arXiv - PHYS - Biological Physics最新文献_第3页

A method for site-specifically tethering the enzyme urease to DNA origami with sustained activity 将脲酶特异性定位于 DNA 折纸并使其具有持续活性的方法

arXiv - PHYS - Biological Physics Pub Date : 2024-09-04 DOI: arxiv-2409.03040

Ian Murphy, Keren Bobilev, Daichi Hayakawa, Eden Ikonen, Thomas E. Videbæk, Shibani Dalal, Wylie W. Ahmed, Jennifer L. Ross, W. Benjamin Rogers

{"title":"A method for site-specifically tethering the enzyme urease to DNA origami with sustained activity","authors":"Ian Murphy, Keren Bobilev, Daichi Hayakawa, Eden Ikonen, Thomas E. Videbæk, Shibani Dalal, Wylie W. Ahmed, Jennifer L. Ross, W. Benjamin Rogers","doi":"arxiv-2409.03040","DOIUrl":"https://doi.org/arxiv-2409.03040","url":null,"abstract":"Attaching enzymes to nanostructures has proven useful to the study of enzyme\u0000functionality under controlled conditions and has led to new technologies.\u0000Often, the utility and interest of enzyme-tethered nanostructures lie in how\u0000the enzymatic activity is affected by how the enzymes are arranged in space.\u0000Therefore, being able to conjugate enzymes to nanostructures while preserving\u0000the enzymatic activity is essential. In this paper, we present a method to\u0000conjugate single-stranded DNA to the enzyme urease while maintaining enzymatic\u0000activity. We show evidence of successful conjugation and quantify the variables\u0000that affect the conjugation yield. We also show that the enzymatic activity is\u0000unchanged after conjugation compared to the enzyme in its native state.\u0000Finally, we demonstrate the tethering of urease to nanostructures made using\u0000DNA origami with high site-specificity. Decorating nanostructures with\u0000enzymatically-active urease may prove to be useful in studying, or even\u0000utilizing, the functionality of urease in disciplines ranging from\u0000biotechnology to soft-matter physics. The techniques we present in this paper\u0000will enable researchers across these fields to modify enzymes without\u0000disrupting their functionality, thus allowing for more insightful studies into\u0000their behavior and utility.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213131","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 model for contractile stress fibers embedded in bulk actomyosin networks 嵌入大量肌动蛋白网络的收缩应力纤维模型

arXiv - PHYS - Biological Physics Pub Date : 2024-09-03 DOI: arxiv-2409.02282

Mariya Savinov, Charles S. Peskin, Alex Mogilner

{"title":"A model for contractile stress fibers embedded in bulk actomyosin networks","authors":"Mariya Savinov, Charles S. Peskin, Alex Mogilner","doi":"arxiv-2409.02282","DOIUrl":"https://doi.org/arxiv-2409.02282","url":null,"abstract":"Contractile cytoskeletal structures such as fine actomyosin meshworks and\u0000stress fibers are essential force-generators for mechanical phenomena in live\u0000cells, including motility, morphogenesis, and mechanosensing. While there have\u0000been many studies on the rheology and assembly of individual stress fibers, few\u0000mathematical models have explicitly modeled the bulk actomyosin network in\u0000which stress fibers are embedded, particularly not in the case of high actin\u0000turnover. Generally the extent of the interplay between embedded stress fibers\u0000and contractile bulk networks is still not well understood. To address this\u0000gap, we design a model of stress fibers embedded in bulk actomyosin networks\u0000which utilizes the immersed boundary method, allowing one to consider various\u0000stress fiber rheologies in the context of an approximately viscous,\u0000compressible, contractile bulk network. We characterize the dynamics of bulk\u0000actomyosin networks with and without embedded stress fibers, and simulate a\u0000laser ablation experiment to demonstrate the effective long-range interactions\u0000between stress fibers as well as how perturbations of stress fibers can result\u0000in symmetry breaking of the bulk actomyosin network.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213183","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 minimal model of smoothly dividing disk-shaped cells 平滑分裂盘状细胞的最小模型

arXiv - PHYS - Biological Physics Pub Date : 2024-09-03 DOI: arxiv-2409.01959

Lukas Hupe, Yoav G. Pollack, Jonas Isensee, Aboutaleb Amiri, Ramin Golestanian, Philip Bittihn

{"title":"A minimal model of smoothly dividing disk-shaped cells","authors":"Lukas Hupe, Yoav G. Pollack, Jonas Isensee, Aboutaleb Amiri, Ramin Golestanian, Philip Bittihn","doi":"arxiv-2409.01959","DOIUrl":"https://doi.org/arxiv-2409.01959","url":null,"abstract":"Replication through cell division is one of the most fundamental processes of\u0000life and a major driver of dynamics in systems ranging from bacterial colonies\u0000to embryogenesis, tissues and tumors. While regulation often plays a role in\u0000shaping self-organization, mounting evidence suggests that many biologically\u0000relevant behaviors exploit principles based on a limited number of physical\u0000ingredients, and particle-based models have become a popular platform to\u0000reconstitute and investigate these emergent dynamics. However, incorporating\u0000division into such models often leads to aberrant mechanical fluctuations that\u0000hamper physically meaningful analysis. Here, we present a minimal model\u0000focusing on mechanical consistency during division. Cells are comprised of two\u0000nodes, overlapping disks which separate from each other during cell division,\u0000resulting in transient dumbbell shapes. Internal degrees of freedom, cell-cell\u0000interactions and equations of motion are designed to ensure force continuity at\u0000all times, including through division, both for the dividing cell itself as\u0000well as interaction partners, while retaining the freedom to define arbitrary\u0000anisotropic mobilities. As a benchmark, we also translate an established model\u0000of proliferating spherocylinders with similar dynamics into our theoretical\u0000framework. Numerical simulations of both models demonstrate force continuity of\u0000the new disk cell model and quantify our improvements. We also investigate some\u0000basic collective behaviors related to alignment and orientational order and\u0000find consistency both between the models and with the literature. A reference\u0000implementation of the model is freely available as a package in the Julia\u0000programming language based on $textit{InPartS.jl}$. Our model is ideally\u0000suited for the investigation of mechanical observables such as velocities and\u0000stresses, and is easily extensible with additional features.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213190","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

Internal Representations in Spiking Neural Networks, criticality and the Renormalization Group 尖峰神经网络的内部表征、临界性和重正化群

arXiv - PHYS - Biological Physics Pub Date : 2024-09-03 DOI: arxiv-2409.02238

João Henrique de Sant'Ana, Nestor Caticha

{"title":"Internal Representations in Spiking Neural Networks, criticality and the Renormalization Group","authors":"João Henrique de Sant'Ana, Nestor Caticha","doi":"arxiv-2409.02238","DOIUrl":"https://doi.org/arxiv-2409.02238","url":null,"abstract":"Optimal information processing in peripheral sensory systems has been\u0000associated in several examples to the signature of a critical or near critical\u0000state. Furthermore, cortical systems have also been described to be in a\u0000critical state in both wake and anesthetized experimental models, both {it in\u0000vitro} and {it in vivo}. We investigate whether a similar signature\u0000characterizes the internal representations (IR) of a multilayer (deep) spiking\u0000artificial neural network performing computationally simple but meaningful\u0000cognitive tasks, using a methodology inspired in the biological setup, with\u0000cortical implanted electrodes in rats, either freely behaving or under\u0000different levels of anesthesia. The increase of the characteristic time of the\u0000decay of the correlation of fluctuations of the IR, found when the network\u0000input changes, are indications of a broad-tailed distribution of IR\u0000fluctuations. The broad tails are present even when the network is not yet\u0000capable of performing the classification tasks, either due to partial training\u0000or to the effect of a low dose of anesthesia in a simple model. However, we\u0000don't find enough evidence of power law distributions of avalanche size and\u0000duration. We interpret the results from a renormalization group perspective to\u0000point out that despite having broad tails, this is not related to a critical\u0000transition but rather similar to fluctuations driven by the reversal of the\u0000magnetic field in a ferromagnetic system. Another example of persistent\u0000correlation of fluctuations of a non critical system is constructed, where a\u0000particle undergoes Brownian motion on a slowly varying potential.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213185","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

Bacteria exhibit optimal diffusivity near surfaces 细菌在表面附近表现出最佳扩散性

arXiv - PHYS - Biological Physics Pub Date : 2024-09-03 DOI: arxiv-2409.01597

Antai Tao, Guangzhe Liu, Rongjing Zhang, Junhua Yuan

引用次数: 0

Compression Causes Expansion and Compaction of the Jammed Polydisperse Particles 压缩导致多分散颗粒膨胀和压实

arXiv - PHYS - Biological Physics Pub Date : 2024-09-02 DOI: arxiv-2409.01108

Daisuke S. Shimamoto, Miho Yanagisawa

引用次数: 0

Physical mechanism reveals bacterial slowdown above a critical number of flagella 物理机制揭示了细菌在鞭毛数量超过临界值时速度减慢的原因

arXiv - PHYS - Biological Physics Pub Date : 2024-09-01 DOI: arxiv-2409.00574

Maria Tătulea-Codrean, Eric Lauga

{"title":"Physical mechanism reveals bacterial slowdown above a critical number of flagella","authors":"Maria Tătulea-Codrean, Eric Lauga","doi":"arxiv-2409.00574","DOIUrl":"https://doi.org/arxiv-2409.00574","url":null,"abstract":"Numerous studies have explored the link between bacterial swimming and the\u0000number of flagella, a distinguishing feature of motile multiflagellated\u0000bacteria. We revisit this open question using augmented slender-body theory\u0000simulations, in which we resolve the full hydrodynamic interactions within a\u0000bundle of helical filaments rotating and translating in synchrony. Unlike\u0000previous studies, our model considers the full torque-speed relationship of the\u0000bacterial flagellar motor, revealing its significant impact on multiflagellated\u0000swimming. Because the viscous load per motor decreases with flagellar number,\u0000the bacterial flagellar motor (BFM) transitions from the high-load to the\u0000low-load regime at a critical number of filaments, leading to bacterial\u0000slowdown as further flagella are added to the bundle. We explain the physical\u0000mechanism behind the observed slowdown as an interplay between the\u0000load-dependent generation of torque by the motor, and the load-reducing\u0000cooperativity between flagella, which consists of both hydrodynamic and\u0000non-hydrodynamic components. The theoretically predicted critical number of\u0000flagella is remarkably close to the values reported for the model organism\u0000textit{Escherichia coli}. Our model further predicts that the critical number\u0000of flagella increases with viscosity, suggesting that bacteria can enhance\u0000their swimming capacity by growing more flagella in more viscous environments,\u0000consistent with empirical observations.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213188","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

DNA transport is topologically sculpted by active microtubule dynamics 活跃的微管动力学对 DNA 运输进行拓扑学雕刻

arXiv - PHYS - Biological Physics Pub Date : 2024-09-01 DOI: arxiv-2409.00569

Dylan P. McCuskey, Raisa E. Achiriloaie, Claire Benjamin, Jemma Kushen, Isaac Blacklow, Omar Mnfy, Jennifer L. Ross, Rae M. Robertson-Anderson, Janet Y. Sheung

{"title":"DNA transport is topologically sculpted by active microtubule dynamics","authors":"Dylan P. McCuskey, Raisa E. Achiriloaie, Claire Benjamin, Jemma Kushen, Isaac Blacklow, Omar Mnfy, Jennifer L. Ross, Rae M. Robertson-Anderson, Janet Y. Sheung","doi":"arxiv-2409.00569","DOIUrl":"https://doi.org/arxiv-2409.00569","url":null,"abstract":"The transport of macromolecules, such as DNA, through the cytoskeleton is\u0000critical to wide-ranging cellular processes from cytoplasmic streaming to\u0000transcription. The rigidity and steric hindrances imparted by the network of\u0000filaments comprising the cytoskeleton often leads to anomalous subdiffusion,\u0000while active processes such as motor-driven restructuring can induce athermal\u0000superdiffusion. Understanding the interplay between these seemingly\u0000antagonistic contributions to intracellular dynamics remains a grand challenge.\u0000Here, we use single-molecule tracking to show that the transport of large\u0000linear and circular DNA through motor-driven microtubule networks can be\u0000non-gaussian and multi-modal, with the degree and spatiotemporal scales over\u0000which these features manifest depending non-trivially on the state of activity\u0000and DNA topology. For example, active network restructuring increases caging\u0000and non-Gaussian transport modes of linear DNA, while dampening these\u0000mechanisms for rings. We further discover that circular DNA molecules exhibit\u0000either markedly enhanced subdiffusion or superdiffusion compared to their\u0000linear counterparts, in the absence or presence of kinesin activity, indicative\u0000of microtubules threading circular DNA. This strong coupling leads to both\u0000stalling and directed transport, providing a direct route towards parsing\u0000distinct contributions to transport and determining the impact of coupling on\u0000the transport signatures. More generally, leveraging macromolecular topology as\u0000a route to programming molecular interactions and transport dynamics is an\u0000elegant yet largely overlooked mechanism that cells may exploit for\u0000intracellular trafficking, streaming, and compartmentalization. This mechanism\u0000could be harnessed for the design of self-regulating, sensing, and\u0000reconfigurable biomimetic matter.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213191","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

Attractive and repulsive terms in multi-object dispersion interactions 多物体色散相互作用中的吸引项和排斥项

arXiv - PHYS - Biological Physics Pub Date : 2024-08-31 DOI: arxiv-2409.00419

Subhojit Pal, Barry W. Ninham, John F. Dobson, Mathias Boström

引用次数: 0

Phase behaviors and dynamics of active particle systems in double-well potential 双阱势能中活性粒子系统的相行为和动力学

arXiv - PHYS - Biological Physics Pub Date : 2024-08-31 DOI: arxiv-2409.00425

Lu Chen, Baopi Liu, Ning Liu

引用次数: 0