arXiv - PHYS - Biological Physics最新文献

{"title":"Error Thresholds in Presence of Epistatic Interactions","authors":"David A. Herrera-Martí","doi":"arxiv-2409.11944","DOIUrl":"https://doi.org/arxiv-2409.11944","url":null,"abstract":"Models for viral populations with high replication error rates (such as RNA\u0000viruses) rely on the quasi-species concept, in which mutational pressure beyond\u0000the so-called ``Error Threshold\" leads to a loss of essential genetic\u0000information and population collapse, an effect known as the ``Error\u0000Catastrophe\". We explain how crossing this threshold, as a result of increasing\u0000mutation rates, can be understood as a second order phase transition, even in\u0000the presence of lethal mutations. In particular, we show that, in fitness\u0000landscapes with a single peak, this collapse is equivalent to a\u0000ferro-paramagnetic transition, where the back-mutation rate plays the role of\u0000the external magnetic field. We then generalise this framework to rugged\u0000fitness landscapes, like the ones that arise from epistatic interactions, and\u0000provide numerical evidence that there is a transition from a high average\u0000fitness regime to a low average fitness one, similarly to single-peaked\u0000landscapes. The onset of the transition is heralded by a sudden change in the\u0000susceptibility to changes in the mutation rate. We use insight from Replica\u0000Symmetry Breaking mechanisms in spin glasses, in particular by considering that\u0000the fluctuations of the genotype similarity distribution are an order\u0000parameter.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"2 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142265671","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}

{"title":"Choice of Reference Surfaces to assess Plant Health through leaf scale temperature monitoring","authors":"Rather Laasani Sanya Shabir, Shivani Chauhan, Navneet Kumar","doi":"arxiv-2409.10968","DOIUrl":"https://doi.org/arxiv-2409.10968","url":null,"abstract":"We use infrared thermal imaging to remotely monitor the temperature of the\u0000leaves and plant which in turn is an indicative of their health and stress; in\u0000particular water stress. A series of experiments were conducted using Fluke\u0000TiX580 thermal imager on tomato plants to correlate the leaf temperature to\u0000different stages such as healthy, dying/wilted, and completely dead/dry. The\u0000leaf temperature was compared to a series of paper-based reference surface\u0000temperatures; these are of different colors and some are dry while some are\u0000wet. All the reference surfaces were insulated at the bottom ensuring the heat\u0000interaction between their top surfaces and ambient only. The surfaces were kept\u0000sufficiently far from one another. The healthy leaf temperature was found to be\u0000close to that of white dry and black wet reference surfaces whereas the wilted\u0000and dying leaves temperature were observed to range between yellow and red\u0000signifying that this temperature range can better predict the onset of water\u0000stress in the leaves. The completely dead/dry leaves were observed to range\u0000between green and blue dry surfaces, respectively. However, most of the dead\u0000leaf temperature data was found to be accumulated closer to the green surface\u0000signifying green dry surface can better indicate a dead leaf condition. The\u0000dying leaves were observed to exhibit 8-10 degree centigrade higher\u0000temperatures as compared to the healthy leaves in similar ambient conditions.\u0000Temperature-based health assessment provides us with a timely intervention to\u0000prevent leaf death compared to the optical monitoring since IR images revealed\u0000elevated leaf temperature 2-3 days before the optical unhealthiness (appearance\u0000of yellowness on the leaf) was noticed.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142265673","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}

{"title":"Physical Insights into Electromagnetic Efficiency of Wireless Implantable Bioelectronics","authors":"Mingxiang Gao, Denys Nikolayev, Zvonimir Sipus, Anja K. Skrivervik","doi":"arxiv-2409.10763","DOIUrl":"https://doi.org/arxiv-2409.10763","url":null,"abstract":"Autonomous implantable bioelectronics rely on wireless connectivity,\u0000necessitating highly efficient electromagnetic (EM) radiation systems. However,\u0000limitations in power, safety, and data transmission currently impede the\u0000advancement of innovative wireless medical devices, such as tetherless neural\u0000interfaces, electroceuticals, and surgical microrobots. To overcome these\u0000challenges and ensure sufficient link and power budgets for wireless\u0000implantable systems, this study explores the mechanisms behind EM radiation and\u0000losses, offering strategies to enhance radiation efficiency in wireless\u0000implantable bioelectronics. Using analytical modeling, the EM waves emitted by\u0000the implant are expanded as a series of spherical harmonics, enabling a\u0000detailed analysis of the radiation mechanisms. This framework is then extended\u0000to approximate absorption losses caused by the lossy and dispersive properties\u0000of tissues through derived analytical expressions. The radiation efficiency and\u0000in-body path loss are quantified and compared in terms of three primary loss\u0000mechanisms. The impact of various parameters on the EM efficiency of\u0000implantable devices is analyzed and quantified, including operating frequency,\u0000implant size, body-air interface curvature, and implantation location.\u0000Additionally, a rapid estimation technique is introduced to determine the\u0000optimal operating frequency for specific scenarios, along with a set of design\u0000principles aimed at improving radiation performance. The design strategies\u0000derived in this work - validated through numerical and experimental\u0000demonstrations on realistic implants - reveal a potential improvement in\u0000implant radiation efficiency or gain by a factor of five to ten, leading to a\u0000corresponding increase in overall link efficiency compared to conventional\u0000designs.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"189 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142265672","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}

{"title":"Pseudo-RNA with parallel aligned single-strands and periodic base sequence as a new universality class","authors":"R. Dengler","doi":"arxiv-2409.10158","DOIUrl":"https://doi.org/arxiv-2409.10158","url":null,"abstract":"We investigate a field theory for RNA-like polymers with periodic base\u0000sequence GCGCG..., where only single-strands aligned in the same direction form\u0000double strands. The field theory is derived from a lattice model that\u0000incorporates excluded volume effects, base sequence, and temperature dependent\u0000renaturation/denaturation. The artificial directionality leads to a novel universality class, not\u0000related to conventional branched polymers and Lee-Yang field theory. This\u0000universality class is unstable against natural pairing, where oppositely\u0000aligned single-strands form double strands. The denaturation/renaturation\u0000transition is a continuous crossover between two $varphi_{n=0}^{4}$ critical\u0000points and the critical point of the new universality class.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"19 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142265675","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}

{"title":"Hydrodynamic hovering of swimming bacteria above surfaces","authors":"Pyae Hein Htet, Debasish Das, Eric Lauga","doi":"arxiv-2409.10447","DOIUrl":"https://doi.org/arxiv-2409.10447","url":null,"abstract":"Flagellated bacteria are hydrodynamically attracted to rigid walls, yet past\u0000work shows a 'hovering' state where they swim stably at a finite height above\u0000surfaces. We use numerics and theory to reveal the physical origin of hovering.\u0000Simulations first show that hovering requires an elongated cell body and\u0000results from a tilt away from the wall. Theoretical models then identify two\u0000essential asymmetries: the response of width-asymmetric cells to active flows\u0000created by length-asymmetric cells. A minimal model reconciles near and\u0000far-field hydrodynamics, capturing all key features of hovering.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142265676","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}

{"title":"The structure of inter-reaction times in reaction-diffusion processes and consequences for counting statistics","authors":"Benjamin Garcia de Figueiredo, Justin M. Calabrese, William F. Fagan, Ricardo Martinez-Garcia","doi":"arxiv-2409.11433","DOIUrl":"https://doi.org/arxiv-2409.11433","url":null,"abstract":"Many natural phenomena are quantified by counts of observable events, from\u0000the annihilation of quasiparticles in a lattice to predator-prey encounters on\u0000a landscape to spikes in a neural network. These events are triggered at random\u0000intervals when an underlying dynamical system occupies a set of reactive states\u0000in its phase space. We derive a general expression for the distribution of\u0000times between events in such counting processes assuming the underlying\u0000triggering dynamics is a stochastic process that converges to a stationary\u0000distribution. Our results contribute to resolving a long-standing dichotomy in\u0000the study of reaction-diffusion processes, showing the inter-reaction point\u0000process interpolates between a reaction- and a diffusion-limited regime. At low\u0000reaction rates, the inter-reaction process is Poisson with a rate depending on\u0000stationary properties of the event-triggering stochastic process. At high\u0000reaction rates, inter-reaction times are dominated by the hitting times to the\u0000reactive states. To further illustrate the power of this approach we apply our\u0000framework to obtain the counting statistics of two counting processes appearing\u0000in several biophysical scenarios. First, we study the common situation of\u0000estimating an animal's activity level by how often it crosses a detector,\u0000showing that the mean number of crossing events can decrease monotonically with\u0000the hitting rate, a seemingly 'paradoxical' result that could possibly lead to\u0000misinterpretation of experimental count data. Second, we derive the ensemble\u0000statistics for the detection of many particles, recovering and generalizing\u0000known results in the biophysics of chemosensation. Overall, we develop a\u0000unifying theoretical framework to quantify inter-event time distributions in\u0000reaction-diffusion systems that clarifies existing debates in the literature\u0000and provide examples of application to real-world scenarios.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"97 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142265670","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}

{"title":"Light-induced cortical excitability reveals programmable shape dynamics in starfish oocytes","authors":"Jinghui Liu, Tom Burkart, Alexander Ziepke, John Reinhard, Yu-Chen Chao, Tzer Han Tan, S. Zachary Swartz, Erwin Frey, Nikta Fakhri","doi":"arxiv-2409.08651","DOIUrl":"https://doi.org/arxiv-2409.08651","url":null,"abstract":"Chemo-mechanical waves on active deformable surfaces are a key component for\u0000many vital cellular functions. In particular, these waves play a major role in\u0000force generation and long-range signal transmission in cells that dynamically\u0000change shape, as encountered during cell division or morphogenesis.\u0000Reconstituting and controlling such chemically controlled cell deformations is\u0000a crucial but unsolved challenge for the development of synthetic cells. Here,\u0000we develop an optogenetic method to elucidate the mechanism responsible for\u0000coordinating surface contraction waves that occur in oocytes of the starfish\u0000Patiria miniata during meiotic cell division. Using spatiotemporally-patterned\u0000light stimuli as a control input, we create chemo-mechanical cortical\u0000excitations that are decoupled from meiotic cues and drive diverse shape\u0000deformations ranging from local pinching to surface contraction waves and cell\u0000lysis. We develop a quantitative model that entails the hierarchy of chemical\u0000and mechanical dynamics, which allows to relate the variety of mechanical\u0000responses to optogenetic stimuli. Our framework systematically predicts and\u0000explains transitions of programmed shape dynamics. Finally, we qualitatively\u0000map the observed shape dynamics to elucidate how the versatility of\u0000intracellular protein dynamics can give rise to a broad range of mechanical\u0000phenomenologies. More broadly, our results pave the way toward real-time\u0000control over dynamical deformations in living organisms and can advance the\u0000design of synthetic cells and life-like cellular functions.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142269512","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}

{"title":"Influence of cell density and in-vivo aging on erythrocyte aggregability: Dissociation dynamics in extensional flow","authors":"Midhun Puthumana Melepattu, Guillaume Maîtrejean, Christian Wagner, Thomas Podgorski","doi":"arxiv-2409.08877","DOIUrl":"https://doi.org/arxiv-2409.08877","url":null,"abstract":"Blood rheology and microcirculation are strongly influenced by red blood cell\u0000(RBC) aggregation. The aggregability of RBCs can vary significantly due to\u0000factors such as their mechanical and membrane surface properties, which are\u0000affected by cell aging in vivo. In this study, we investigate RBC aggregability\u0000as a function of their density, a marker of cell age and mechanical properties,\u0000by separating RBCs from healthy donors into different density fractions using\u0000Percoll density gradient centrifugation. We examine the dissociation rates of\u0000aggregates in a controlled medium supplemented with Dextran, employing an\u0000extensional flow technique based on hyperbolic microfluidic constrictions and\u0000image analysis, assisted by a convolutional neural network (CNN). In contrast\u0000to other techniques, our microfluidic experimental approach highlights the\u0000behavior of RBC aggregates in dynamic flow conditions relevant to\u0000microcirculation. Our results demonstrate that aggregate dissociation is\u0000strongly correlated with cell density and that aggregates formed from the\u0000denser fractions of RBCs are significantly more robust than those from the\u0000average cell population. This study provides insight into the effect of RBC\u0000aging in vivo on their mechanical properties and aggregability, underscoring\u0000the importance of further exploration of RBC aggregation in the context of\u0000cellular senescence and its potential implications for hemodynamics.\u0000Additionally, it suggests that this technique can complement existing methods\u0000for improved evaluation of RBC aggregability in health and disease.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142265674","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}

{"title":"Hybrid roles of adaptation and optimization in formation of vascular network","authors":"Yawei Wang, Zilu Qin, Yubo Fan","doi":"arxiv-2409.07824","DOIUrl":"https://doi.org/arxiv-2409.07824","url":null,"abstract":"It was hypothesized that the structures of biological transport networks are\u0000the result of either energy consumption or adaptation dynamics. Although\u0000approaches based on these hypotheses can produce optimal network and form loop\u0000structures, we found that neither possesses complete ability to generate\u0000complex networks that resemble vascular network in living organisms, which\u0000motivated us to propose a hybrid approach. This approach can replicate the path\u0000dependency phenomenon of main branches and produce an optimal network that\u0000resembles the real vascular network. We further show that there is a clear\u0000transition in the structural pattern of the vascular network, shifting from\u0000`chive-like' to dendritic configuration after a period of sequenced adaptation\u0000and optimization.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"104 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213125","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}

{"title":"Settling aerodynamics is a driver of symmetry in deciduous tree leaves","authors":"Matthew D. Biviano, Kaare H. Jensen","doi":"arxiv-2409.05514","DOIUrl":"https://doi.org/arxiv-2409.05514","url":null,"abstract":"Leaves shed by deciduous trees contain 40% of the annually sequestered\u0000carbon, and include nutrients vital to the expansion and health of forest\u0000ecosystems. To achieve this, leaves must fall quickly to land near the parent\u0000tree -- otherwise, they are lost to the wind, like pollen or gliding seeds.\u0000However, the link between leaf shape and sedimentation speed remains unclear.\u0000To gauge the relative performance of extant leaves, we developed an automated\u0000sedimentation apparatus (ASAP) capable of performing $sim100$ free fall\u0000experiments per day on biomimetic paper leaves. The majority of 25\u0000representative leaves settle at rates similar to our control (a circular disc).\u0000Strikingly, the Arabidopsid mutant asymmetric leaves1 (as1) fell 15% slower\u0000than the wild type. Applying the as1-digital mutation to deciduous tree leaves\u0000revealed a similar speed reduction. Data correlating shape and settling across\u0000a broad range of natural, mutated, and artificial leaves support\u0000thefast-leaf-hypothesis: Deciduous leaves are symmetric and relatively unlobed\u0000in part because this maximizes their settling speed and concomitant nutrient\u0000retention.","PeriodicalId":501040,"journal":{"name":"arXiv - PHYS - Biological Physics","volume":"68 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142213126","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}