arXiv: Biological Physics最新文献_第3页

arXiv: Biological Physics Pub Date : 2017-12-30 DOI: 10.1007/978-3-030-00630-3_21

H. Turlier, T. Betz

引用次数: 7

Molecular Dynamics Studies of the Bufallo Prion Protein Structured Region at Higher Temperatures 高温下布法罗朊病毒蛋白结构区的分子动力学研究

arXiv: Biological Physics Pub Date : 2017-06-04 DOI: 10.2174/1875036202013010129

Jiapu Zhang

引用次数: 0

Investigations of Auditory Filters Based Excitation Patterns for Assessment of Noise Induced Hearing Loss 基于听觉过滤器的激励模式在噪声性听力损失评估中的研究

arXiv: Biological Physics Pub Date : 2017-05-30 DOI: 10.24425/123919

W. Al-Dayyeni, Pengfei Sun, Jun Qin

引用次数: 3

Stochastic Ratcheting on a Funneled Energy Landscape is Necessary for Highly Efficient Contractility of Actomyosin Force Dipoles 漏斗能量景观上的随机棘轮是肌动球蛋白力偶极子高效收缩的必要条件

arXiv: Biological Physics Pub Date : 2017-05-23 DOI: 10.1103/physrevx.8.021006

James Komianos, G. Papoian

{"title":"Stochastic Ratcheting on a Funneled Energy Landscape is Necessary for Highly Efficient Contractility of Actomyosin Force Dipoles","authors":"James Komianos, G. Papoian","doi":"10.1103/physrevx.8.021006","DOIUrl":"https://doi.org/10.1103/physrevx.8.021006","url":null,"abstract":"Current understanding of how contractility emerges in disordered actomyosin networks of non-muscle cells is still largely based on the intuition derived from earlier works on muscle contractility. This view, however, largely overlooks the free energy gain following passive cross-linker binding, which, even in the absence of active fluctuations, provides a thermodynamic drive towards highly overlapping filamentous states. In this work, we shed light on this phenomenon, showing that passive cross-linkers, when considered in the context of two anti-parallel filaments, generate noticeable contractile forces. However, as binding free energy of cross-linkers is increased, a sharp onset of kinetic arrest follows, greatly diminishing effectiveness of this contractility mechanism, allowing the network to contract only with weakly resisting tensions at its boundary. We have carried out stochastic simulations elucidating this mechanism, followed by a mean-field treatment that predicts how contractile forces asymptotically scale at small and large binding energies, respectively. Furthermore, when considering an active contractile filament pair, based on non-muscle myosin II, we found that the non-processive nature of these motors leads to highly inefficient force generation, due to recoil slippage of the overlap during periods when the motor is dissociated. However, we discovered that passive cross-linkers can serve as a structural ratchet during these unbound motor time spans, resulting in vast force amplification. Our results shed light on the non-equilibrium effects of transiently binding proteins in biological active matter, as observed in the non-muscle actin cytoskeleton, showing that highly efficient contractile force dipoles result from synergy of passive cross-linker and active motor dynamics, via a ratcheting mechanism on a funneled energy landscape.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"35 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131225295","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: 17

Universal entrainment mechanism controls contact times with motile cells 通用夹带机制控制与运动细胞的接触时间

arXiv: Biological Physics Pub Date : 2017-04-18 DOI: 10.1103/PhysRevFluids.3.033103

A. Mathijssen, Raphaël Jeanneret, M. Polin

引用次数: 24

Fractional cable model for signal conduction in spiny neuronal dendrites 棘神经元树突信号传导的分数索模型

arXiv: Biological Physics Pub Date : 2017-02-17 DOI: 10.1063/1.4981944

S. Vitali, F. Mainardi

引用次数: 3

Noise and function 噪音与功能

arXiv: Biological Physics Pub Date : 2016-08-17 DOI: 10.1017/9781316584200.009

Steven Weinstein, Theodore P. Pavlic

{"title":"Noise and function","authors":"Steven Weinstein, Theodore P. Pavlic","doi":"10.1017/9781316584200.009","DOIUrl":"https://doi.org/10.1017/9781316584200.009","url":null,"abstract":"Noise is widely understood to be something that interferes with a signal or process. Thus, it is generally thought to be destructive, obscuring signals and interfering with function. However, early in the 20th century, mechanical engineers found that mechanisms inducing additional vibration in mechanical systems could prevent sticking and hysteresis. This so-called \"dither\" noise was later introduced in an entirely different context at the advent of digital information transmission and recording in the early 1960s. Ironically, the addition of noise allows one to preserve information that would otherwise be lost when the signal or image is digitized. As we shall see, the benefits of added noise in these contexts are closely related to the phenomenon which has come to be known as stochastic resonance, the original version of which appealed to noise to explain how small periodic fluctuations in the eccentricity of the earth's orbit might be amplified in such a way as to bring about the observed periodic transitions in climate from ice age to temperate age and back. These noise-induced transitions have since been invoked to explain a wide array of biological phenomena, including the foraging and tracking behavior of ants. Many biological phenomena, from foraging to gene expression, are noisy, involving an element of randomness. In this paper, we illustrate the general principles behind dithering and stochastic resonance using examples from image processing, and then show how the constructive use of noise can carry over to systems found in nature.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"115 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114444361","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: 2

From a thin film model for passive suspensions towards the description of osmotic biofilm spreading 从被动悬浮液的薄膜模型到渗透生物膜扩散的描述

arXiv: Biological Physics Pub Date : 2016-07-28 DOI: 10.3934/matersci.2016.3.1138

S. Trinschek, Karin John, U. Thiele

{"title":"From a thin film model for passive suspensions towards the description of osmotic biofilm spreading","authors":"S. Trinschek, Karin John, U. Thiele","doi":"10.3934/matersci.2016.3.1138","DOIUrl":"https://doi.org/10.3934/matersci.2016.3.1138","url":null,"abstract":"Biofilms are ubiquitous macro-colonies of bacteria that develop at various interfaces (solid- liquid, solid-gas or liquid-gas). The formation of biofilms starts with the attachment of individual bac- teria to an interface, where they proliferate and produce a slimy polymeric matrix - two processes that result in colony growth and spreading. Recent experiments on the growth of biofilms on agar substrates under air have shown that for certain bacterial strains, the production of the extracellular matrix and the resulting osmotic influx of nutrient-rich water from the agar into the biofilm are more crucial for the spreading behaviour of a biofilm than the motility of individual bacteria. We present a model which de- scribes the biofilm evolution and the advancing biofilm edge for this spreading mechanism. The model is based on a gradient dynamics formulation for thin films of biologically passive liquid mixtures and suspensions, supplemented by bioactive processes which play a decisive role in the osmotic spreading of biofilms. It explicitly includes the wetting properties of the biofilm on the agar substrate via a dis- joining pressure and can therefore give insight into the interplay between passive surface forces and bioactive growth processes.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"39 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114201395","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: 15

Flagellar flows around bacterial swarms 鞭毛在细菌群周围流动

arXiv: Biological Physics Pub Date : 2016-07-27 DOI: 10.1103/PHYSREVFLUIDS.1.043202

Justas Dauparas, E. Lauga

{"title":"Flagellar flows around bacterial swarms","authors":"Justas Dauparas, E. Lauga","doi":"10.1103/PHYSREVFLUIDS.1.043202","DOIUrl":"https://doi.org/10.1103/PHYSREVFLUIDS.1.043202","url":null,"abstract":"Flagellated bacteria on nutrient-rich substrates can differentiate into a swarming state and move in dense swarms across surfaces. A recent experiment measured the flow in the fluid around an Escherichia coli swarm (Wu, Hosu and Berg, 2011 Proc. Natl. Acad. Sci. USA 108 4147). A systematic chiral flow was observed in the clockwise direction (when viewed from above) ahead of the swarm with flow speeds of about $10~mu$m/s, about 3 times greater than the radial velocity at the edge of the swarm. The working hypothesis is that this flow is due to the action of cells stalled at the edge of a colony that extend their flagellar filaments outwards, moving fluid over the virgin agar. In this work we quantitatively test his hypothesis. We first build an analytical model of the flow induced by a single flagellum in a thin film and then use the model, and its extension to multiple flagella, to compare with experimental measurements. The results we obtain are in agreement with the flagellar hypothesis. The model provides further quantitative insight into the flagella orientations and their spatial distributions as well as the tangential speed profile. In particular, the model suggests that flagella are on average pointing radially out of the swarm and are not wrapped tangentially.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"37 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122336934","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: 10

Can graphene bilayers be the membrane mimetic materials 石墨烯双层能否成为膜类材料

arXiv: Biological Physics Pub Date : 2016-06-30 DOI: 10.17725/rensit.2016.08.025

O. Gradov

引用次数: 0