Made available in DSpace on 2016-03-15T19:37:54Z (GMT). No. of bitstreams: 1 Fernando Biazi Nascimento.pdf: 3885211 bytes, checksum: 52d266afc3ffddce2e0abc915e2471a1 (MD5) Previous issue date: 2014-10-23 / Fundo Mackenzie de Pesquisa / The present work consists of an implementation of time distribution protocol based on PTP disclosed in the IEC 61588:2009 / IEEE 1588-2008 standard to be used in low-power wireless devices. The distribution of time is important to determine the order of occurrence of events marked in distinct counts that can then be related. And the problems of lack of synchronicity are evident in circumstances ranging from the study of historical facts up to the investigation of intruders in modern equipments connected to the internet. The work included development of a completely new software for the microcontroller MSP430F2274TM using the CC2480TMnetwork controller. The implementation of the protocol considers one of the mechanisms described by the standard and remains very close to it, not fully conformant mainly because of lack of resources on the used device, but the expected behavior was kept. The devices synchronize the time between them and sintonize their time counting, in a way to reduce, as much as possible, the adjustments of further synchronizations. / O presente trabalho consiste em uma implementação de protocolo de distribuição de tempo baseado no PTP, definido na norma IEC 61588:2009/IEEE 1588-2008 a ser utilizado em dispositivos sem fio de baixo consumo de energia. A distribuição de tempo é importante para determinar a ordem de ocorrência de eventos marcados em contagens distintas que podem então ser relacionadas. E os problemas de falta de sincronia são evidentes em circunstâncias que vão de estudo de fatos históricos até a verificação de intrusos em equipamentos modernos conectados à internet. O trabalho contou com desenvolvimento de um software completamente novo para o micro-controlador MSP430F2274TM utilizando o controlador de rede CC2480TM. A implementação do protocolo considera um dos mecanismos apresentados pela norma e ficou muito próxima, não atendendo-a plenamente principalmente por falta de recursos no dispositivo utilizado, mas manteve o comportamento previsto. Os dispositivos sincronizam os tempos entre eles e sintonizam suas contagens de tempo, de forma a reduzir, tanto quanto possível, o ajuste de futuras sincronizações.

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.

Diplomová práce pojednává o chaotických dynamických systémech se zvláštním zaměřením na jejich synchronizaci. Proces synchronizace je aplikován použitím dvou různých metod, a to - metodou úplné synchronizace na dva Lorenzovy systémy a metodou negativní zpětné vazby na dva Rösslerovy systémy. Dále je prozkoumána možná aplikace synchronizace chaotických systémů v oblasti soukromé komunikace, která je doplněná algoritmy v prostředí MATLAB.

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 Bibliography

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This thesis investigates time synchronization, which is crucial in various applications, such as power grid monitoring, communication systems, and in the fusion of information from different sensors. Global Navigation Satellite Systems (GNSS) are currently the state-of-the-art for time synchronization in distributed wireless sensor networks. However, due to GNSS being vulnerable to jamming, alternative methods are required to ensure robustness in critical systems. Preferably, a system would not be controlled by a single country or organization, e.g., GPS. Therefore, time synchronization methods utilizing commonly available signals, such as radio or television broadcasting, are of interest. Long Term Evolution (LTE), the fourth-generation (4G) cellular network, is widely accessible and the framework is internationally standardized. Consequently, the scope of the thesis is limited to LTE-based methods for time synchronization.  Based on the desired receiver-to-receiver characteristics, Scalable Wireless Network Synchronization (SWINS) and Reference Broadcast Synchronization (RBS) were selected to obtain time synchronization. RBS is an active synchronization method requiring communication within the sensor network, while the passive SWINS method solely relies on self-captured measurements. Time synchronization performance was evaluated using Matlab. Simulations show an increased accuracy for SWINS in synchronized LTE networks, while RBS is superior in unsynchronized cellular networks. Both LTE-based methods show performance comparable to the time synchronization accuracy guaranteed with publicly available GPS signals. A sensitivity analysis with varying disturbances shows that jointly estimating time offset and position is preferred to sole time offset estimation if the transceiver position uncertainty exceeds 50 meters.

Master of Science / Department of Animal Sciences and Industry / Jeffrey S. Stevenson / Lactating dairy cows from 2 Kansas farms were used to determine the effectiveness of exogenous progesterone in the form of an intravaginal insert (controlled internal drug release; CIDR) in conjunction with an ovulation-synchronization protocol. Cows were enrolled in a Presynch + Ovsynch protocol after parturition, where they received 2 injections of PGF[subscript]2[alpha], 14 d apart (Presynch) beginning between 30 and 36 DIM. Cows (n = 155) detected in estrus after the second PGF[subscript]2[alpha] injection of Presynch were inseminated (early AI). Remaining cows were assigned randomly to be treated with the Cosynch-72 protocol (GnRH 12 d after last Presynch PGF[subscript]2[alpha] injection, PGF[subscript]2[alpha] 7 d after GnRH, and timed AI + GnRH injection 72 h later) and served as controls (n = 159), or to be treated with the Cosynch-72 protocol and receive a progesterone insert (Ovsynch + CIDR; n = 175) for 7 d between GnRH and PGF[subscript]2[alpha]. Blood was collected at d −22 and −10 (relative to TAI at d 0) to determine cycling status based on progesterone concentrations and again at d 11 post AI to determine luteal competency. Treated cows were assigned body condition scores (BCS) on d −22 and −10. Pregnancy status was confirmed by palpation of the uterus per rectum and its contents on d 38 post-timed AI and verified again 4 wk later. Treatment with the progesterone insert increased timed AI pregnancies per AI in Cosynch- 72 + CIDR-treated cows when compared with controls (38 vs. 24%), but did not differ from early AI cows (38%). Pregnancy loss was numerically less in progesterone-treated cows than in controls (4.4 vs. 11.8%). Our study shows that increased pregnancies per AI can be achieved by the use of a progesterone insert in a reduced population of cows not yet inseminated, but treated with a progesterone insert.

ITC/USA 2005 Conference Proceedings / The Forty-First Annual International Telemetering Conference and Technical Exhibition / October 24-27, 2005 / Riviera Hotel & Convention Center, Las Vegas, Nevada / As requirements for the amount of test data continues to increase, instrumentation engineers are under pressure to deploy data acquisition systems that reduce the amount of associated wiring and overall system complexity. Smart sensor buses have been long considered as one approach to address this issue by placing the appropriate signal conditioners close to their respective sensors and providing data back over a common bus. However, the inability to adequately synchronize the operation of the sensor bus to the system master, which is required to correlate analog data measurements, has precluded their use. The ongoing development and deployment of smart sensor buses has reached the phase in which integration into a larger data acquisition system environment must be considered. Smart sensor buses, such as IntelliBus™, have their own unique mode of operation based on a pre-determined sampling schedule, which however, is typically asynchronous to the operation of the (master or controller) data acquisition system and must be accounted for when attempting to synchronize the two systems. IRIG Chapter 4 type methods for inserting data into a format, as exemplified by the handling of MIL-STD-1553 data, could be employed, with the disadvantage of eliminating any knowledge as to when a particular measurement was sampled, unless it is time stamped (similar to the time stamping function that is provided to mark receipt of 1553 command words). This can result in excessive time data as each sensor bus can manage a large number of analog sensor inputs and multiple sensor buses must be accommodated by the data acquisition system. The paper provides an example, using the Boeing developed IntelliBus system and the L3 Communications - Telemetry East NetDAS system, of how correlated data can be acquired from a smart sensor bus as a major subsystem component of a larger integrated data acquisition system. The focus will be specifically on how the IntelliBus schedule can be synchronized to that of the NetDAS formatter. Sample formats will be provided along with a description of how a standalone NetDAS stack and an integrated NetDAS-IntelliBus system would be programmed to create the required output, taking into account the unique sampling characteristics of the sensor bus.

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ITC/USA 2009 Conference Proceedings / The Forty-Fifth Annual International Telemetering Conference and Technical Exhibition / October 26-29, 2009 / Riviera Hotel & Convention Center, Las Vegas, Nevada / Space-time Coding (STC) for Multiple-Input Multiple-Output (MIMO) wireless communication systems is an effective technique for providing robust wireless link performance in telemetry systems. This paper investigates the degradation in system performance when synchronization errors between the transmitter and receiver are present. Specifically, expressions that quantify the increase in symbol-error-rate as a function of symbol synchronization error are derived for a two-transmit and single receive antenna MISO system using binary frequency shift keying waveforms. These results are then extended to the MIMO case. The analytic results are verified with simulation results that show close agreement between the theoretical expressions and Monte Carlo simulation runs.