Preliminary list of poster contributions
| Ao, Xue | Biased diffusion of active particles in confined geometries | Abstract |
| Becker, Thijs | Diffusion of Interacting Particles in Discrete Geometries | Abstract |
| Chacón-Acosta, Guillermo | Effective One-dimensional Diffusion on Curved Surfaces | Abstract |
| Contino, Matteo | Microorganism motility in 2D porous materials | Abstract |
| Flegel, Franziska | Dynamical localization and eigenstate localization | Abstract |
| Fouladvand, Ebrahim | A molecular dynamics study of a two dimensional system of hard ellipses | Abstract |
| Godec, Aljaz | Ultraweak ergodicity breaking in superdiffusive Levy walks | Abstract |
| Groß, Torsten | Self-organized escape of linear chains in nonlinear potentials | Abstract |
| Guerrier, Claire | Modeling vesicle trafficking in the pre-synaptic terminal | Abstract |
| Hafner, Anne | Intermittent Motion of Motor Proteins in Biological Environments | Abstract |
| Kang, Shuo | Probing the first-passsage time of single molecules in a nanochannel | Abstract |
| Khatami, Maryam | Trapping Self-propelled Particles | Abstract |
| Klein, Sarah | Cooperative Cargo Transport by Teams of Molecular Motors | Abstract |
| Kolb, Jakob | Reaction rates over fluctuating barriers | Abstract |
| Kroy, Klaus | Internal Brownian dynamics boosts friction of recoiling DNA | Abstract |
| Li, Yunyun | Rectification of channeled particles and waves in a rotational field | Abstract |
| Malgaretti, Paolo | Electrokinetic transport in confined geometries | Abstract |
| Milster, Sebastian | Active Brownian particles with repulsive interactions in confined vessels | Abstract |
| Misiunas, Karolis | Hindered diffusion coefficients of spherical particles confined by microchannels | Abstract |
| Motz, Thomas | Improved entropic splitter for particle separation | Abstract |
| Nelissen, Kwinten | Enhanced Absorption by tuning pore loading in discrete geometries | Abstract |
| Pineda, Inti | Effective diffusion coefficient for two-dimensional narrow asymmetric channels | Abstract |
| Roy, Anjan | Tagged particle diffusion in one-dimensional systems with Hamiltonian Dynamics | Abstract |
| Sadjadi, Zeinab | Influence of Cytoskeletal Anisotropy on Transport Properties of Molecular Motors | Abstract |
| Sitta, Christoph | Kinks in diffusion profiles and sharp penetration fronts in dissolving semi-crystalline polymers | Abstract |
| Thiel, Felix | Weak ergodicity breaking in subordinated Gaussian processes | Abstract |
| Yang, Jing | Periplasmal physics: The rotational dynamics of spirochetal flagella | Abstract |
| Biased diffusion of active particles in confined geometries Ao, Xue ( University of Augsburg, Institute for Physics, Augsburg, Germany) |
Stimulated by recent developments in synthesizing nano- and microsized 'active' particles with partially functionalized surface [1], much theoretical effort is put in the modelling of their dynamics [2], which is distinguishedly different to those of 'passive' particles exhibiting standard Brownian motion. However, while most studies focuses on the unconfined movement [3], the influence of geometrical restriction on the active particles' dynamics is hardly considered. In this poster we focus on the ongoing project of investigations on the transport of 'active' microswimmers through channels and pores. At the preliminary stage, theoretical modeling in 2D and a subsequent numerical simulation has been performed to study the dynamics of the active particle. The role of the confinement for the biased transport of the active particle, which is the challenge of this project, is expected to be roughly comprehended from the preliminary results. After the function of the geometrical confinement on the dynamics of an active particle is unveiled by our further research, the detailed understanding, modeling and control of these transport processes can serve as basis for the development of separation devices. |
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| Diffusion of Interacting Particles in Discrete Geometries Becker, Thijs (Hasselt University, Faculty of Sciences, Hasselt, Belgium) |
We evaluate the self-diffusion and transport diffusion of interacting particles in a discrete geometry consisting of a linear chain of cavities, with interactions within a cavity described by a free-energy function. Exact analytical expressions are obtained in the absence of correlations, showing that the self- diffusion can exceed the transport diffusion if the free-energy function is concave. The effect of correlations is elucidated by comparison with numerical results. Quantitative agreement is obtained with recent experimental data for diffusion in a nanoporous zeolitic imidazolate framework material, ZIF-8. |
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| Effective One-dimensional Diffusion on Curved Surfaces Chacón-Acosta, Guillermo (Universidad Autonoma Metropolitana-Cuajimalpa , Applied Mathematics and Systems , Mexico City, Mexico) |
We present the derivation of a general effective diffusion coefficient to describe the two dimensional (2D) diffusion in a narrow and smoothly asymmetric channel of varying width that lies on a curved surface. We generalize the well known Kalinay-Percus projection method for the asymmetric channels, to project the anisotropic two dimensional diffusion equation on a smooth curved manifold, into an effective one dimensional generalized Fick-Jacobs-like equation that is modified due to the curvature of the surface. We study the perturbation series up to the n-th order, and we derive the full effective diffusion coefficient for the two dimensional diffusion in a narrow asymmetric channel with modifications due to the curved metric. This is the analogous of the Dagdug-Pineda coefficient extended for curved spaces. Finally, we present several examples of symmetric surfaces, namely, the sphere, the pseudosphere, the catenoid and the torus, and we study the diffusion on a conical asymmetric channel with varying slope on them. |
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| Microorganism motility in 2D porous materials Contino, Matteo (University of Warwick, Physics, Coventry, United Kingdom) |
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| Dynamical localization and eigenstate localization Flegel, Franziska (Humboldt-Universität zu Berlin, Institut für Physik, AG Statistische Physik und nichtlineare Dynamik, Berlin, Germany) |
We investigate the phenomenon of dynamical localization in a 1D trap model with Pareto-distributed waiting times in the subdiffusive case by considering the spectral properties of the corresponding transition matrix. |
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| A molecular dynamics study of a two dimensional system of hard ellipses Fouladvand, Ebrahim (Zanjan University & IPM, Institute for studies in Theyoritical physics and mathmatics (IPM), Physics, Tehran, Iran, Islamic Republic of) |
We have simulated the dynamics of a two dimensional system of hard ellipses by event-oriented molecular dynamics in NEV ensemble. Various quantities namely longitudinal and transverse velocity auto-correlation functions, translational and rotational diffusion mean squared displacements, pressure, intermediate self scattering function, radial distribution function and angular spatial correlation have been obtained and their dependence on packing fraction is characterised. Despite absence of prominent positional ordering, the orientational degree of freedom behaves nontrivially and exhibits interesting features. Slowing down is observed in the angular part of the motion near isotropic-nematic phase transition. It is shown that above a certain packing fraction the rotational mean squared displacement exhibits a three stage temporal regime including a plateau. Comparison to 2D system of hard needles is made and it is shown that from positional viewpoint, the ellipse system is more ordered. |
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| Ultraweak ergodicity breaking in superdiffusive Levy walks Godec, Aljaz (University of Potsdam, Institute for Physics and Astronomy, Theoretical Physics, Germany) |
We study the ergodic properties of superdiffusive, spatiotemporally coupled L{'e}vy walk (LW) processes. We consider separately the effect of finite system size and finite length of trajectories. We reveal a distinct scatter of the scaling exponents of the time averaged mean squared displacement $overline{ delta^2}$ around the ensemble value $3-alpha$ ($1 |
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| Self-organized escape of linear chains in nonlinear potentials Groß, Torsten (Humboldt-Universität zu Berlin, Institut für Physik, ) |
An enhancement of localized nonlinear modes in coupled systems gives rise to a novel type of escape process. A deterministic concentration of energy into small chain sections causes their transgression over a potential barrier and a subsequent escape of the entire chain from a meta-stable potential basin. The emergence of localized breathers can cause a deterministic chain to escape even more efficiently than one driven by thermal fluctuations. Nevertheless, the latter also exhibits breather modes that foster an escape. Through the understanding of such collective behaviour we intend to offer a new perspective on escape processes. |
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| Modeling vesicle trafficking in the pre-synaptic terminal Guerrier, Claire (Ecole Normale Superieure, Institut de Biologie de l'ENS, Paris, France) |
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| Intermittent Motion of Motor Proteins in Biological Environments Hafner, Anne (Universität des Saarlandes, Fachrichtung Theoretische Physik, Saarbrücken, Germany) |
Motor proteins exhibit different types of anomalous diffusive behavior depending on whether or not they attach to cytoskeletal filaments. While they experience subdiffusive dynamics within the cytoplasm due to a crowded environment, they usually move superdiffusively at short time scales due to the active transport on the filament network, followed by a normal diffusion at long times. Here we study an intermittent motion, composed of two different modes of motility, which mimic the properties of the biological environment. By means of extensive Monte Carlo simulations we investigate how the overall transport properties depend on the structural properties of the filament network, the stepping strategy in the crowded cytoplasm, and the motor processivity. The fraction of time spent in each state (set by binding/unbinding rates between filament and cytoplasm) acts as an order parameter for the efficiency of the long-distance transfer of materials. In the case that the motors are not allowed to diffuse in the surrounding medium after detachment from filaments, they just halt motion on the cytoskeleton. We address the influence of such waiting times on the transport properties. |
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| Probing the first-passsage time of single molecules in a nanochannel Kang, Shuo (University Twente, MESA+ Institute for Nanotechnology, TNW, Enschede, Netherlands) |
The diffusive mass transport of individual redox molecules was probed experimentally in microfabricated nanogap transducers. The first-passage times of single molecules exiting a detection region were extracted and the resulting distribution was compared with quantitative analytical predictions. The results suggest that different adsorption processes dominate at trace analyte levels. |
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| Trapping Self-propelled Particles Khatami, Maryam (Sharif University of Technology, sharif university of technology, Physics, Tehran, Iran, Islamic Republic of) |
Trapping of micron-sized self-propelled particles such as bacteria and other microbes is of essential importance in health sciences and biophysics. By means of a computer simulation of a two-dimensional system of self-propelled particles, we have shown that a star trap can effectively catch these particles. Changing star trap's number of teeth and its gaps' width, a geometry has been reached which minimizes trapping time. This kind of trap is also useful in high concentrations of particles. |
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| Cooperative Cargo Transport by Teams of Molecular Motors Klein, Sarah (Universite Paris - Sud, Laboratoire de Physique Théorique ORSAY, ORSAY Dedex, France) |
Many different types of cargos are transported bidirectionally along microtubules by teams of molecular motors. The motion of this cargo-motors system has been experimentally characterized in vivo as processive with rather persistent directionality. Different theoretical approaches have been suggested in order to explore the origin of this kind of motion [1,2]. We introduce a model to propagate a cargo in continuous time while we consider the single motor positions. In this contribution we discuss the short and long time regimes of diffusion. Furthermore, we analyze the influence of the number of motors on the cooperative motion. |
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| Reaction rates over fluctuating barriers Kolb, Jakob (Helmholtz-Zentrum Berlin für Materialien und Energie, Helmholtz Zentrum Berlin(HZB), Soft Matter and Functional Materials, Berlin, Germany) |
Recent studies on tunable nano-reactors with a thermosensitive polymer shell have shown curious effects in reaction rates right at the polymer critical solution temperature. The shell is presumably stochastically fluctuating between states with different permeability for the substrate. To investigate this effect a simplified system of diffusing particles in the vicinity of a spherical sink shielded by a metastable potential barrier is investigated. We derive an implicit solution for the resulting Fokker-Planck equation to obtain the diffusion-controlled reaction rate and verify these results with Brownian dynamics computer simulations. The system shows resonant activation as previously seen with thermally activated escape over fluctuating barriers. |
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| Internal Brownian dynamics boosts friction of recoiling DNA Kroy, Klaus (Universität Leipzig, Institut für Theoretische Physik, Fakultät für Physik und Geowissenschaften, ) |
Macroscopic objects are usually manipulated by force and observed with light. On the nanoscale, however, this is often done oppositely: individual macromolecules are manipulated by light and monitored with force. This procedure, which is the basis of single-molecule force spectroscopy, has led to much of our quantitative understanding of how DNA works, and is now routinely applied to explore molecular structure and interactions, DNA–protein reactions and protein folding. Here we develop the technique further by introducing a dynamic force spectroscopy set-up for a non-invasive inspection of the tension dynamics in a taut strand of DNA. The internal contraction after a sudden release of the molecule is shown to give rise to a drastically enhanced viscous friction, as revealed by the slow relaxation of an attached colloidal tracer. Our systematic theory explains the data quantitatively and provides a powerful tool for the rational design of new dynamic force spectroscopy assays. THIS POSTER IS PRESENTED TOGETHER WITH U.F. Keyser (Cambridge) |
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| Rectification of channeled particles and waves in a rotational field Li, Yunyun (Tongji University, School of Physical Science and Engineering, Shanghai, China, People's Republic of) |
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| Electrokinetic transport in confined geometries Malgaretti, Paolo (Universitat de Barcelona, Facultat de Física, Departament de Física Fonamental, Barcelona, Spain) |
We study the motion of charged and neutral tracers, in an z-z electrolyte embedded in a varying section channel. Making use of systematic approximations, we map the convection diffusion equation governing the motion of tracers density in an effective $1D$ equation describing the dynamic along the channel where its varying-section is encoded as an effective entropic potential. We describe the onset of a novel electro-osmotic flow velocity pattern whit regions of the channel in which the electrolyte moves against the average fluid flow. When we put charged tracer in such a framework their velocities are strongly affected hence leading to a modulation of the current that can even switch its sign. For higher values of the channel corrugation some tracers move against the average fluid flow hence leading to an alternative device for particle separation. Finally negative mobility of neutral tracers, optically trapped along the longitudinal axis of the channel, spontaneously arises as the net effect of the geometrically-modulated fluid flux. |
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| Active Brownian particles with repulsive interactions in confined vessels Milster, Sebastian (Humboldt-Universität zu Berlin, Physics, Berlin, Germany) |
This works investigates active Brownian particles in two dimensions described by the Schienbein-Gruler velocity dependent friction model. Applying binary repulsive interactions via a Debye potential the system exhibits collective motion and spontaneous symmetry breaking in dependence of the chosen confinement. Various geometrical setups have been applied and parameters as noise intensity, particle density and interaction strength have been examined to extract the regimes for the emergence of distinct patterns. In circular vessels the particles move vortically in either direction of rotation. Thermal fluctuations as well as a broken cyclic symmetry reduce the stability of the collective state and facilitate switching in the rotational direction. |
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| Hindered diffusion coefficients of spherical particles confined by microchannels Misiunas, Karolis (University of Cambridge, Cavendish Laboratory, Department of Physics, Cambirdge, United Kingdom) |
We present here the measurement of the diffusivity of spherical particles closely confined by narrow microchannels. Our experiments yield a 2D map of the position-dependent diffusion coefficients parallel and perpendicular to the channel axis with a resolution of down to 129 nm. The diffusivity was measured simultaneously in the channel interior, the bulk reservoirs as well as the channel entrance region. In the channel interior we found strongly anisotropic diffusion. While the perpendicular diffusion coefficient decreased with the distance to the confining walls down to approximately 25% of the value on the channel axis, the parallel diffusion coefficient remained constant throughout the entire channel width. In addition to the experiment, we performed finite element simulations for the diffusivity in the channel interior and found good agreement with the measurements. Our results reveal the distinctive influence of strong confinement on Brownian motion which is of significance to microfluidics as well as quantitative models of facilitated membrane transport. |
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| Improved entropic splitter for particle separation Motz, Thomas (University of Ulm, Theorie der kondensierten Materie, Ulm, Germany) |
Entropic transport of finite sized particles through confined geometries is investigated by numerical Langevin simulations. It is assumed that spherical particles, which are not interacting among each other, are exposed to a combination of a static force and a time dependent force. The confinement is a highly asymmetric periodical structure which is characterized by a corrugated profile that causes a preferential direction of the diffusing particles. The width of the bottlenecks have the same order of magnitude as the particles' radii. With this set-up an efficient size-dependent particle separation is possible.newline The goal of this work is to find parameters of the asymmetric geometry and the applied time dependent external forces that deliver a high efficiency for the splitting of spherical particles with different radii. Therefore, the role of the geometrical parameters bottleneck width and total width of the confinement on the one hand, and the influences of different amplitudes and frequencies of the external oscillating force on the other hand are investigated. The results of this work should be useful when implementing a device experimentally, which enables to split particles like DNA fragments dependent on their size. |
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| Enhanced Absorption by tuning pore loading in discrete geometries Nelissen, Kwinten (Universiteit Antwerpen, Universiteit Hasselt, Physics, Antwerp, Belgium) |
Diffusion refers to the process were particles are flowing in the direction of a falling concentration. Till recently, this particle flux was found to be slowed down by imposing an opposing flux, but in an experiment published in Phys. Rev. Lett. [1], this rate was found to be enhanced rather than slowed down by an opposing flux of particles. Here, we will show that the absorption of guest particles in zeolite-like structures can be enhanced by preloading the pores with a certain concentration of host particles. This enhancement is explained by the strong interparticle interaction and the specific form of the confining geometry. Further an optimal absorption was found for critical pore loadings. [1] C. Chmelik, H. Bux, J. Caro, L. Heinke, F. Hibbe, T. Titze, and J. Karger, Phys. Rev. Lett. 104, 085902 (2010). |
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| Effective diffusion coefficient for two-dimensional narrow asymmetric channels Pineda, Inti (Universidad Autonoma Metropolitana-Iztapalapa, Department of Physics, Mexico City, Mexico) |
The transport of molecules and small particles spatially constrained has gained increasing attention over the last decade, as such systems are ubiquitous in both nature and technology. Typical structures like pores, tubes or fibers, are quasi one-dimensional, such that we need to solve 2 + 1 or 3 +1 dimensional differential equations to describe correctly transport along them. The so-called Fick-Jacobs approach dramatically simplifies the problem if one assumes that a solute distribution in any cross-section of the channel is uniform at equilibrium. This study focuses on the mapping of the diffusion equation in a two-dimensional narrow and smoothly asymmetric channel of varying width onto the longitudinal coordinate. We present a generalization to the case of an asymmetric channel using the projection method introduced earlier by Kalinay and Percus. We derive an expansion of the effective diffusion coefficient, which represents corrections to the Fick-Jacobs equation and contains all the well-known previous results as special cases. Finally, using Brownian dynamics we study some specific two-dimensional asymmetric channel configurations to test the applicability of this effective diffusion coefficient formula. |
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| Tagged particle diffusion in one-dimensional systems with Hamiltonian Dynamics Roy, Anjan (Raman Research Institute, Theoretical Physics, Bangalore, India) |
Observing the dynamics of a single tagged particle in a many particle system constitute a simple way of probing the complex dynamics of an interacting may body sytem. We present our results on tagged particle diffusion in a one-dimensional gas of classical point particles evolving under Hamiltonian dynamics between fixed and periodic walls. Systems studied include equal and alternate mass hard particle gas, the harmonic chain and anharmonic chains such as Fermi-Pasta-Ulam and Lennard-Jones chains. We have studied both short time regime when the effect of boundary is not felt and the tagged particle behaves as if in an infinite system, as well as long time regime when finite size effect comes into play. |
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| Influence of Cytoskeletal Anisotropy on Transport Properties of Molecular Motors Sadjadi, Zeinab (Universität des Saarlandes, Theoretische Physik , FR 7.1 Theoretical Physics, Saarbrucken, Germany) |
Cytoskeleton consists of a variety of interconnected biopolymer networks, including filamentous actin, microtubules, and several types of intermediate filaments. Motor proteins perform directed motion along cytoskeleton due to the structural asymmetry of the filaments. The long-distance intracellular transport becomes feasible through the active transport on microtubule networks which span through the entire cell. On the other hand, the dynamics is relatively slow on actin filaments which can be found e.g. near the cell membrane, and have a more random structure i.e. a more uniform polarity. One usually observes a gradual change in the cytoskeletal anisotropy from the nucleus to the cell membrane, as the relative contribution of the microtubules and actin filaments changes. We study the effect of cytoskeletal anisotropy on the transport properties of motor proteins. Different scenarios for the gradient of anisotropy are investigated in the framework of a previously developed analytical approach, and the results are compared with Monte Carlo simulations. Collaborators: * Zeinab Sadjadi M. Reza Shaebani |
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| Kinks in diffusion profiles and sharp penetration fronts in dissolving semi-crystalline polymers Sitta, Christoph (Heinrich-Heine-Universität Düsseldorf, Institut für Theoretische Physik II: Weiche Materie, Düsseldorf, Germany) |
The movement of small molecules in solid materials has far reaching implications for such diverse problems as steel embrittlement and food production. Diffusion of solvents in and through polymer matrices is important for applications as wide-ranging as drug-delivery and packaging and has been widely discussed. When a resulting change in solvent concentration causes the polymer to pass through its glass or melting transition, the diffusional behaviour has often been described as non-Fickian. Using modern neutron radiography, we have followed on a microscopic level the in-situ dissolution of a tablet of semi-crystalline poly(ethylene oxide) which exhibits such a melting transition when contacted with water. We show that the pronounced kink visible in the measured time-dependent concentration profiles can be explained using Fickian diffusion equations with a concentration-dependent diffusion coefficient. Fundamentally, the success of our approach has important implications. Practically, its use should facilitate the rational design of many applications where small molecules move in materials. |
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| Weak ergodicity breaking in subordinated Gaussian processes Thiel, Felix (Humboldt-Universität zu Berlin, Institut für Physik, Berlin, Germany) |
Weak ergodicity breaking denotes the non-coincidence of time and ensemble averages in systems with a fully accessible state space. It may occur due to non-stationarity or aging of the process and can also lead to randomness in time averaged quantities calculated from different realizations. This heterogeneity of the process's ensemble is quantified with the so called “ergodicity breaking parameter”. This parameter is calculated for a certain class random processes, namely those that can be represented as X(t) = Y(U(t)), with a Gaussian process Y(u) and a non-decreasing process U(t). The result is presented for Y(u) being a fractional Brownian motion and U(t) being a renewal process with Levy-distributed inter-renewal times. |
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| Periplasmal physics: The rotational dynamics of spirochetal flagella Yang, Jing (École Normale Supérieure de Paris, École normale supérieure - Paris, Biology, Paris, France) |
Spirochetes are distinguished by the location of their flagella, which reside within the periplasm: the tiny space between the bacterial cell wall and the outer membrane. In Borrelia burgdorferi (the causative agent of Lyme disease), rotation of the flagella leads to cellular undulations that drive swimming. Exactly how these shape changes arise due to the forces and torques acting between the flagella and the cell body is unknown. By applying low-Reynolds number hydrodynamic theory to the motion of an elastic flagellum rotating in the periplasm, we show that the flagella are most likely separated from the bacterial cell wall by a lubricating layer of fluid. We obtain analytical solutions for the force and torque on the rotating flagellum through lubrication analysis, as well as through scaling analysis, and find that the results are in close agreement numerical simulations. |
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