Pub Date : 2017-12-30DOI: 10.1007/978-3-030-00630-3_21
H. Turlier, T. Betz
{"title":"Fluctuations in Active Membranes","authors":"H. Turlier, T. Betz","doi":"10.1007/978-3-030-00630-3_21","DOIUrl":"https://doi.org/10.1007/978-3-030-00630-3_21","url":null,"abstract":"","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"28 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134501689","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}
Pub Date : 2017-06-04DOI: 10.2174/1875036202013010129
Jiapu Zhang
Molecular dynamics (MD) studies of buffalo prion protein (BufPrP$^text{C}$) [Zhang JP et al.(2016) J Biomol Struct Dyn 34(4):762-777] showed that the structure of this protein is very stable at room temperature (whether under neutral pH or low pH environments). In order to understand the reason why buffalo is lowly susceptible to prion diseases and why BufPrP$^text{C}$ is so stable at room temperature, this paper will prolong our MD running time at room temperature and extend our research to higher temperatures to study this BufPrP$^text{C}$ structure furthermore. From the salt bridge point of view we found an important reason why BufPrP$^text{C}$ is so stable at room temperature and this might be a nice clue of drug discovery or drug design for the treatment of prion diseases.
水牛朊病毒蛋白(BufPrP$^text{C}$)的分子动力学(MD)研究[Zhang JP et al.(2016) J Biomol Struct, 34(4):762-777]表明，该蛋白在室温下(无论是在中性pH还是低pH环境下)具有非常稳定的结构。为了了解水牛对朊病毒疾病的易感性较低的原因，以及为什么BufPrP$^text{C}$在室温下如此稳定，本文将延长我们的MD在室温下的运行时间，并将我们的研究扩展到更高的温度，进一步研究BufPrP$^text{C}$结构。从盐桥的角度，我们发现了BufPrP$^text{C}$在室温下如此稳定的一个重要原因，这可能是治疗朊病毒疾病的药物发现或药物设计的一个很好的线索。
{"title":"Molecular Dynamics Studies of the Bufallo Prion Protein Structured Region at Higher Temperatures","authors":"Jiapu Zhang","doi":"10.2174/1875036202013010129","DOIUrl":"https://doi.org/10.2174/1875036202013010129","url":null,"abstract":"Molecular dynamics (MD) studies of buffalo prion protein (BufPrP$^text{C}$) [Zhang JP et al.(2016) J Biomol Struct Dyn 34(4):762-777] showed that the structure of this protein is very stable at room temperature (whether under neutral pH or low pH environments). In order to understand the reason why buffalo is lowly susceptible to prion diseases and why BufPrP$^text{C}$ is so stable at room temperature, this paper will prolong our MD running time at room temperature and extend our research to higher temperatures to study this BufPrP$^text{C}$ structure furthermore. From the salt bridge point of view we found an important reason why BufPrP$^text{C}$ is so stable at room temperature and this might be a nice clue of drug discovery or drug design for the treatment of prion diseases.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"2013 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131216879","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}
Noise induced hearing loss (NIHL) as one of major avoidable occupational related health issues has been studied for decades. To assess NIHL, the excitation pattern (EP) has been considered as one of mechanisms to estimate movements of basilar membrane (BM) in cochlea. In this study, two auditory filters, dual resonance nonlinear (DRNL) filter and rounded-exponential (ROEX) filter, have been applied to create two EPs, referring as the velocity EP and the loudness EP, respectively. Two noise hazard metrics are also proposed based on the developed EPs to evaluate hazardous levels caused by different types of noise. Moreover, Gaussian noise and pure-tone noise have been simulated to evaluate performances of the developed EPs and noise metrics. The results show that both developed EPs can reflect the responses of BM to different types of noise. For Gaussian noise, there is a frequency shift between the velocity EP and the loudness EP. For pure-tone noise, both EPs can reflect the frequencies of input noise accurately. The results suggest that both EPs can be potentially used for assessment of NIHL.
{"title":"Investigations of Auditory Filters Based Excitation Patterns for Assessment of Noise Induced Hearing Loss","authors":"W. Al-Dayyeni, Pengfei Sun, Jun Qin","doi":"10.24425/123919","DOIUrl":"https://doi.org/10.24425/123919","url":null,"abstract":"Noise induced hearing loss (NIHL) as one of major avoidable occupational related health issues has been studied for decades. To assess NIHL, the excitation pattern (EP) has been considered as one of mechanisms to estimate movements of basilar membrane (BM) in cochlea. In this study, two auditory filters, dual resonance nonlinear (DRNL) filter and rounded-exponential (ROEX) filter, have been applied to create two EPs, referring as the velocity EP and the loudness EP, respectively. Two noise hazard metrics are also proposed based on the developed EPs to evaluate hazardous levels caused by different types of noise. Moreover, Gaussian noise and pure-tone noise have been simulated to evaluate performances of the developed EPs and noise metrics. The results show that both developed EPs can reflect the responses of BM to different types of noise. For Gaussian noise, there is a frequency shift between the velocity EP and the loudness EP. For pure-tone noise, both EPs can reflect the frequencies of input noise accurately. The results suggest that both EPs can be potentially used for assessment of NIHL.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124931466","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}
Pub Date : 2017-05-23DOI: 10.1103/physrevx.8.021006
James Komianos, G. Papoian
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.
{"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}
Pub Date : 2017-04-18DOI: 10.1103/PhysRevFluids.3.033103
A. Mathijssen, Raphaël Jeanneret, M. Polin
Contact between particles and motile cells underpins a wide variety of biological processes, from nutrient capture and ligand binding to grazing, viral infection, and cell-cell communication. The window of opportunity for these interactions depends on the basic mechanism determining contact time, which is currently unknown. By combining experiments on three different species—Chlamydomonas reinhardtii, Tetraselmis subcordiforms, and Oxyrrhis marina—with simulations and analytical modeling, we show that the fundamental physical process regulating proximity to a swimming microorganism is hydrodynamic particle entrainment. The resulting distribution of contact times is derived within the framework of Taylor dispersion as a competition between advection by the cell surface and microparticle diffusion, and predicts the existence of an optimal tracer size that is also observed experimentally. Spatial organization of flagella, swimming speed, and swimmer and tracer size influence entrainment features and provide tradeoffs that may be tuned to optimize the estimated probabilities for microbial interactions like predation and infection.
{"title":"Universal entrainment mechanism controls contact times with motile cells","authors":"A. Mathijssen, Raphaël Jeanneret, M. Polin","doi":"10.1103/PhysRevFluids.3.033103","DOIUrl":"https://doi.org/10.1103/PhysRevFluids.3.033103","url":null,"abstract":"Contact between particles and motile cells underpins a wide variety of biological processes, from nutrient capture and ligand binding to grazing, viral infection, and cell-cell communication. The window of opportunity for these interactions depends on the basic mechanism determining contact time, which is currently unknown. By combining experiments on three different species—Chlamydomonas reinhardtii, Tetraselmis subcordiforms, and Oxyrrhis marina—with simulations and analytical modeling, we show that the fundamental physical process regulating proximity to a swimming microorganism is hydrodynamic particle entrainment. The resulting distribution of contact times is derived within the framework of Taylor dispersion as a competition between advection by the cell surface and microparticle diffusion, and predicts the existence of an optimal tracer size that is also observed experimentally. Spatial organization of flagella, swimming speed, and swimmer and tracer size influence entrainment features and provide tradeoffs that may be tuned to optimize the estimated probabilities for microbial interactions like predation and infection.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"7 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128341973","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}
The cable model is widely used in several fields of science to describe the propagation of signals. A relevant medical and biological example is the anomalous subdiffusion in spiny neuronal dendrites observed in several studies of the last decade. Anomalous subdiffusion can be modelled in several ways introducing some fractional component into the classical cable model. The Chauchy problem associated to these kind of models has been investigated by many authors, but up to our knowledge an explicit solution for the signalling problem has not yet been published. Here we propose how this solution can be derived applying the generalized convolution theorem (known as Efros theorem) for Laplace transforms.The fractional cable model considered in this paper is defined by replacing the first order time derivative with a fractional derivative of order α ∈ (0, 1) of Caputo type. The signalling problem is solved for any input function applied to the accessible end of a semi-infinite cable, which satisfies the requir...
{"title":"Fractional cable model for signal conduction in spiny neuronal dendrites","authors":"S. Vitali, F. Mainardi","doi":"10.1063/1.4981944","DOIUrl":"https://doi.org/10.1063/1.4981944","url":null,"abstract":"The cable model is widely used in several fields of science to describe the propagation of signals. A relevant medical and biological example is the anomalous subdiffusion in spiny neuronal dendrites observed in several studies of the last decade. Anomalous subdiffusion can be modelled in several ways introducing some fractional component into the classical cable model. The Chauchy problem associated to these kind of models has been investigated by many authors, but up to our knowledge an explicit solution for the signalling problem has not yet been published. Here we propose how this solution can be derived applying the generalized convolution theorem (known as Efros theorem) for Laplace transforms.The fractional cable model considered in this paper is defined by replacing the first order time derivative with a fractional derivative of order α ∈ (0, 1) of Caputo type. The signalling problem is solved for any input function applied to the accessible end of a semi-infinite cable, which satisfies the requir...","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"138 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129246268","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}
Pub Date : 2016-08-17DOI: 10.1017/9781316584200.009
Steven Weinstein, Theodore P. Pavlic
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.
{"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}
Pub Date : 2016-07-28DOI: 10.3934/matersci.2016.3.1138
S. Trinschek, Karin John, U. Thiele
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.
{"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}
Pub Date : 2016-07-27DOI: 10.1103/PHYSREVFLUIDS.1.043202
Justas Dauparas, E. Lauga
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.
在营养丰富的基质上，鞭毛细菌可以分化成群体状态，密集地在表面上移动。最近的一项实验测量了大肠杆菌群周围流体的流动(Wu, Hosu和Berg, 2011 Proc. Natl.)。学会科学。美国108 4147)。在蜂群前方顺时针方向观察到系统的手性流动(从上方观察)，流动速度约为$10~mu$m/s，约为蜂群边缘径向速度的3倍。可行的假设是，这种流动是由于停在菌落边缘的细胞向外伸展鞭毛丝的作用，使液体在原始琼脂上流动。在这项工作中，我们定量地检验了他的假设。我们首先建立了薄膜中单个鞭毛诱导的流动的解析模型，然后将该模型及其扩展到多个鞭毛，与实验测量结果进行比较。我们得到的结果与鞭毛假说一致。该模型提供了进一步的定量洞察鞭毛的方向和空间分布，以及切向速度分布。特别是，该模型表明鞭毛平均呈放射状指向群外，而不是切向包裹。
{"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}
Pub Date : 2016-06-30DOI: 10.17725/rensit.2016.08.025
O. Gradov
Since the pioneering works of the founder of membrane mimetic chemistry Janos H. Fendler it is known that a number of atomic or molecular clusters and films (including nanoscale ones) are capable of mimicking the membrane functions. Membrane mimetic materials can be either soft matter or solid state materials. Conducting films (including those with magnetic properties) and semiconductors are also known to possess membrane mimetic properties. If we consider the agent exchange through the membrane in the operator form, the chemical composition of the membranes and their models, as well as the difference between the atomic and molecular clusters or layers become not so essential, and hence, membrane mimetic chemistry of nano- and mesostructures do not differ significantly within the agent-based approach. This invited review containing several parts reflects the main aspects of the author's report at the conference "Graphene: a molecule and 2D-crystal" (September 8-12, 2015, Novosibirsk, Russia) and considers various aspects of the similarity between the graphene nanostructures, membranes and bionic membrane-like nanomaterials.
自从膜模拟化学的创始人Janos H. Fendler的开创性工作以来，人们已经知道许多原子或分子团簇和薄膜(包括纳米级的)能够模仿膜的功能。膜模拟材料可以是软物质也可以是固态材料。导电薄膜(包括具有磁性的薄膜)和半导体也已知具有膜模拟特性。如果我们以操作符的形式考虑介质通过膜的交换，那么膜的化学组成及其模型，以及原子和分子簇或层之间的差异就变得不那么重要了，因此，在基于介质的方法中，纳米和介观结构的膜模拟化学没有显着差异。这篇特邀综述包含几个部分，反映了作者在“石墨烯:分子和2d晶体”会议(2015年9月8-12日，俄罗斯新西伯利亚)上报告的主要方面，并考虑了石墨烯纳米结构、膜和仿生膜样纳米材料之间的相似性。
{"title":"Can graphene bilayers be the membrane mimetic materials","authors":"O. Gradov","doi":"10.17725/rensit.2016.08.025","DOIUrl":"https://doi.org/10.17725/rensit.2016.08.025","url":null,"abstract":"Since the pioneering works of the founder of membrane mimetic chemistry Janos H. Fendler it is known that a number of atomic or molecular clusters and films (including nanoscale ones) are capable of mimicking the membrane functions. Membrane mimetic materials can be either soft matter or solid state materials. Conducting films (including those with magnetic properties) and semiconductors are also known to possess membrane mimetic properties. If we consider the agent exchange through the membrane in the operator form, the chemical composition of the membranes and their models, as well as the difference between the atomic and molecular clusters or layers become not so essential, and hence, membrane mimetic chemistry of nano- and mesostructures do not differ significantly within the agent-based approach. This invited review containing several parts reflects the main aspects of the author's report at the conference \"Graphene: a molecule and 2D-crystal\" (September 8-12, 2015, Novosibirsk, Russia) and considers various aspects of the similarity between the graphene nanostructures, membranes and bionic membrane-like nanomaterials.","PeriodicalId":360136,"journal":{"name":"arXiv: Biological Physics","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130596389","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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