Ian Murphy, Keren Bobilev, Daichi Hayakawa, Eden Ikonen, Thomas E. Videbæk, Shibani Dalal, Wylie W. Ahmed, Jennifer L. Ross, W. Benjamin Rogers
Attaching enzymes to nanostructures has proven useful to the study of enzyme functionality under controlled conditions and has led to new technologies. Often, the utility and interest of enzyme-tethered nanostructures lie in how the enzymatic activity is affected by how the enzymes are arranged in space. Therefore, being able to conjugate enzymes to nanostructures while preserving the enzymatic activity is essential. In this paper, we present a method to conjugate single-stranded DNA to the enzyme urease while maintaining enzymatic activity. We show evidence of successful conjugation and quantify the variables that affect the conjugation yield. We also show that the enzymatic activity is unchanged after conjugation compared to the enzyme in its native state. Finally, we demonstrate the tethering of urease to nanostructures made using DNA origami with high site-specificity. Decorating nanostructures with enzymatically-active urease may prove to be useful in studying, or even utilizing, the functionality of urease in disciplines ranging from biotechnology to soft-matter physics. The techniques we present in this paper will enable researchers across these fields to modify enzymes without disrupting their functionality, thus allowing for more insightful studies into their behavior and utility.
将酶连接到纳米结构已被证明有助于在受控条件下研究酶的功能，并催生了新技术。通常情况下，酶系纳米结构的实用性和趣味性在于酶的活性如何受到酶在空间排列方式的影响。在本文中，我们介绍了一种在保持酶活性的同时将单链 DNA 与脲酶共轭的方法。我们展示了成功共轭的证据，并量化了影响共轭产量的变量。最后，我们展示了利用 DNA 折纸技术将脲酶系在纳米结构上，而且具有高度的位点特异性。用具有酶活性的脲酶装饰纳米结构可能会有助于研究甚至利用脲酶在从生物技术到软物质物理学等学科中的功能。我们在本文中介绍的技术将使这些领域的研究人员能够在不破坏酶功能的情况下改造酶，从而对酶的行为和用途进行更深入的研究。
{"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":"5 1","pages":""},"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}
Contractile cytoskeletal structures such as fine actomyosin meshworks and stress fibers are essential force-generators for mechanical phenomena in live cells, including motility, morphogenesis, and mechanosensing. While there have been many studies on the rheology and assembly of individual stress fibers, few mathematical models have explicitly modeled the bulk actomyosin network in which stress fibers are embedded, particularly not in the case of high actin turnover. Generally the extent of the interplay between embedded stress fibers and contractile bulk networks is still not well understood. To address this gap, we design a model of stress fibers embedded in bulk actomyosin networks which utilizes the immersed boundary method, allowing one to consider various stress fiber rheologies in the context of an approximately viscous, compressible, contractile bulk network. We characterize the dynamics of bulk actomyosin networks with and without embedded stress fibers, and simulate a laser ablation experiment to demonstrate the effective long-range interactions between stress fibers as well as how perturbations of stress fibers can result in symmetry breaking of the bulk actomyosin network.
{"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":"71 1","pages":""},"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}
Lukas Hupe, Yoav G. Pollack, Jonas Isensee, Aboutaleb Amiri, Ramin Golestanian, Philip Bittihn
Replication through cell division is one of the most fundamental processes of life and a major driver of dynamics in systems ranging from bacterial colonies to embryogenesis, tissues and tumors. While regulation often plays a role in shaping self-organization, mounting evidence suggests that many biologically relevant behaviors exploit principles based on a limited number of physical ingredients, and particle-based models have become a popular platform to reconstitute and investigate these emergent dynamics. However, incorporating division into such models often leads to aberrant mechanical fluctuations that hamper physically meaningful analysis. Here, we present a minimal model focusing on mechanical consistency during division. Cells are comprised of two nodes, overlapping disks which separate from each other during cell division, resulting in transient dumbbell shapes. Internal degrees of freedom, cell-cell interactions and equations of motion are designed to ensure force continuity at all times, including through division, both for the dividing cell itself as well as interaction partners, while retaining the freedom to define arbitrary anisotropic mobilities. As a benchmark, we also translate an established model of proliferating spherocylinders with similar dynamics into our theoretical framework. Numerical simulations of both models demonstrate force continuity of the new disk cell model and quantify our improvements. We also investigate some basic collective behaviors related to alignment and orientational order and find consistency both between the models and with the literature. A reference implementation of the model is freely available as a package in the Julia programming language based on $textit{InPartS.jl}$. Our model is ideally suited for the investigation of mechanical observables such as velocities and stresses, and is easily extensible with additional features.
{"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":"94 1","pages":""},"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}
Optimal information processing in peripheral sensory systems has been associated in several examples to the signature of a critical or near critical state. Furthermore, cortical systems have also been described to be in a critical state in both wake and anesthetized experimental models, both {it in vitro} and {it in vivo}. We investigate whether a similar signature characterizes the internal representations (IR) of a multilayer (deep) spiking artificial neural network performing computationally simple but meaningful cognitive tasks, using a methodology inspired in the biological setup, with cortical implanted electrodes in rats, either freely behaving or under different levels of anesthesia. The increase of the characteristic time of the decay of the correlation of fluctuations of the IR, found when the network input changes, are indications of a broad-tailed distribution of IR fluctuations. The broad tails are present even when the network is not yet capable of performing the classification tasks, either due to partial training or to the effect of a low dose of anesthesia in a simple model. However, we don't find enough evidence of power law distributions of avalanche size and duration. We interpret the results from a renormalization group perspective to point out that despite having broad tails, this is not related to a critical transition but rather similar to fluctuations driven by the reversal of the magnetic field in a ferromagnetic system. Another example of persistent correlation of fluctuations of a non critical system is constructed, where a particle undergoes Brownian motion on a slowly varying potential.
在一些例子中，外周感觉系统的最佳信息处理与临界或接近临界状态的特征有关。此外，在唤醒和麻醉实验模型中，大脑皮层系统也被描述为处于临界状态，包括{it invitro}和{it in vivo}。我们使用一种受生物设置启发的方法，在大鼠的皮层植入电极，在自由行为或不同程度的麻醉状态下，研究执行计算简单但有意义的认知任务的多层（深度）尖峰人工神经网络的内部表征（IR）是否具有类似的特征。当网络输入发生变化时，红外波动相关性衰减的特征时间会增加，这表明红外波动呈宽尾分布。即使由于部分训练或简单模型中低剂量麻醉的影响，网络尚未具备执行分类任务的能力时，宽尾也会出现。但是，我们没有发现雪崩大小和持续时间的幂律分布的足够证据。我们从重正化群的角度解释了这一结果，指出尽管雪崩具有宽尾，但这与临界转换无关，而是类似于铁磁系统中磁场反转所驱动的波动。我们还构建了非临界系统波动持续相关性的另一个例子，即粒子在缓慢变化的电势上进行布朗运动。
{"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":"38 1","pages":""},"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}
In natural environments, solid surfaces present both opportunities and challenges for bacteria. On one hand, they serve as platforms for biofilm formation, crucial for bacterial colonization and resilience in harsh conditions. On the other hand, surfaces can entrap bacteria, constraining their environmental exploration compared to the freedom they experience in bulk liquid. Here, through systematic single-cell behavioral measurements, phenomenological modeling, and theoretical analysis, we reveal how bacteria strategically navigate these factors. We observe that bacterial surface residence time decreases sharply with increasing tumble bias, transitioning to a plateau at a tumble bias of around 0.25, consistent with the mean tumble bias of wild-type Escherichia coli. Furthermore, we find that bacterial surface diffusivity peaks near the mean tumble bias of wild-type E. coli. This reflects a bet-hedging strategy: some bacteria swiftly escape from the surface, while others, with longer surface residence times, explore this two-dimensional environment most efficiently.
{"title":"Bacteria exhibit optimal diffusivity near surfaces","authors":"Antai Tao, Guangzhe Liu, Rongjing Zhang, Junhua Yuan","doi":"arxiv-2409.01597","DOIUrl":"https://doi.org/arxiv-2409.01597","url":null,"abstract":"In natural environments, solid surfaces present both opportunities and\u0000challenges for bacteria. On one hand, they serve as platforms for biofilm\u0000formation, crucial for bacterial colonization and resilience in harsh\u0000conditions. On the other hand, surfaces can entrap bacteria, constraining their\u0000environmental exploration compared to the freedom they experience in bulk\u0000liquid. Here, through systematic single-cell behavioral measurements,\u0000phenomenological modeling, and theoretical analysis, we reveal how bacteria\u0000strategically navigate these factors. We observe that bacterial surface\u0000residence time decreases sharply with increasing tumble bias, transitioning to\u0000a plateau at a tumble bias of around 0.25, consistent with the mean tumble bias\u0000of wild-type Escherichia coli. Furthermore, we find that bacterial surface\u0000diffusivity peaks near the mean tumble bias of wild-type E. coli. This reflects\u0000a bet-hedging strategy: some bacteria swiftly escape from the surface, while\u0000others, with longer surface residence times, explore this two-dimensional\u0000environment most efficiently.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"112 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213187","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}
This study focused on the expansion in polydisperse granular materials owing to mechanical annealing, which involved compression and decompression. Following minor annealing, the polydisperse systems exhibited compaction as well as the systems having uniform-sized particles. However, following extensive annealing, only the polydisperse systems were observed to expand. Pressure history and structure analysis indicated that this expansion results from the size segregation of the particles. We attribute this segregation to particle-size-dependent effective attraction. The results of this study highlight the strong history dependence of the packing fraction and structure in polydisperse particles and reveal a potential-energy-driven segregation mechanism.
{"title":"Compression Causes Expansion and Compaction of the Jammed Polydisperse Particles","authors":"Daisuke S. Shimamoto, Miho Yanagisawa","doi":"arxiv-2409.01108","DOIUrl":"https://doi.org/arxiv-2409.01108","url":null,"abstract":"This study focused on the expansion in polydisperse granular materials owing\u0000to mechanical annealing, which involved compression and decompression.\u0000Following minor annealing, the polydisperse systems exhibited compaction as\u0000well as the systems having uniform-sized particles. However, following\u0000extensive annealing, only the polydisperse systems were observed to expand.\u0000Pressure history and structure analysis indicated that this expansion results\u0000from the size segregation of the particles. We attribute this segregation to\u0000particle-size-dependent effective attraction. The results of this study\u0000highlight the strong history dependence of the packing fraction and structure\u0000in polydisperse particles and reveal a potential-energy-driven segregation\u0000mechanism.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213212","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}
Numerous studies have explored the link between bacterial swimming and the number of flagella, a distinguishing feature of motile multiflagellated bacteria. We revisit this open question using augmented slender-body theory simulations, in which we resolve the full hydrodynamic interactions within a bundle of helical filaments rotating and translating in synchrony. Unlike previous studies, our model considers the full torque-speed relationship of the bacterial flagellar motor, revealing its significant impact on multiflagellated swimming. Because the viscous load per motor decreases with flagellar number, the bacterial flagellar motor (BFM) transitions from the high-load to the low-load regime at a critical number of filaments, leading to bacterial slowdown as further flagella are added to the bundle. We explain the physical mechanism behind the observed slowdown as an interplay between the load-dependent generation of torque by the motor, and the load-reducing cooperativity between flagella, which consists of both hydrodynamic and non-hydrodynamic components. The theoretically predicted critical number of flagella is remarkably close to the values reported for the model organism textit{Escherichia coli}. Our model further predicts that the critical number of flagella increases with viscosity, suggesting that bacteria can enhance their swimming capacity by growing more flagella in more viscous environments, consistent with empirical observations.
{"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":"1 1","pages":""},"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}
Dylan P. McCuskey, Raisa E. Achiriloaie, Claire Benjamin, Jemma Kushen, Isaac Blacklow, Omar Mnfy, Jennifer L. Ross, Rae M. Robertson-Anderson, Janet Y. Sheung
The transport of macromolecules, such as DNA, through the cytoskeleton is critical to wide-ranging cellular processes from cytoplasmic streaming to transcription. The rigidity and steric hindrances imparted by the network of filaments comprising the cytoskeleton often leads to anomalous subdiffusion, while active processes such as motor-driven restructuring can induce athermal superdiffusion. Understanding the interplay between these seemingly antagonistic contributions to intracellular dynamics remains a grand challenge. Here, we use single-molecule tracking to show that the transport of large linear and circular DNA through motor-driven microtubule networks can be non-gaussian and multi-modal, with the degree and spatiotemporal scales over which these features manifest depending non-trivially on the state of activity and DNA topology. For example, active network restructuring increases caging and non-Gaussian transport modes of linear DNA, while dampening these mechanisms for rings. We further discover that circular DNA molecules exhibit either markedly enhanced subdiffusion or superdiffusion compared to their linear counterparts, in the absence or presence of kinesin activity, indicative of microtubules threading circular DNA. This strong coupling leads to both stalling and directed transport, providing a direct route towards parsing distinct contributions to transport and determining the impact of coupling on the transport signatures. More generally, leveraging macromolecular topology as a route to programming molecular interactions and transport dynamics is an elegant yet largely overlooked mechanism that cells may exploit for intracellular trafficking, streaming, and compartmentalization. This mechanism could be harnessed for the design of self-regulating, sensing, and reconfigurable biomimetic matter.
大分子（如 DNA）通过细胞骨架的运输对于从细胞质流到转录等广泛的细胞过程至关重要。组成细胞骨架的丝网所具有的刚性和立体阻碍往往会导致反常的亚扩散，而马达驱动的重组等活跃过程则会诱发热超扩散。在这里，我们利用单分子追踪技术证明，大线性和环状 DNA 通过马达驱动的微管网络的传输可以是高斯和多模式的，这些特征的表现程度和时空尺度取决于活动状态和 DNA 拓扑结构。例如，活跃的网络重组会增加线性 DNA 的笼状和非高斯传输模式，而抑制环状 DNA 的这些机制。我们进一步发现，在没有或有驱动蛋白活动的情况下，与线性 DNA 分子相比，环状 DNA 分子表现出明显增强的亚扩散或超扩散，这表明微管在穿环状 DNA。这种强耦合导致了沉积和定向传输，为解析传输的不同贡献和确定耦合对传输特征的影响提供了直接途径。更广泛地说，利用大分子拓扑学作为分子相互作用和运输动力学的编程途径，是细胞可能利用来进行胞内运输、流式运输和区隔的一种古老但却被忽视的机制。这种机制可用于设计自我调节、传感和可重新配置的生物仿生物质。
{"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":"107 1","pages":""},"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}
Subhojit Pal, Barry W. Ninham, John F. Dobson, Mathias Boström
We consider the dispersion (van der Waals, vdW) interaction among N parallel elongated objects such as DNA/RNA strands or metallic nanotubes, which are polarizable primarily along the long axis. Within a quasi-one-dimensional model, we prove that the irreducible N -object vdW energy contribution is negative (attractive) for even N and positive (repulsive) for odd N. We confirm these results up to $N=4$ via a 3-dimensional plasma cylinder model. This suggests a preference for even-N clustering of elongated structures in nanoscience and biology. This work could have implications e.g. for nanotube bundle formation and for the clustering of long-chain biomolecules at separations exceeding chemical bond lengths.
我们考虑了 N 个平行长物体（如 DNA/RNA 链或金属纳米管）之间的色散（范德华，vdW）相互作用，这些物体主要沿长轴具有极性。在一个准一维模型中，我们证明了不可还原的 N 个物体 vdW 能量贡献对偶数 N 为负（吸引力），对奇数 N 为正（排斥力）。这表明在纳米科学和生物学中，拉长结构更倾向于偶数 N 聚类。这项工作可能会对纳米管束的形成以及长链生物分子在超过化学键长度的间隔内的聚类等方面产生影响。
{"title":"Attractive and repulsive terms in multi-object dispersion interactions","authors":"Subhojit Pal, Barry W. Ninham, John F. Dobson, Mathias Boström","doi":"arxiv-2409.00419","DOIUrl":"https://doi.org/arxiv-2409.00419","url":null,"abstract":"We consider the dispersion (van der Waals, vdW) interaction among N parallel\u0000elongated objects such as DNA/RNA strands or metallic nanotubes, which are\u0000polarizable primarily along the long axis. Within a quasi-one-dimensional\u0000model, we prove that the irreducible N -object vdW energy contribution is\u0000negative (attractive) for even N and positive (repulsive) for odd N. We confirm\u0000these results up to $N=4$ via a 3-dimensional plasma cylinder model. This\u0000suggests a preference for even-N clustering of elongated structures in\u0000nanoscience and biology. This work could have implications e.g. for nanotube\u0000bundle formation and for the clustering of long-chain biomolecules at\u0000separations exceeding chemical bond lengths.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"8 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213193","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}
In this paper, we investigate the phase behaviors and dynamics of self-propelled particles with active reorientation in double-well potential. We observe the self-propelled particles exhibit flocking and clustering in an asymmetric potential trap. By MD simulations, we obtain a phase diagram of flocking with active reorientation and potential asymmetry as parameters. We compare the responses of inactive and active particles to the potential. It shows that active reorientation of particles amplifies the degree of aggregation on one side in the asymmetric potential well. Furthermore, we calculate the mean squared displacement and identify distinct diffusion regimes. These results highlight active particles with active reorientation exhibit greater sensitivity in double-well potentials.
{"title":"Phase behaviors and dynamics of active particle systems in double-well potential","authors":"Lu Chen, Baopi Liu, Ning Liu","doi":"arxiv-2409.00425","DOIUrl":"https://doi.org/arxiv-2409.00425","url":null,"abstract":"In this paper, we investigate the phase behaviors and dynamics of\u0000self-propelled particles with active reorientation in double-well potential. We\u0000observe the self-propelled particles exhibit flocking and clustering in an\u0000asymmetric potential trap. By MD simulations, we obtain a phase diagram of\u0000flocking with active reorientation and potential asymmetry as parameters. We\u0000compare the responses of inactive and active particles to the potential. It\u0000shows that active reorientation of particles amplifies the degree of\u0000aggregation on one side in the asymmetric potential well. Furthermore, we\u0000calculate the mean squared displacement and identify distinct diffusion\u0000regimes. These results highlight active particles with active reorientation\u0000exhibit greater sensitivity in double-well potentials.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213195","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}
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