Highly scalable aggregate computations in cyber-physical systems: physical environment meets communication protocols

In this paper, we focus on large-scale and dense Cyber- Physical Systems, and discuss methods that tightly integrate communication and computing with the underlying physical environment. We present Physical Dynamic Priority Dominance ((PD)2) protocol that exemplifies a key mechanism to devise low time-complexity communication protocols for large-scale networked sensor systems. We show that using this mechanism, one can compute aggregate quantities such as the maximum or minimum of sensor readings in a time-complexity that is equivalent to essentially one message exchange. We also illustrate the use of this mechanism in a more complex task of computing the interpolation of smooth as well as non-smooth sensor data in very low timecomplexity.

A Logic and tool for local reasoning about security protocols

Trabalho apresentado no âmbito do Mestrado em Engenharia Informática, como requisito parcial para obtenção do grau de Mestre em Engenharia Informática

Synchronization in Von Bertalanffy’s models

Many data have been useful to describe the growth of marine mammals, invertebrates and reptiles, seabirds, sea turtles and fishes, using the logistic, the Gom-pertz and von Bertalanffy's growth models. A generalized family of von Bertalanffy's maps, which is proportional to the right hand side of von Bertalanffy's growth equation, is studied and its dynamical approach is proposed. The system complexity is measured using Lyapunov exponents, which depend on two biological parameters: von Bertalanffy's growth rate constant and the asymptotic weight. Applications of synchronization in real world is of current interest. The behavior of birds ocks, schools of fish and other animals is an important phenomenon characterized by synchronized motion of individuals. In this work, we consider networks having in each node a von Bertalanffy's model and we study the synchronization interval of these networks, as a function of those two biological parameters. Numerical simulation are also presented to support our approaches.

Evaluation of different immunization protocols with P. brasiliensis antigens in Guinea pigs

The objective of the present study was to develop an efficient and reproducible protocol of immunization of guinea pigs with P. brasiliensis antigens as an animal model for future studies of protective immunity mechanisms. We tested three different antigens (particulate, soluble and combined) and six protocols in the presence and absence of Freund's complete adjuvant and with different numbers of immunizing doses and variable lenght of time between the last immunizing dose and challenge. The efficacy of the immunizing protocol was evaluated by measuring the humoral and cellular anti-P. brasiliensis immune response of the animals, using immuno-diffusion, skin test and macrophage migration inhibition test. It was observed that: 1. Three immunizing doses of the antigens induced a more marked response than two doses; 2. The highest immune response was obtained with the use of Freund's complete adjuvant; 3. Animals challenged a long time (week 6) after the last immunizing dose showed good anti-P. brasiliensis immune response; 4. The particulate antigen induced the lowest immune response. The soluble and the combined antigens were equally efficient in raising good humoral and cellular anti-P. brasiliensis immune response

Complete synchronization and delayed synchronization in couplings

We consider a general coupling of two identical chaotic dynamical systems, and we obtain the conditions for synchronization. We consider two types of synchronization: complete synchronization and delayed synchronization. Then, we consider four different couplings having different behaviors regarding their ability to synchronize either completely or with delay: Symmetric Linear Coupled System, Commanded Linear Coupled System, Commanded Coupled System with delay and symmetric coupled system with delay. The values of the coupling strength for which a coupling synchronizes define its Window of synchronization. We obtain analytically the Windows of complete synchronization, and we apply it for the considered couplings that admit complete synchronization. We also obtain analytically the Window of chaotic delayed synchronization for the only considered coupling that admits a chaotic delayed synchronization, the commanded coupled system with delay. At last, we use four different free chaotic dynamics (based in tent map, logistic map, three-piecewise linear map and cubic-like map) in order to observe numerically the analytically predicted windows.

Generalized synchronization in a system of several non-autonomous oscillators coupled by a medium

An abstract theory on general synchronization of a system of several oscillators coupled by a medium is given. By generalized synchronization we mean the existence of an invariant manifold that allows a reduction in dimension. The case of a concrete system modeling the dynamics of a chemical solution on two containers connected to a third container is studied from the basics to arbitrary perturbations. Conditions under which synchronization occurs are given. Our theoretical results are complemented with a numerical study.

Multi-Objective and Financial Portfolio Optimization of Carrier-Sense Multiple Access Protocols with Cooperative Diversity

8th International Workshop on Multiple Access Communications (MACOM2015), Helsinki, Finland.

Energy-efficient MAC protocols for WBANs: Opportunities and challenges

Wireless body area networks (WBANs) are expected to play a significant role in smart healthcare systems. One of the most important attributes of WBANs is to increase network lifetime by introducing novel and low-power techniques on the energy-constrained sensor nodes. Medium access control (MAC) protocols play a significant role in determining the energy consumption in WBANs. Existing MAC protocols are unable to accommodate communication requirements in WBANs. There is a need to develop novel, scalable and reliable MAC protocols that must be able to address all these requirements in a reliable manner. In this special issue, we attracted high quality research and review papers on the recent advances in MAC protocols for WBANs.

Synchronization properties of multi-oscillator circadian systems

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

Planning and verification of multipath routing protocols

Conventionally the problem of the best path in a network refers to the shortest path problem. However, for the vast majority of networks present nowadays this solution has some limitations which directly affect their proper functioning, as well as an inefficient use of their potentialities. Problems at the level of large networks where graphs of high complexity are commonly present as well as the appearing of new services and their respective requirements, are intrinsically related to the inability of this solution. In order to overcome the needs present in these networks, a new approach to the problem of the best path must be explored. One solution that has aroused more interest in the scientific community considers the use of multiple paths between two network nodes, where they can all now be considered as the best path between those nodes. Therefore, the routing will be discontinued only by minimizing one metric, where only one path between nodes is chosen, and shall be made by the selection of one of many paths, thereby allowing the use of a greater diversity of the present paths (obviously, if the network consents). The establishment of multi-path routing in a given network has several advantages for its operation. Its use may well improve the distribution of network traffic, improve recovery time to failure, or it can still offer a greater control of the network by its administrator. These factors still have greater relevance when networks have large dimensions, as well as when their constitution is of high complexity, such as the Internet, where multiple networks managed by different entities are interconnected. A large part of the growing need to use multipath protocols is associated to the routing made based on policies. Therefore, paths with different characteristics can be considered with equal level of preference, and thus be part of the solution for the best way problem. To perform multi-path routing using protocols based only on the destination address has some limitations but it is possible. Concepts of graph theory of algebraic structures can be used to describe how the routes are calculated and classified, enabling to model the routing problem. This thesis studies and analyzes multi-path routing protocols from the known literature and derives a new algebraic condition which allows the correct operation of these protocols without any network restriction. It also develops a range of software tools that allows the planning and the respective verification/validation of new protocols models according to the study made.

A comparison of four DNA extraction protocols for the analysis of urine from patients with visceral leishmaniasis

Introduction Polymerase chain reaction (PCR) may offer an alternative diagnostic option when clinical signs and symptoms suggest visceral leishmaniasis (VL) but microscopic scanning and serological tests provide negative results. PCR using urine is sensitive enough to diagnose human visceral leishmaniasis (VL). However, DNA quality is a crucial factor for successful amplification. Methods A comparative performance evaluation of DNA extraction methods from the urine of patients with VL using two commercially available extraction kits and two phenol-chloroform protocols was conducted to determine which method produces the highest quality DNA suitable for PCR amplification, as well as the most sensitive, fast and inexpensive method. All commercially available kits were able to shorten the duration of DNA extraction. Results With regard to detection limits, both phenol: chloroform extraction and the QIAamp DNA Mini Kit provided good results (0.1 pg of DNA) for the extraction of DNA from a parasite smaller than Leishmania (Leishmania) infantum (< 100fg of DNA). However, among 11 urine samples from subjects with VL, better performance was achieved with the phenol:chloroform method (8/11) relative to the QIAamp DNA Mini Kit (4/11), with a greater number of positive samples detected at a lower cost using PCR. Conclusion Our results demonstrate that phenol:chloroform with an ethanol precipitation prior to extraction is the most efficient method in terms of yield and cost, using urine as a non-invasive source of DNA and providing an alternative diagnostic method at a low cost.

Rely-guarantee protocols for safe interference over shared memory

Mutable state can be useful in certain algorithms, to structure programs, or for efficiency purposes. However, when shared mutable state is used in non-local or nonobvious ways, the interactions that can occur via aliases to that shared memory can be a source of program errors. Undisciplined uses of shared state may unsafely interfere with local reasoning as other aliases may interleave their changes to the shared state in unexpected ways. We propose a novel technique, rely-guarantee protocols, that structures the interactions between aliases and ensures that only safe interference is possible. We present a linear type system outfitted with our novel sharing mechanism that enables controlled interference over shared mutable resources. Each alias is assigned separate, local roles encoded in a protocol abstraction that constrains how an alias can legally use that shared state. By following the spirit of rely-guarantee reasoning, our rely-guarantee protocols ensure that only safe interference can occur but still allow many interesting uses of shared state, such as going beyond invariant and monotonic usages. This thesis describes the three core mechanisms that enable our type-based technique to work: 1) we show how a protocol models an alias’s perspective on how the shared state evolves and constrains that alias’s interactions with the shared state; 2) we show how protocols can be used while enforcing the agreed interference contract; and finally, 3) we show how to check that all local protocols to some shared state can be safely composed to ensure globally safe interference over that shared memory. The interference caused by shared state is rooted at how the uses of di↵erent aliases to that state may be interleaved (perhaps even in non-deterministic ways) at run-time. Therefore, our technique is mostly agnostic as to whether this interference was the result of alias interleaving caused by sequential or concurrent semantics. We show implementations of our technique in both settings, and highlight their di↵erences. Because sharing is “first-class” (and not tied to a module), we show a polymorphic procedure that enables abstract compositions of protocols. Thus, protocols can be specialized or extended without requiring specific knowledge of the interference produce by other protocols to that state. We show that protocol composition can ensure safety even when considering abstracted protocols. We show that this core composition mechanism is sound, decidable (without the need for manual intervention), and provide an algorithm implementation.

Secure multiParty computation protocols

Dissertação de Mestrado em Engenharia Informática

Bimodal information increases spontaneous interpersonal synchronization of goal directed upper limb movements

When interacting with each other, people often synchronize spontaneously their movements, e.g. during pendulum swinging, chair rocking[5], walking [4][7], and when executing periodic forearm movements[3].Although the spatiotemporal information that establishes the coupling, leading to synchronization, might be provided by several perceptual systems, the systematic study of different sensory modalities contribution is widely neglected. Considering a) differences in the sensory dominance on the spatial and temporal dimension[5] , b) different cue combination and integration strategies [1][2], and c) that sensory information might provide different aspects of the same event, synchronization should be moderated by the type of sensory modality. Here, 9 naïve participants placed a bottle periodically between two target zones, 40 times, in 12 conditions while sitting in front of a confederate executing the same task. The participant could a) see and hear, b) see , c) hear the confederate, d) or audiovisual information about the movements of the confederate was absent. The couple started in 3 different relative positions (i.e., in-phase, anti-phase, out of phase). A retro-reflective marker was attached to the top of the bottles. Bottle displacement was captured by a motion capture system. We analyzed the variability of the continuous relative phase reflecting the degree of synchronization. Results indicate the emergence of spontaneous synchronization, an increase with bimodal information, and an influence of the initial phase relation on the particular synchronization pattern. Results have theoretical implication for studying cue combination in interpersonal coordination and are consistent with coupled oscillator models.

Sensorimotor synchronization when walking side by side with a point light walker

[Excerpt] Synchronization of periodic movements like side-by-side walking [7] is frequently modeled by coupled oscillators [5] and the coupling strength is defined quantitatively [3]. In contrast, in most studies on sensorimotor synchronization (SMS), simple movements like finger taps are synchronized with simple stimuli like metronomes [4]. While the latter paradigm simplifies matters and allows for the assessment of the relative weights of sensory modalities through systematic variation of the stimuli [1], it might lack ecological validity. Conversely, using more complex movements and stimuli might complicate the specification of mechanisms underlying coupling. We merged the positive aspects of both approaches to study the contribution of auditory and visual information on synchronization during side-by-side walking. As stimuli, we used Point Light Walkers (PLWs) and auralized steps sound; both were constructed from previously captured walking individuals [2][6]. PLWs were retro-projected on a screen and matched according to gender, hip height, and velocity. The participant walked for 7.20m side by side with 1) a PLW, 2) steps sound, or 3) both displayed in temporal congruence. Instruction to participants was to synchronize with the available stimuli. [...]