Multiscale Computations on Neural Networks: From the Individual Neuron Interactions to the Macroscopic-Level Analysis

We show how the Equation-Free approach for multi-scale computations can be exploited to systematically study the dynamics of neural interactions on a random regular connected graph under a pairwise representation perspective. Using an individual-based microscopic simulator as a black box coarse-grained timestepper and with the aid of simulated annealing we compute the coarse-grained equilibrium bifurcation diagram and analyze the stability of the stationary states sidestepping the necessity of obtaining explicit closures at the macroscopic level. We also exploit the scheme to perform a rare-events analysis by estimating an effective Fokker-Planck describing the evolving probability density function of the corresponding coarse-grained observables

Opinions and Outlooks on Morphological Computation

Morphological Computation is based on the observation that biological systems seem to carry out relevant computations with their morphology (physical body) in order to successfully interact with their environments. This can be observed in a whole range of systems and at many different scales. It has been studied in animals – e.g., while running, the functionality of coping with impact and slight unevenness in the ground is "delivered" by the shape of the legs and the damped elasticity of the muscle-tendon system – and plants, but it has also been observed at the cellular and even at the molecular level – as seen, for example, in spontaneous self-assembly. The concept of morphological computation has served as an inspirational resource to build bio-inspired robots, design novel approaches for support systems in health care, implement computation with natural systems, but also in art and architecture. As a consequence, the field is highly interdisciplinary, which is also nicely reflected in the wide range of authors that are featured in this e-book. We have contributions from robotics, mechanical engineering, health, architecture, biology, philosophy, and others

Development of a Plasmonic On-Chip System to Characterize Changes from External Perturbations in Cardiomyocytes

Today’s heart-on-a-chip devices are hoped to be the state-of-the-art cell and tissue characterizing tool, in clinically applicable regenerative medicine and cardiac tissue engineering. Due to the coupled electromechanical activity of cardiomyocytes (CM), a comprehensive heart-on-a-chip device as a cell characterizing tool must encompass the capability to quantify cellular contractility, conductivity, excitability, and rhythmicity. This dissertation focuses on developing a successful and statistically relevant surface plasmon resonance (SPR) biosensor for simultaneous recording of neonatal rat cardiomyocytes’ electrophysiological profile and mechanical motion under normal and perturbed conditions. The surface plasmon resonance technique can quantify (1) molecular binding onto a metal film, (2) bulk refractive index changes of the medium near (nm) the metal film, and (3) dielectric property changes of the metal film. We used thin gold metal films (also called chips) as our plasmonic sensor and obtained a periodic signal from spontaneously contracting CMs on the chip. Furthermore, we took advantage of a microfluidic module for controlled drug delivery to CMs on-chip, inhibiting and promoting their signaling pathways under dynamic flow. We identified that ionic channel activity of each contraction period of a live CM syncytium on a gold metal sensor would account for the non-specific ion adsorption onto the metal surface in a periodic manner. Moreover, the contraction of cardiomyocytes following their ion channel activity displaces the medium, changing its bulk refractive index near the metal surface. Hence, the real-time electromechanical activity of CMs using SPR sensors may be extracted as a time series we call the Plasmonic Cardio-Eukaryography Signal (P-CeG). The P-CeG signal render opportunities, where state-of-the-art heart-on-a-chip device complexities may subside to a simpler, faster and cheaper platform for label-free, non-invasive, and high throughput cellular characterization

A Bio-inspired architecture for adaptive quadruped locomotion over irregular terrain

Tese de doutoramento Programa Doutoral em Engenharia Electrónica e de ComputadoresThis thesis presents a tentative advancement on walking control of small quadruped and humanoid position controlled robots, addressing the problem of walk generation by combining dynamical systems approach to motor control, insights from neuroethology research on vertebrate motor control and computational neuroscience. Legged locomotion is a complex dynamical process, despite the seemingly easy and natural behavior of the constantly present proficiency of legged animals. Research on locomotion and motor control in vertebrate animals from the last decades has brought to the attention of roboticists, the potential of the nature’s solutions to robot applications. Recent knowledge on the organization of complex motor generation and on mechanics and dynamics of locomotion has been successfully exploited to pursue agile robot locomotion. The work presented on this manuscript is part of an effort on the pursuit in devising a general, model free solution, for the generation of robust and adaptable walking behaviors. It strives to devise a practical solution applicable to real robots, such as the Sony’s quadruped AIBO and Robotis’ DARwIn- OP humanoid. The discussed solutions are inspired on the functional description of the vertebrate neural systems, especially on the concept of Central Pattern Generators (CPGs), their structure and organization, components and sensorimotor interactions. They use a dynamical systems approach for the implementation of the controller, especially on the use of nonlinear oscillators and exploitation of their properties. The main topics of this thesis are divided into three parts. The first part concerns quadruped locomotion, extending a previous CPG solution using nonlinear oscillators, and discussing an organization on three hierarchical levels of abstraction, sharing the purpose and knowledge of other works. It proposes a CPG solution which generates the walking motion for the whole-leg, which is then organized in a network for the production of quadrupedal gaits. The devised solution is able to produce goal-oriented locomotion and navigation as directed through highlevel commands from local planning methods. In this part, active balance on a standing quadruped is also addressed, proposing a method based on dynamical systems approach, exploring the integration of parallel postural mechanisms from several sensory modalities. The solutions are all successfully tested on the quadruped AIBO robot. In the second part, is addressed bipedal walking for humanoid robots. A CPG solution for biped walking based on the concept of motion primitives is proposed, loosely based on the idea of synergistic organization of vertebrate motor control. A set of motion primitives is shown to produce the basis of simple biped walking, and generalizable to goal-oriented walking. Using the proposed CPG, the inclusion of feedback mechanisms is investigated, for modulation and adaptation of walking, through phase transition control according to foot load information. The proposed solution is validated on the humanoid DARwIn-OP, and its application is evaluated within a whole-body control framework. The third part sidesteps a little from the other two topics. It discusses the CPG as having an alternative role to direct motor generation in locomotion, serving instead as a processor of sensory information for a feedback based motor generation. In this work a reflex based walking controller is devised for the compliant quadruped Oncilla robot, to serve as purely feedback based walking generation. The capabilities of the reflex network are shown in simulations, followed by a brief discussion on its limitations, and how they could be improved by the inclusion of a CPG.Esta tese apresenta uma tentativa de avanço no controlo de locomoção para pequenos robôs quadrúpedes e bipedes controlados por posição, endereçando o problema de geração motora através da combinação da abordagem de sistemas dinâmicos para o controlo motor, e perspectivas de investigação neuroetologia no controlo motor vertebrado e neurociência computacional. Andar é um processo dinâmico e complexo, apesar de parecer um comportamento fácil e natural devido à presença constante de animais proficientes em locomoção terrestre. Investigação na área da locomoção e controlo motor em animais vertebrados nas últimas decadas, trouxe à atenção dos roboticistas o potencial das soluções encontradas pela natureza aplicadas a aplicações robóticas. Conhecimento recente relativo à geração de comportamentos motores complexos e da mecânica da locomoção tem sido explorada com sucesso na procura de locomoção ágil na robótica. O trabalho apresentado neste documento é parte de um esforço no desenho de uma solução geral, e independente de modelos, para a geração robusta e adaptável de comportamentos locomotores. O foco é desenhar uma solução prática, aplicável a robôs reais, tal como o quadrúpede Sony AIBO e o humanóide DARwIn-OP. As soluções discutidas são inspiradas na descrição funcional do sistema nervoso vertebrado, especialmente no conceito de Central Pattern Generators (CPGs), a sua estrutura e organização, componentes e interacção sensorimotora. Estas soluções são implementadas usando uma abordagem em sistemas dinâmicos, focandos o uso de osciladores não lineares e a explorando as suas propriedades. Os tópicos principais desta tese estão divididos em três partes. A primeira parte explora o tema de locomoção quadrúpede, expandindo soluções prévias de CPGs usando osciladores não lineares, e discutindo uma organização em três níveis de abstracção, partilhando as ideias de outros trabalhos. Propõe uma solução de CPG que gera os movimentos locomotores para uma perna, que é depois organizado numa rede, para a produção de marcha quadrúpede. A solução concebida é capaz de produzir locomoção e navegação, comandada através de comandos de alto nível, produzidos por métodos de planeamento local. Nesta parte também endereçado o problema da manutenção do equilíbrio num robô quadrúpede parado, propondo um método baseado na abordagem em sistemas dinâmicos, explorando a integração de mecanismos posturais em paralelo, provenientes de várias modalidades sensoriais. As soluções são todas testadas com sucesso no robô quadrupede AIBO. Na segunda parte é endereçado o problema de locomoção bípede. É proposto um CPG baseado no conceito de motion primitives, baseadas na ideia de uma organização sinergética do controlo motor vertebrado. Um conjunto de motion primitives é usado para produzir a base de uma locomoção bípede simples e generalizável para navegação. Esta proposta de CPG é usada para de seguida se investigar a inclusão de mecanismos de feedback para modulação e adaptação da marcha, através do controlo de transições entre fases, de acordo com a informação de carga dos pés. A solução proposta é validada no robô humanóide DARwIn-OP, e a sua aplicação no contexto do framework de whole-body control é também avaliada. A terceira parte desvia um pouco dos outros dois tópicos. Discute o CPG como tendo um papel alternativo ao controlo motor directo, servindo em vez como um processador de informação sensorial para um mecanismo de locomoção puramente em feedback. Neste trabalho é desenhado um controlador baseado em reflexos para a geração da marcha de um quadrúpede compliant. As suas capacidades são demonstradas em simulação, seguidas por uma breve discussão nas suas limitações, e como estas podem ser ultrapassadas pela inclusão de um CPG.The presented work was possible thanks to the support by the Portuguese Science and Technology Foundation through the PhD grant SFRH/BD/62047/2009

Relational Basis of the Organism's Self-organization A Philosophical Discussion

In this thesis, I discuss the organism’s self-organization from the perspective of relational ontology. I critically examine scientific and philosophical sources that appeal to the concept of self-organization. By doing this, I aim to carry out a thorough investigation into the underlying reasons of emergent order within the ontogeny of the organism. Moreover, I focus on the relation between universal dynamics of organization and the organization of living systems. I provide a historical review of the development of modern ideas related to self-organization. These ideas have been developed in relation to various research areas including thermodynamics, molecular biology, developmental biology, systems theory, and so on. In order to develop a systematic understanding of the concept, I propose a conceptual distinction between transitional self-organization and regulative self-organization. The former refers to the spontaneous emergence of order, whereas the latter refers to the self-maintaining characteristic of the living systems. I show the relation between these two types of organization within biological processes. I offer a critical analysis of various theories within the organizational approach. Several ideas and notions in these theories originate from the early studies in cybernetics. More recently, autopoiesis and the theory of biological autonomy asserted certain claims that were critical toward the ideas related to self-organization. I advocate a general theory of self-organization against these criticisms. I also examine the hierarchical nature of the organism’s organization, as this is essential to understand regulative self-organization. I consider the reciprocal relation between bottom-up and top-down dynamics of organization as the basis of the organism’s individuation. To prove this idea, I appeal to biological research on molecular self-assembly, pattern formation (including reaction-diffusion systems), and the self-organized characteristic of the immune system. Finally, I promote the idea of diachronic emergence by drawing support from biological self-organization. I discuss the ideas related to constraints, potentiality, and dynamic form in an attempt to reveal the emergent nature of the organism. To demonstrate the dynamicity of form, I examine research into biological oscillators. I draw the following conclusions: synchronic condition of the organism is irreducibly processual and relational, and this is the basis of the organism’s potentiality for various organizational states

THE EFFECTS OF CONSECUTIVE SOFTBALL WINDMILL PITCHES ON COORDINATION PATTERNS AND VARIABILITY, MUSCULAR STRENGTH, AND PITCHING PERFORMANCE

Upper and lower extremity musculoskeletal injuries occur at a similar rate in softball pitchers. Most of these injuries can be considered chronic in nature, which may result in symptoms being treated instead of considering the underlying mechanism for injury. Previous literature has primarily focused on discrete values such as joint ranges and kinematic peaks. The primary purpose was to examine inter-segmental and intra-limb coordination of the softball windmill pitch throughout a simulated game of softball and to determine if variability of these patterns change throughout multiple pitch counts. The secondary purpose is to identify if a difference between pre-pitching and post-pitching strength can be detected to determine if muscular fatigue, as defined by the inability to sustain the expected power output around a joint, has occurred. Pitching performance, defined as pitch velocity and accuracy, were also assessed. A total of 14 softball pitchers (17.9±2.3 years, 166.4±8.67 cm, 72.3±12.6 kg) successfully completed all strength assessments and pitching sequence. Pitchers completed strength assessments of the at baseline and immediately after a pitching sequence consisting of 105 fastballs. Vector coding was used to measure coordination and variability of Drive Leg Thigh v Pelvis, Pelvis v Torso, Pelvis v Humerus and Humerus v Forearm. Paired t-test or Wilcoxon Signed Ranks test was used to determine change in muscular strength. One-way repeated measures analysis of variance was performed to establish if differences in pitch velocity or accuracy varied between innings. Appropriate order parameter to encapsulate the behavior of the windmill pitch could not be established due to lack of fatigue or incorrect coordinative structures measured. Results demonstrated a significant increase in stride leg knee extension and trunk flexion peak torque, as percent body weight, after consecutive pitches. Differences were seen in pitch velocity but not accuracy across innings. While this study did not demonstrate the negative effects of consecutive pitching that were expected, results can provide a foundation for future research into windmill pitch mechanics to assist with injury prevention and performance optimization

Effects of circadian rhythm phase alteration on physiological and psychological variables: Implications to pilot performance (including a partially annotated bibliography)

The effects of environmental synchronizers upon circadian rhythmic stability in man and the deleterious alterations in performance and which result from changes in this stability are points of interest in a review of selected literature published between 1972 and 1980. A total of 2,084 references relevant to pilot performance and circadian phase alteration are cited and arranged in the following categories: (1) human performance, with focus on the effects of sleep loss or disturbance and fatigue; (2) phase shift in which ground based light/dark alteration and transmeridian flight studies are discussed; (3) shiftwork; (4)internal desynchronization which includes the effect of evironmental factors on rhythmic stability, and of rhythm disturbances on sleep and psychopathology; (5) chronotherapy, the application of methods to ameliorate desynchronization symptomatology; and (6) biorythm theory, in which the birthdate based biorythm method for predicting aircraft accident susceptability is critically analyzed. Annotations are provided for most citations