Variance-Constrained Capacity of the Molecular Timing Channel with Synchronization Error

Molecular communication is set to play an important role in the design of complex biological and chemical systems. An important class of molecular communication systems is based on the timing channel, where information is encoded in the delay of the transmitted molecule - a synchronous approach. At present, a widely used modeling assumption is the perfect synchronization between the transmitter and the receiver. Unfortunately, this assumption is unlikely to hold in most practical molecular systems. To remedy this, we introduce a clock into the model - leading to the molecular timing channel with synchronization error. To quantify the behavior of this new system, we derive upper and lower bounds on the variance-constrained capacity, which we view as the step between the mean-delay and the peak-delay constrained capacity. By numerically evaluating our bounds, we obtain a key practical insight: the drift velocity of the clock links does not need to be significantly larger than the drift velocity of the information link, in order to achieve the variance-constrained capacity with perfect synchronization.

Distributed Region-Based Memory Allocation and Synchronization

We present DRASync, a region-based allocator that implements a global address space abstraction for MPI programs with pointer-based data structures. The main features of DRASync are: (a) it amortizes communication among nodes to allow efficient parallel allocation in a global address space; (b) it takes advantage of bulk deallocation and good locality with pointer-based data structures; (c) it supports ownership semantics of regions by nodes akin to reader–writer locks, which makes for a high-level, intuitive synchronization tool in MPI programs, without sacrificing message-passing performance. We evaluate DRASync against a state-of-the-art distributed allocator and find that it produces comparable performance while offering a higher-level abstraction to programmers.

Parkinson’s Is Time on Your Side? Evidence for Difficulties with Sensorimotor Synchronization

There is lack of consistent evidence as to how well PD patients are able to accurately time their movements across space with an external acoustic signal. For years, research based on the finger-tapping paradigm, the most popular paradigm for exploring the brain's ability to time movement, has provided strong evidence that patients are not able to accurately reproduce an isochronous interval [i.e., Ref. (1)]. This was undermined by Spencer and Ivry (2) who suggested a specific deficit in temporal control linked to emergent, rhythmical movement not event-based actions, which primarily involve the cerebellum. In this study, we investigated motor timing of seven idiopathic PD participants in event-based sensorimotor synchronization task. Participants were asked to move their finger horizontally between two predefined target zones to synchronize with the occurrence of two sound events at two time intervals (1.5 and 2.5 s). The width of the targets and the distance between them were manipulated to investigate impact of accuracy demands and movement amplitude on timing performance. The results showed that participants with PD demonstrated specific difficulties when trying to accurately synchronize their movements to a beat. The extent to which their ability to synchronize movement was compromised was found to be related to the severity of PD, but independent of the spatial constraints of the task.

On the structure and performance of a novel blind source separation based carrier phase synchronization error compensator

In this paper we carry out a detailed performance analysis of a novel blind-source-seperation (BSS) based DSP algorithm that tackles the carrier phase synchronization error problem. The results indicate that the mismatch can be effectively compensated during the normal operation as well as in the rapidly changing environments. Since the compensation is carried out before any modulation specific processing, the proposed method works with all standard modulation formats and lends itself to efficient real-time custom integrated hardware or software implementations.

Synchronization properties of multi-oscillator circadian systems

Dissertation presented to obtain the Ph.D degree in Computational Biology

Wireless GPS-based phase-locked synchronization system for outdoor environment.

Synchronization of data coming from different sources is of high importance in biomechanics to ensure reliable analyses. This synchronization can either be performed through hardware to obtain perfect matching of data, or post-processed digitally. Hardware synchronization can be achieved using trigger cables connecting different devices in many situations; however, this is often impractical, and sometimes impossible in outdoors situations. The aim of this paper is to describe a wireless system for outdoor use, allowing synchronization of different types of - potentially embedded and moving - devices. In this system, each synchronization device is composed of: (i) a GPS receiver (used as time reference), (ii) a radio transmitter, and (iii) a microcontroller. These components are used to provide synchronized trigger signals at the desired frequency to the measurement device connected. The synchronization devices communicate wirelessly, are very lightweight, battery-operated and thus very easy to set up. They are adaptable to every measurement device equipped with either trigger input or recording channel. The accuracy of the system was validated using an oscilloscope. The mean synchronization error was found to be 0.39 μs and pulses are generated with an accuracy of <2 μs. The system provides synchronization accuracy about two orders of magnitude better than commonly used post-processing methods, and does not suffer from any drift in trigger generation.

The role of the nuclear receptor Nr5a2 in ovulation in mice

Le récepteur nucléaire Nr5a2 est exprimé dans l’ovaire, plus spécifiquement dans les cellules de granulosa et lutéales. Une déplétion conditionnelle de Nr5a2 dans les cellules de granulosa au stade de follicule primaire par croisement de souris Nr5a2-flox et Amhr2-Cre (Nr5a2f/fAmhr2Cre/+) génère des problèmes au niveau de l’expansion du cumulus, de l’ovulation et de la lutéinisation. Ainsi, nous estimons que Nr5a2 régule les connexions intercellulaires dans le follicule ovarien via la connexine 43 (Cx43), une protéine de jonction impliquée dans l’expansion du cumulus. Le premier objectif de l’étude était de déterminer si l’absence d’expansion du cumulus chez les souris Amhr2Cre-cKO est liée à l’absence de communication intercellulaire adéquate entre les cellules de granulosa et de cumulus dans les follicules préovulatoires. À cette fin, des ovaires de souris immatures Amhr2Cre-cKO et non transgéniques ont été prélevés (n=3) après un traitement de superstimulation utilisant les gonadotropines eCG suivie de hCG afin d’induire l’ovulation. Nous avons ainsi démontré, par RT-PCR, une sous-expression de Cx43 avant et au moment du stimulus ovulatoire (0 h et 2 h) chez le groupe Amhr2Cre-cKO (P<0.01), ce qui pourrait mener à un problème dans l’acquisition de la compétence développementale de l’oocyte. D’un autre côté, au moment de l’ovulation (12 h), l’ARNm de Cx43 est surexprimé dans le groupe Amhr2Cre-cKO, ce qui pourrait prévenir les cellules du cumulus de se détacher l’une de l’autre. Nous avons ainsi conclu que Cx43 est un gène sous le contrôle de Nr5a2 et qu’une régulation erronée de ce gène est une cause possible du problème d’expansion du cumulus chez les souris Amhr2Cre-cKO. Afin d’examiner le rôle de Nr5a2 dans l’ovulation et la lutéinisation à différents stades de la maturation folliculaire, nous suggérons que Nr5a2 module la séquence temporelle des événements menant à l’ovulation. En croisant des souris Nr5a2-flox et Cyp19-Cre (Nr5a2f/fCyp19Cre/+), l’expression de Nr5a2 a été interrompue dans les cellules de granulosa des follicules antraux et préovulatoires. Aucune portée n’a été obtenue de ces souris (n=4) durant un essai d’accouplement de 6 mois. Chez les souris Cyp19Cre-cKO on remarque la présence de structures s’apparentant à des cellules de type lutéales et les femelles âgées d’un an présentent des kystes folliculaires hémorragiques et une hypertrophie de l’épithélium en surface de l’ovaire. Les deux modèles transgéniques démontrent donc une absence de l’expansion du cumulus et de l’ovulation. En conclusion, Nr5a2 semble réguler différemment la folliculogenèse et l’ovulation dans les cellules de granulosa des follicules primaires et antraux.

The involvement of nitric oxide in bovine follicular development and ovulation

Comprendre les événements paracriniens qui régulent la fertilité chez la vache est nécessaire non seulement en raison de l'importance agricole de cette espèce, mais aussi pour son utilisation potentielle comme modèle chez l’humain. L'oxyde nitrique (NO), un gaz de radicaux libres, a été impliqué dans la croissance folliculaire et l'ovulation chez les rongeurs et d'autres espèces, mais chez la vache c’est une énigme fascinante : le NO est produit par les cellules de la granulosa bovine et est régulé par la FSH, mais la présence et le profil d'expression des enzymes responsables de la synthèse de NO (NOS) dans les cellules de la granulosa tout au long de la croissance folliculaire ne sont pas claires. Les objectifs de cette thèse sont: (1) élucider le mécanisme de contrôle des NOS et les conséquences de la production d'oxyde nitrique pour le fonctionnement des cellules de la granulosa au cours du développement folliculaire chez la vache et (2) déterminer la régulation des NOS pendant la cascade ovulatoire induite par LH chez les cellules de la granulosa bovine et si l'activité des NOS pour l’expression des gènes critiques dans la cascade ovulatoire chez cette espèce. Les résultats sont séparés en 2 articles. Dans le premier article, la régulation de NOS2 dans les cellules de la granulosa bovine a été explorée. L'abondance des ARNm codant pour NOS2 a été stimulée par la FSH et l’IGF1 en augmentant l’estradiol, et un blocage de l'action de l’estradiol a conséquemment réduit les niveaux d'ARNm codant pour NOS2. De plus, l'inhibition de l'activité des NOS a augmenté l'apoptose dans les cellules de la granulosa in vitro. Dans le second article, il a été démontré que le pic de LH induit une activation des NOS dans les cellules de la granulosa, et que l'activité de NOS induit la production de NO, ce qui est essentiel pour l’expression des gènes critiques dans la cascade ovulatoire induite par LH comme EREG/AREG/PTGS2. Ensemble, les résultats présentés dans ces 2 articles suggèrent que les niveaux physiologiques d'activité des NOS peuvent contribuer à la croissance et la survie des cellules de la granulosa et indiquent également que NO peut être essentiel pour l'ovulation chez les bovins.

Biopacemaker acceleration without increased synchronization by chronic exposure to phorbol myristate acetate

L'activité électrique du coeur est initiée par la génération spontanée de potentiels d'action venant des cellules pacemaker du noeud sinusal (SN). Toute dysfonction au niveau de cette région entraîne une instabilité électrique du coeur. La majorité des patients souffrant d'un noeud sinusal déficient nécessitent l'implantation chirurgicale d'un pacemaker électronique; cependant, les limitations de cette approche incitent à la recherche d'une alternative thérapeutique. La base moléculaire des courants ioniques jouant un rôle crucial dans l'activité du noeud sinusal sont de plus en plus connues. Une composante importante de l'activité des cellules pacemakers semble être le canal HCN, responsable du courant pacemaker If. Le facteur T-box 3 (Tbx3), un facteur de transcription conservé durant le processus de l'évolution, est nécessaire au développement du système de conduction cardiaque. De précédentes études ont démontré que dans différentes lignées cellulaires le Phorbol 12-myristate 13-acetate (PMA) active l'expression du gène codant Tbx3 via des réactions en cascade partant de la protéine kinase C (PKC). L'objectif principal de cette étude est de tester si le PMA peut augmenter la fréquence et la synchronisation de l'activité spontanée du pacemaker biologique en culture. Plus précisément, nous avons étudié les effets de l'exposition chronique au PMA sur l'expression du facteur de transcription Tbx3, sur HCN4 et l'activité spontanée chez des monocouches de culture de myocytes ventriculaires de rats néonataux (MVRN). Nos résultats démontrent que le PMA augmente significativement le facteur transcription de Tbx3 et l'expression ARNm de HCN4, favorisant ainsi l'augmentation du rythme et de la stabilité de l'activité autonome. De plus, une diminution significative de la vitesse de conduction a été relevée et est attribuée à la diminution du couplage intercellulaire. La diminution de la vitesse de conduction pourrait expliquer l'effet négatif du PMA sur la synchronisation de l'activité autonome du pacemaker biologique. Ces résultats ont été confirmés par un modèle mathématique multicellulaire suggérant que des fréquences et résistances intercellulaires plus élevée pourraient induire une activité plus stable et moins synchrone. Cette étude amène de nouvelles connaissances très importantes destinées à la production d'un pacemaker biologique efficient et robuste.

Nonlinear Dynamics of Semiconductor LasersControl and Synchronization of Chaos:

Nonlinear dynamics of laser systems has become an interesting area of research in recent times. Lasers are good examples of nonlinear dissipative systems showing many kinds of nonlinear phenomena such as chaos, multistability and quasiperiodicity. The study of these phenomena in lasers has fundamental scientific importance since the investigations on these effects reveal many interesting features of nonlinear effects in practical systems. Further, the understanding of the instabilities in lasers is helpful in detecting and controlling such effects. Chaos is one of the most interesting phenomena shown by nonlinear deterministic systems. It is found that, like many nonlinear dissipative systems, lasers also show chaos for certain ranges of parameters. Many investigations on laser chaos have been done in the last two decades. The earlier studies in this field were concentrated on the dynamical aspects of laser chaos. However, recent developments in this area mainly belong to the control and synchronization of chaos. A number of attempts have been reported in controlling or suppressing chaos in lasers since lasers are the practical systems aimed to operated in stable or periodic mode. On the other hand, laser chaos has been found to be applicable in high speed secure communication based on synchronization of chaos. Thus, chaos in laser systems has technological importance also. Semiconductor lasers are most applicable in the fields of optical communications among various kinds of laser due to many reasons such as their compactness, reliability modest cost and the opportunity of direct current modulation. They show chaos and other instabilities under various physical conditions such as direct modulation and optical or optoelectronic feedback. It is desirable for semiconductor lasers to have stable and regular operation. Thus, the understanding of chaos and other instabilities in semiconductor lasers and their xi control is highly important in photonics. We address the problem of controlling chaos produced by direct modulation of laser diodes. We consider the delay feedback control methods for this purpose and study their performance using numerical simulation. Besides the control of chaos, control of other nonlinear effects such as quasiperiodicity and bistability using delay feedback methods are also investigated. A number of secure communication schemes based on synchronization of chaos semiconductor lasers have been successfully demonstrated theoretically and experimentally. The current investigations in these field include the study of practical issues on the implementations of such encryption schemes. We theoretically study the issues such as channel delay, phase mismatch and frequency detuning on the synchronization of chaos in directly modulated laser diodes. It would be helpful for designing and implementing chaotic encryption schemes using synchronization of chaos in modulated semiconductor laser

Studies on the Effect of Randomness on the Synchronization of Coupled Systems and on the Dynamics of Intermittently driven systems

Nonlinear dynamics has emerged into a prominent area of research in the past few Decades.Turbulence, Pattern formation,Multistability etc are some of the important areas of research in nonlinear dynamics apart from the study of chaos.Chaos refers to the complex evolution of a deterministic system, which is highly sensitive to initial conditions. The study of chaos theory started in the modern sense with the investigations of Edward Lorentz in mid 60's. Later developments in this subject provided systematic development of chaos theory as a science of deterministic but complex and unpredictable dynamical systems. This thesis deals with the effect of random fluctuations with its associated characteristic timescales on chaos and synchronization. Here we introduce the concept of noise, and two familiar types of noise are discussed. The classifications and representation of white and colored noise are introduced. Based on this we introduce the concept of randomness that we deal with as a variant of the familiar concept of noise. The dynamical systems introduced are the Rossler system, directly modulated semiconductor lasers and the Harmonic oscillator. The directly modulated semiconductor laser being not a much familiar dynamical system, we have included a detailed introduction to its relevance in Chaotic encryption based cryptography in communication. We show that the effect of a fluctuating parameter mismatch on synchronization is to destroy the synchronization. Further we show that the relation between synchronization error and timescales can be found empirically but there are also cases where this is not possible. Studies show that under the variation of the parameters, the system becomes chaotic, which appears to be the period doubling route to chaos.

Nonlinear Dynamics of Nd:YAG lasers: Hopf bifurcation, Multistability and Chaotic Synchronization

In this thesis we have presented some aspects of the nonlinear dynamics of Nd:YAG lasers including synchronization, Hopf bifurcation, chaos control and delay induced multistability.We have chosen diode pumped Nd:YAG laser with intracavity KTP crystal operating with two mode and three mode output as our model system.Different types of orientation for the laser cavity modes were considered to carry out the studies. For laser operating with two mode output we have chosen the modes as having parallel polarization and perpendicular polarization. For laser having three mode output, we have chosen them as two modes polarized parallel to each other while the third mode polarized orthogonal to them.

Studies on function projective synchronization in chaotic and hyperchaotic systems

FPS is a more general form of synchronization. Hyperchaotic systems possessing more than one positive Lypaunov exponent exhibit highly complex behaviour and are more suitable for some applications like secure communications. In this thesis we report studies of FPS and MFPS of a few chaotic and hyperchaotic systems. When all the parameters of the system are known we show that active nonlinear control method can be efectively used to obtain FPS. Adaptive nonlinear control and OPCL control method are employed for obtaining FPS and MFPS when some or all parameters of the system are uncertain. A secure communication scheme based on MFPS is also proposed in theory. All our theoretical calculations are verified by numerical simulations.

Synchronization and control of chaos in coupled chaotic multimode Nd:YAG lasers

In this Letter we numerically investigate the dynamics of a system of two coupled chaotic multimode Nd:YAG lasers with two mode and three mode outputs. Unidirectional and bidirectional coupling schemes are adopted; intensity time series plots, phase space plots and synchronization plots are used for studying the dynamics. Quality of synchronization is measured using correlation index plots. It is found that for laser with two mode output bidirectional direct coupling scheme is found to be effective in achieving complete synchronization, control of chaos and amplification in output intensity. For laser with three mode output, bidirectional difference coupling scheme gives much better chaotic synchronization as compared to unidirectional difference coupling but at the cost of higher coupling strength. We also conclude that the coupling scheme and system properties play an important role in determining the type of synchronization exhibited by the system.