2,325 research outputs found

    Realizing the physics of motile cilia synchronization with driven colloids

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    Cilia and flagella in biological systems often show large scale cooperative behaviors such as the synchronization of their beats in "metachronal waves". These are beautiful examples of emergent dynamics in biology, and are essential for life, allowing diverse processes from the motility of eukaryotic microorganisms, to nutrient transport and clearance of pathogens from mammalian airways. How these collective states arise is not fully understood, but it is clear that individual cilia interact mechanically,and that a strong and long ranged component of the coupling is mediated by the viscous fluid. We review here the work by ourselves and others aimed at understanding the behavior of hydrodynamically coupled systems, and particularly a set of results that have been obtained both experimentally and theoretically by studying actively driven colloidal systems. In these controlled scenarios, it is possible to selectively test aspects of the living motile cilia, such as the geometrical arrangement, the effects of the driving profile and the distance to no-slip boundaries. We outline and give examples of how it is possible to link model systems to observations on living systems, which can be made on microorganisms, on cell cultures or on tissue sections. This area of research has clear clinical application in the long term, as severe pathologies are associated with compromised cilia function in humans.Comment: 31 pages, to appear in Annual Review of Condensed Matter Physic

    Fundamentals and applications of spatial dissipative solitons in photonic devices : [Chapter 6]

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    We review the properties of optical spatial dissipative solitons (SDS). These are stable, self‐localized optical excitations sitting on a uniform, or quasi‐uniform, background in a dissipative environment like a nonlinear optical cavity. Indeed, in optics they are often termed “cavity solitons.” We discuss their dynamics and interactions in both ideal and imperfect systems, making comparison with experiments. SDS in lasers offer important advantages for applications. We review candidate schemes and the tremendous recent progress in semiconductor‐based cavity soliton lasers. We examine SDS in periodic structures, and we show how SDS can be quantitatively related to the locking of fronts. We conclude with an assessment of potential applications of SDS in photonics, arguing that best use of their particular features is made by exploiting their mobility, for example in all‐optical delay lines

    Dissipative solitons in pattern-forming nonlinear optical systems : cavity solitons and feedback solitons

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    Many dissipative optical systems support patterns. Dissipative solitons are generally found where a pattern coexists with a stable unpatterned state. We consider such phenomena in driven optical cavities containing a nonlinear medium (cavity solitons) and rather similar phenomena (feedback solitons) where a driven nonlinear optical medium is in front of a single feedback mirror. The history, theory, experimental status, and potential application of such solitons is reviewed

    Modeling, Analysis, and Optimization Issues for Large Space Structures

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    Topics concerning the modeling, analysis, and optimization of large space structures are discussed including structure-control interaction, structural and structural dynamics modeling, thermal analysis, testing, and design

    Vibrational Strong Coupling in THz Plasmonic Nanocavities

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    Vibrational Strong Coupling in THz Plasmonic Nanocavitie

    Quodons in Mica 2013

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    Quodons in Mica 2013 INDEX 1. Introduction. 3. JFR Archilla, SMM Coelho, FD Auret, V Dubinko and V Hizhnyakov. Experimental observation of moving discrete breathers in germanium. 5. L Brzihik. Bisolectrons in harmonic and anharmonic lattices. 6. AP Chetverikov. Solitons and charge transport in triangular and quadratic Morse lattices. 7. LA Cisneros-Ake. Travelling coherent structures in the electron transport in 2D anharmonic crystal lattices. 8. SMM Coelho, FD Auret, JM Nel and JFR Archilla. The origin of defects induced in ultra-pure germanium by Electron Beam Deposition. 10. S Comorosan and M Apostol. Theory vs. Reality - Localized excitations induced by optical manipulation of proteins, as a different approach to link experiments with theory. 12. L Cruzeiro. The amide I band of crystalline acetanilide: old data under new light. 13. SV Dmitriev and AA Kistanov. Moving discrete breathers in crystals with NaCl structure. 15. V Dubinko, JFR Archilla, SMM Coelho and V Hizhnyakov. Modeling of the annealing of radiation-induced defects in germanium by moving discrete breathers. 16. JC Eilbeck. Numerical simulations of nonlinear modes in mica: past, present and future. 17. A Ferrando, C Mili\'an, DE Ceballos-Herrera and Dmitry V. Skryabin. Soliplasmon resonances at metal-dielectric interfaces. 19. YuB Gaididei. Energy localization in nonlinear systems with flexible geometry. 20. D Hennig. Existence and non-existence of breather solutions in damped and driven nonlinear lattices. 21. P Jason and M Johansson. Existence, dynamics and mobility of Quantum Compactons in an extended Bose-Hubbard model. 22. N. Jiménez, JFR Archilla, Y. Kosevich, V. Sánchez-Morcillo and LM García-Raffi. A crowdion in mica. Between K40 recoil and transmission sputtering. 24. M Johansson. Strongly localized moving discrete solitons (breathers): new ways to beat the Peierls-Nabarro barrier. 26. YA Kosevich and AV Savin. Energy transport in molecular chains with combined anharmonic potentials of pair interatomic interaction. 28. B Malomed, C Mejía-Cortés and RA Vicencio. Mobile discrete solitons in the one-dimensional lattice with the cubic-quintic nonlinearity. 29. FM Russell. Recording process in iron-rich muscovite crystals. 30. L Salasnich. Bright solitons of attractive Bose-Einstein condensates confined in quasi-1D optical lattice. 31. V Sánchez-Morcillo, LM, Garcíaa-Raffi, V. Romero-Garcíaa, R. Picó, A. Cebrecos, and Kestutis Staliunas. Wave localization in chirped sonic crystals. 32. P Selyschev, V Sugakov and T Didenko. Peculiarities of the change of temperature and heat transfer under irradiation. 33. K Staliunas. Taming of Modulation Instability: Manipulation, and Complete Suppression of Instability by Spatio-Temporal Periodic Modulation. 34. G Tsironis. Gain-Driven Breathers in PT-Symmetric Metamaterials. 36. JAD Wattis and IA Butt. Moving breather modes in two-dimensional lattices.Ministerio de Ciencia e Innovación FIS2008-0484

    Hydrodynamics of flagellar swimming and synchronization

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    What is flagellar swimming? Cilia and flagella are whip-like cell appendages that can exhibit regular bending waves. This active process emerges from the non-equilibrium dynamics of molecular motors distributed along the length of cilia and flagella. Eukaryotic cells can possess many cilia and flagella that beat in a coordinated fashion, thus transporting fluids, as in mammalian airways or the ventricular system inside the brain. Many unicellular organisms posses just one or two flagella, rendering them microswimmers that are propelled through fluids by the flagellar beat including sperm cells and the biflagellate green alga Chlamydomonas. Objectives. In this thesis in theoretical biological physics, we seek to understand the nonlinear dynamics of flagellar swimming and synchronization. We investigate the flow fields induced by beating flagella and how in turn external hydrodynamic flows change speed and shape of the flagellar beat. This flagellar load-response is a prerequisite for flagellar synchronization. We want to find the physical principals underlying stable synchronization of the two flagella of Chlamydomonas cells. Results. First, we employed realistic hydrodynamic simulations of flagellar swimming based on experimentally measured beat patterns. For this, we developed analysis tools to extract flagellar shapes from high-speed videoscopy data. Flow-signatures of flagellated swimmers are analysed and their effect on a neighboring swimmer is compared to the effect of active noise of the flagellar beat. We were able to estimate a chemomechanical energy efficiency of the flagellar beat and determine its waveform compliance by comparing findings from experiments, in which a clamped Chlamydomonas is exposed to external flow, to predictions from an effective theory that we designed. These mechanical properties have interesting consequences for the synchronization dynamics of Chlamydomonas, which are revealed by computer simulations. We propose that direct elastic coupling between the two flagella of Chlamydomonas, as suggested by recent experiments, in combination with waveform compliance is crucial to facilitate in-phase synchronization of the two flagella of Chlamydomonas.:1 Introduction 1.1 Physics of cell motility: flagellated swimmers as model system 2 1.1.1 Tissue cells and unicellular eukaryotic organisms have cilia and flagella 2 1.1.2 The conserved architecture of flagella 3 1.1.3 Synchronization in collections of flagella 5 1.2 Hydrodynamics at the microscale 9 1.2.1 Navier-Stokes equation 10 1.2.2 The limit of low Reynolds number 10 1.2.3 Multipole expansion of flow fields 11 1.3 Self-propulsion by viscous forces 13 1.3.1 Self propulsion requires broken symmetries 13 1.3.2 Signatures of flowfields: pusher & puller 15 1.4 Overview of the thesis 16 2 Flow signatures of flagellar swimming 2.1 Self-propulsion of flagellated swimmers 20 2.1.1 Representation of flagellar shapes 20 2.1.2 Computation of hydrodynamic friction forces 21 2.1.3 Material frame and rigid-body transformations 22 2.1.4 The grand friction matrix 23 2.1.5 Dynamics of swimming 23 2.2 The hydrodynamic far field: pusher and puller 26 2.2.1 The flow generated by a swimmer 26 2.2.2 Force dipole characterization 27 2.2.3 Flagellated swimmers alternate between pusher and puller 29 2.2.4 Implications for two interacting Chlamydomonas cells 31 2.3 Inertial screening of oscillatory flows 32 2.3.1 Convection and oscillatory acceleration 33 2.3.2 The oscilet: fundamental solution of unsteady flow 35 2.3.3 Screening length of oscillatory flows 35 2.4 Energetics of flagellar self-propulsion 36 2.4.1 Impact of inertial screening on hydrodynamic dissipation 37 2.4.2 Case study: the green alga Chlamydomonas 38 2.4.3 Discussion: evolutionary optimization and the number of molecular motors 38 2.5 Summary 39 3 The load-response of the flagellar beat 3.1 Experimental collaboration: flagellated swimmers exposed to flows 41 3.1.1 Description of the experimental setup 42 3.1.2 Computed flow profile in the micro-fluidic device 43 3.1.3 Image processing and flagellar tracking 43 3.1.4 Mode decomposition and limit-cycle reconstruction 47 3.1.5 Changes of limit-cycle dynamics: deformation, translation, acceleration 49 3.2 An effective theory of flagellar oscillations 50 3.2.1 A balance of generalized forces 50 3.2.2 Hydrodynamic friction in generalized coordinates 51 3.2.3 Intra-flagellar friction 52 3.2.4 Calibration of active flagellar driving forces 52 3.2.5 Stability of the limit cycle of the flagellar beat 53 3.2.6 Equations of motion 55 3.3 Comparison of theory and experiment 56 3.3.1 Flagellar mean curvature 57 3.3.2 Susceptibilities of phase speed and amplitude 57 3.3.3 Higher modes and stalling of the flagellar beat at high external load 59 3.3.4 Non-isochrony of flagellar oscillations 63 3.4 Summary 63 4 Flagellar load-response facilitates synchronization 4.1 Synchronization to external driving 65 4.2 Inter-flagellar synchronization in the green alga Chlamydomonas 67 4.2.1 Equations of motion for inter-flagellar synchronization 68 4.2.2 Synchronization strength for free-swimming and clamped cells 70 4.2.3 The synchronization strength depends on energy efficiency and waveform compliance 73 4.2.4 The case of an elastically clamped cell 74 4.2.5 Basal body coupling facilitates in-phase synchronization 75 4.2.6 Predictions for experiments 78 4.3 Summary 80 5 Active flagellar fluctuations 5.1 Effective description of flagellar oscillations 84 5.2 Measuring flagellar noise 84 5.2.1 Active phase fluctuations are much larger than thermal noise 84 5.2.2 Amplitude fluctuations are correlated 85 5.3 Active flagellar fluctuations result in noisy swimming paths 86 5.3.1 Effective diffusion of swimming circles of sperm cell 86 5.3.2 Comparison of the effect of noise and hydrodynamic interactions 87 5.4 Summary 88 6 Summary and outlook 6.1 Summary of our results 89 6.2 Outlook on future work 90 A Solving the Stokes equation A.1 Multipole expansion 95 A.2 Resistive-force theory 96 A.3 Fast multipole boundary element method 97 B Linearized Navier-Stokes equation B.1 Linearized Navier-Stokes equation 101 B.2 The case of an oscillating sphere 102 B.3 The small radius limit 103 B.4 Greens function 104 C Hydrodynamic friction C.1 A passive particle 107 C.2 Multiple Particles 107 C.3 Generalized coordinates 108 D Data analysis methods D.1 Nematic filter 111 D.1.1 Nemat 111 D.1.2 Nematic correlation 111 D.2 Principal-component analysis 112 D.3 The quality of the limit-cycle projections of experimental data 113 E Adler equation F Sensitivity analysis for computational results F.1 The distance function of basal coupling 117 F.2 Computed synchronization strength for alternative waveform 118 F.3 Insensitivity of computed load-response to amplitude correlation time 118 List of Symbols List of Figures Bibliograph
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