Bio-inspired Mechanisms for Artificial Self-organised Systems

Self-organization is a growing interdisciplinary field of research about a phenomenon that can be observed in the Universe, in Nature and in social contexts. Research on self-organization tries to describe and explain forms, complex patterns and behaviours that arise from a collection of entities without an external organizer. As researchers in artificial systems, our aim is not to mimic self-organizing phenomena arising in Nature, but to understand and to control underlying mechanisms allowing desired emergence of forms, complex patterns and behaviours. Rather than attempting to eliminate such self-organization in artificial systems, we think that this might be deliberately harnessed in order to reach desirable global properties. In this paper we analyze three forms of self-organization: stigmergy, reinforcement mechanisms and cooperation. The amplification phenomena founded in stigmergic process or in reinforcement process are different forms of positive feedbacks that play a major role in building group activity or social organization. Cooperation is a functional form for self-organization because of its ability to guide local behaviours in order to obtain a relevant collective one. For each forms of self-organisation, we present a case study to show how we transposed it to some artificial systems and then analyse the strengths and weaknesses of such an approach

Supramolecular chemistry for nanomedicine

Mimicking Nature, supramolecular chemistry represents the chemistry beyond the molecule, in view that intermolecularinteractions constitute the driving force for the preparation of molecular and supramolecular assemblies, using the chemicalinformation contained in molecular building blocks. Upon molecular recognition between discrete units, chemical processessuch as self-assembly and self-organisation start operating, and are the leading processes to build up supramolecular aggregates and materials. When those materials have dimensions on thenanometric scale, a recently emerging scientific discipline is defined,Nanoscience. Nanomaterials are promising tools for many applications, and their use in biomedical and clinical applicationsdefines the so-called Nanomedicine. In this review we present a few selected examples of nanomaterials designed for therapeutical purposes, emphasizing the importance of the preparation methodology in terms of their therapeutical use.

Organisational Values as "Attractors of Chaos": An Emerging Cultural Change to Manage Organisational Complexity

Business organisations are excellent representations of what in physics and mathematics are designated "chaotic" systems. Because a culture of innovation will be vital for organisational survival in the 21st century, the present paper proposes that viewing organisations in terms of "complexity theory" may assist leaders in fine-tuning managerial philosophies that provide orderly management emphasizing stability within a culture of organised chaos, for it is on the "boundary of chaos" that the greatest creativity occurs. It is argued that 21st century companies, as chaotic social systems, will no longer be effectively managed by rigid objectives (MBO) nor by instructions (MBI). Their capacity for self-organisation will be derived essentially from how their members accept a shared set of values or principles for action (MBV). Complexity theory deals with systems that show complex structures in time or space, often hiding simple deterministic rules. This theory holds that once these rules are found, it is possible to make effective predictions and even to control the apparent complexity. The state of chaos that self-organises, thanks to the appearance of the "strange attractor", is the ideal basis for creativity and innovation in the company. In this self-organised state of chaos, members are not confined to narrow roles, and gradually develop their capacity for differentiation and relationships, growing continuously toward their maximum potential contribution to the efficiency of the organisation. In this way, values act as organisers or "attractors" of disorder, which in the theory of chaos are equations represented by unusually regular geometric configurations that predict the long-term behaviour of complex systems. In business organisations (as in all kinds of social systems) the starting principles end up as the final principles in the long term. An attractor is a model representation of the behavioral results of a system. The attractor is not a force of attraction or a goal-oriented presence in the system; it simply depicts where the system is headed based on its rules of motion. Thus, in a culture that cultivates or shares values of autonomy, responsibility, independence, innovation, creativity, and proaction, the risk of short-term chaos is mitigated by an overall long-term sense of direction. A more suitable approach to manage the internal and external complexities that organisations are currently confronting is to alter their dominant culture under the principles of MBV.

Organisational values as "attractors of chaos": An emerging cultural change to manage organisational complexity

Business organisations are excellent representations of what in physics and mathematics are designated "chaotic" systems. Because a culture of innovation will be vital for organisational survival in the 21st century, the present paper proposes that viewing organisations in terms of "complexity theory" may assist leaders in fine-tuning managerial philosophies that provide orderly management emphasizing stability within a culture of organised chaos, for it is on the "boundary of chaos" that the greatest creativity occurs. It is argued that 21st century companies, as chaotic social systems, will no longer be effectively managed by rigid objectives (MBO) nor by instructions (MBI). Their capacity for self-organisation will be derived essentially from how their members accept a shared set of values or principles for action (MBV). Complexity theory deals with systems that show complex structures in time or space, often hiding simple deterministic rules. This theory holds that once these rules are found, it is possible to make effective predictions and even to control the apparent complexity. The state of chaos that self-organises, thanks to the appearance of the "strange attractor", is the ideal basis for creativity and innovation in the company. In this self-organised state of chaos, members are not confined to narrow roles, and gradually develop their capacity for differentiation and relationships, growing continuously toward their maximum potential contribution to the efficiency of the organisation. In this way, values act as organisers or "attractors" of disorder, which in the theory of chaos are equations represented by unusually regular geometric configurations that predict the long-term behaviour of complex systems. In business organisations (as in all kinds of social systems) the starting principles end up as the final principles in the long term. An attractor is a model representation of the behavioral results of a system. The attractor is not a force of attraction or a goal-oriented presence in the system; it simply depicts where the system is headed based on its rules of motion. Thus, in a culture that cultivates or shares values of autonomy, responsibility, independence, innovation, creativity, and proaction, the risk of short-term chaos is mitigated by an overall long-term sense of direction. A more suitable approach to manage the internal and external complexities that organisations are currently confronting is to alter their dominant culture under the principles of MBV.

Epistemología y cibernética

Si el observador y el observado forman parte del mismo objeto descrito, la convergencia entre el sujeto cognoscente y el objeto por conocer no puede sustraerse del principio de reflexividad, que propicia una mejor y más profunda solidez del corpus científico generado. La superioridad del principio de reflexividad se fundamenta en la naturaleza autorreferente de los sistemas sociales, esto es, en la capacidad que desarrollan los sistemas para tomar conciencia de sí y delimitarse respecto a un entorno o ambiente. A través de tal delimitación los sistemas acceden a la autoobservación, sin ella los sistemas no son capaces de generar todos los componentes que precisan para sus operaciones, esto es, no son capaces de llevar a cabo sus procesos autopoiéticos.

Las Imágenes del malestar. Representaciones del yo y la construcción de subjetividad en la producción audiovisual contemporánea y en los nuevos dispositivos tecnológicos

El tema de la investigación propuesto aquí, se centra en el malestar social, y la representación de éste desde un punto de vista personal y autobiográfico, algo que en estas página denomino Autorepresentación del malestar social. ¿Cómo se autorepresenta el malestar y qué prácticas artísticas se emplean para ello? ¿Cuáles son la transformaciones que provocan estas prácticas artísticas en el terreno audiovisual? En este sentido, exploraremos dos vías de análisis: por un lado nos interesa observar cuales han sido las modificaciones que el poder ha desarrollado para establecer nuevas formas de explotación, y por otro lado, veremos como estas modificaciones están generando una nueva praxis social donde las prácticas artísticas cobran un nuevo y reforzado sentido, así como una nueva capacidad política, individual y colectiva a un mismo tiempo, cargada de una fuerza transformadora capaz de componer nuevos espacios de sujeto. Analizaremos, desde la representación del yo en la vida cotidiana, el género y las relaciones interpersonales, hasta las transformaciones contemporáneas del trabajo, y los cambios en la construcción de la subjetividad. El principal elemento en el que se apoyaran nuestras investigaciones será el anàlisis de producciones audiovisuales contemporáneas y la distribución de estas en algunas de las redes de comunicación contemporáneas, intentando mostrar, de esta manera, la interacción y los efectos directos que provocan en la realidad social.

Embodied Autonomy in Digital Ecosystems: From Bio-Inspired Agents to Cognitive Systems

This paper proposes to promote autonomy in digital ecosystems so that it provides agents with information to improve the behavior of the digital ecosystem in terms of stability. This work proposes that, in digital ecosystems, autonomous agents can provide fundamental services and information. The final goal is to run the ecosystem, generate novel conditions and let agents exploit them. A set of evaluation measures must be defined as well. We want to provide an outline of some global indicators, such as heterogeneity and diversity, and establish relationships between agent behavior and these global indicators to fully understand interactions between agents, and to understand the dependence and autonomy relations that emerge between the interacting agents. Individual variations, interaction dependencies, and environmental factors are determinants of autonomy that would be considered. The paper concludes with a discussion of situations when autonomy is a milestone

Algorithmic aspects of bio-inspired string operations

We present building blocks for algorithms for the efficient reduction of square factor, i.e. direct repetitions in strings. So the basic problem is this: given a string, compute all strings that can be obtained by reducing factors of the form zz to z. Two types of algorithms are treated: an offline algorithm is one that can compute a data structure on the given string in advance before the actual search for the square begins; in contrast, online algorithms receive all input only at the time when a request is made. For offline algorithms we treat the following problem: Let u and w be two strings such that w is obtained from u by reducing a square factor zz to only z. If we further are given the suffix table of u, how can we derive the suffix table for w without computing it from scratch? As the suffix table plays a key role in online algorithms for the detection of squares in a string, this derivation can make the iterated reduction of squares more efficient. On the other hand, we also show how a suffix array, used for the offline detection of squares, can be adapted to the new string resulting from the deletion of a square. Because the deletion is a very local change, this adaption is more eficient than the computation of the new suffix array from scratch.

Can wild ungulate carcasses provide enough biomass to maintain avian scavenger populations? An empirical assessment using a bio-inspired computational model

Background: The reduction in the amount of food available for European avian scavengers as a consequence of restrictive public health policies is a concern for managers and conservationists. Since 2002, the application of several sanitary regulations has limited the availability of feeding resources provided by domestic carcasses, but theoretical studies assessing whether the availability of food resources provided by wild ungulates are enough to cover energetic requirements are lacking. Methodology/Findings: We assessed food provided by a wild ungulate population in two areas of NE Spain inhabited by three vulture species and developed a P System computational model to assess the effects of the carrion resources provided on their population dynamics. We compared the real population trend with to a hypothetical scenario in which only food provided by wild ungulates was available. Simulation testing of the model suggests that wild ungulates constitute an important food resource in the Pyrenees and the vulture population inhabiting this area could grow if only the food provided by wild ungulates would be available. On the contrary, in the Pre-Pyrenees there is insufficient food to cover the energy requirements of avian scavenger guilds, declining sharply if biomass from domestic animals would not be available. Conclusions/Significance: Our results suggest that public health legislation can modify scavenger population trends if a large number of domestic ungulate carcasses disappear from the mountains. In this case, food provided by wild ungulates could be not enough and supplementary feeding could be necessary if other alternative food resources are not available (i.e. the reintroduction of wild ungulates), preferably in European Mediterranean scenarios sharing similar and socio-economic conditions where there are low densities of wild ungulates. Managers should anticipate the conservation actions required by assessing food availability and the possible scenarios in order to make the most suitable decisions.

Leadership and overcoming coordination failure with asymmetric costs

We study how the heterogeneity of agents affects the extent to which changes in financial incentives can pull a group out of a situation of coordination failure. We focus on the connections between cost asymmetries and leadership. Experimental subjects interact in groups of four in a series of weak-link games. The treatment variable is the distribution of high and low effort cost across subjects. We present data for one, two and three low-cost subjects as well as control sessions with symmetric costs. The overall pattern of coordination improvement is common across treatments. Early coordination improvements depend on the distribution of high and low effort costs across subjects, but these differences disappear with time. We find that initial leadership in overcoming coordination failure is not driven by low-cost subjects but by subjects with the most frequent cost. This conformity effect can be due to a kind of group identity or to the cognitive simplicity of acting with identical others.

Could cell membranes produce acoustic streaming? Making the case for synechococcus self-propulsion

Sir James Lighthill proposed in 1992 that acoustic streaming occurs in the inner ear, as part of the cochlear amplifier mechanism. Here we hypothesize that some of the most ancient organisms use acoustic streaming not only for self-propulsion but also to enhance their nutrient uptake. We focus on a motile strain of Synechococcus, a yanobacteria whose mechanism for self-propulsion is not known. Molecular motors could work like piezoelectric transducers acting on the crystalline structure surrounding the outer cell membrane. Our calculations show that a traveling surface acoustic wave (SAW)could account for the observed velocities. These SAW waves will also produce a non-negligible Stokes layer surrounding the cell: motion within this region being essentially chaotic. Therefore, an AS mechanism would be biologically advantageous, enhancing localized diffusion processes and consequently, chemical reactions. We believe that acoustic streaming, produced by nanometer scale membrane vibrations could be widespread in cell biology. Other possible instances are yeast cells and erythrocytes. Flows generated by acoustic streaming may also be produced by silica coated diatoms along their raphe. We note that microelectromechanical (MEMS) acoustic streaming devices were first introduced in the 1990’s. Nature may have preceded this invention by 2.7 Gyr.

Desarrollo de una colección de Líneas Casi Isogénicas (NIL) para el estudio de caracteres de interés agronómico en especies del género Fragaria

Fragaria vesca posee varias características que la hacen interesante como especie modelo en la familia Rosaceae. Además, su naturaleza diploide permite sortear la complejidad genética de la fresa cultivada. Considerando que los genomas de las especies diploides y octoploides de Fragaria mantienen una relación de sintenia y colinearidad, estamos desarrollando una colección de Líneas Casi Isogénicas (NIL) en Fragaria diploide, usando Fragaria bucharica, una variedad asiática, como donante de introgresiones y Fragaria vesca var. Reine des Vallées, una variedad francesa comúnmente cultivada en España para usos industriales, como parental recurrente. Para obtener introgresiones de F. bucharica en un fondo genético homogéneo de F. vesca, se desarrolló un retrocruzamiento y se obtuvo una población BC1 que fue analizada para la presencia de alelos de F. bucharica a lo largo de los 7 grupos de ligamiento (LG) del mapa de referencia de Fragaria. Los individuos con bajo número de introgresiones de gran tamaño, que en conjunto abarcaron todo el genoma de F. bucharica, fueron seleccionados y retrocruzados con el parental recurrente. La descendencia fue analizada para los loci segregantes y los individuos BC2 con 1 ó 2 introgresiones fueron seleccionados como líneas donadoras de introgresiones de las NIL. Hasta el momento se han descrito tres fenotipos dominantes diferentes bajo condiciones de invernadero en varias NIL heterozigóticas: Las plantas con introgresiones en LG2 presentan estolones. Las plantas con introgresiones en LG1 y LG3 presentan floración temprana. Las plantas con introgresiones en LG6 presentan floración estacional. Actualmente se está trabajando en la selección y caracterización de introgresiones de pequeño tamaño mediante la autofecundación de las líneas seleccionadas. La caracterización fenotípica de los recombinantes seleccionados permitirá localizar y estimar los patrones de herencia de los genes implicados en los caracteres descritos, además de la identificación de nuevos caracteres recesivos que aparecerán en homozigosis.

Implementació de cursos d'Electrònica i Tècniques de Microscòpia en modalitat docent semipresencial amb estratègies de treball cooperatiu i avaluació continuada en entorn de programari lliure Moodle

L’objectiu principal del present projecte MQD és la implementació de cursos semipresencials en el campus virtual MOODLE per a la docència de les assignatures d’Electrònica troncals de l’ensenyament de Física que depenen del nostre departament i de l’assignatura Tècniques de Microscòpia, que és optativa i comuna als Màsters de Nanociència i Nanotecnologia i d’Enginyeria Física. Plantegem metodologies docents basades en: (1) reduir la presencialitat, (2) afavorir l'autoaprenentatge, (3) aplicar estratègies d’avaluació formativa i avaluació acreditativa continuada i (4) fer ús de les TIC com a suport a la docència. La versatilitat de la plataforma Moodle per compartir recursos permetrà generar un material docent accessible per altres professors. D’altra banda, la possibilitat de Moodle per a la gestió de grups, organització i revisió de tasques facilitarà el seguiment de l’activitat d’autoaprenentatge i de treball cooperatiu així com de l’avaluació final dels aprenentatges. Durant la duració d'aquest projecte MQD s'han implementat els segúents entorns: - Curs d'Electrònica Física, semipresencial, amb treball cooperatiu i amb implantació d'avaluació continuada - Entorn de Coordinació del Master de Nanociència i Nanotecnologia - Curs de l'assignatura optativa de Màster Oficial de Nanociència i Nanotecnologia "Tècniques de Microscòpia"

Nanomotors: new strategies of (bio)sensing based on motion

Nanomotors are nanoscale devices capable of converting energy into movement and forces. Among them, self-propelled nanomotors offer considerable promise for developing new and novel bioanalytical and biosensing strategies based on the direct isolation of target biomolecules or changes in their movement in the presence of target analytes. The mainachievements of this project consists on the development of receptor-functionalized nanomotors that offer direct and rapid target detection, isolation and transport from raw biological samples without preparatory and washing steps. For example, microtube engines functionalized with aptamer, antibody, lectin and enzymes receptors were used for the direct isolation of analytes of biomedical interest, including proteins and whole cells, among others. A target protein was also isolated from a complex sample by using an antigen-functionalized microengine navigating into the reservoirs of a lab-on-a-chip device. The new nanomotorbased target biomarkers detection strategy not only offers highly sensitive, rapid, simple and low cost alternative for the isolation and transport of target molecules, but also represents a new dimension of analytical information based on motion. The recognition events can be easily visualized by optical microscope (without any sophisticated analytical instrument) to reveal the target presence and concentration. The use of artificial nanomachines has shown not only to be useful for (bio)recognition and (bio)transport but also for detection of environmental contamination and remediation. In this context, micromotors modified with superhydrophobic layer demonstrated that effectively interacted, captured, transported and removed oil droplets from oil contaminated samples. Finally, a unique micromotor-based strategy for water-quality testing, that mimics live-fish water-quality testing, based on changes in the propulsion behavior of artificial biocatalytic microswimmers in the presence of aquatic pollutants was also developed. The attractive features of the new micromachine-based target isolation and signal transduction protocols developed in this project offer numerous potential applications in biomedical diagnostics, environmental monitoring, and forensic analysis.

Simulation methods with extended stability for stiff biochemical kinetics

Background: With increasing computer power, simulating the dynamics of complex systems in chemistry and biology is becoming increasingly routine. The modelling of individual reactions in (bio)chemical systems involves a large number of random events that can be simulated by the stochastic simulation algorithm (SSA). The key quantity is the step size, or waiting time, τ, whose value inversely depends on the size of the propensities of the different channel reactions and which needs to be re-evaluated after every firing event. Such a discrete event simulation may be extremely expensive, in particular for stiff systems where τ can be very short due to the fast kinetics of some of the channel reactions. Several alternative methods have been put forward to increase the integration step size. The so-called τ-leap approach takes a larger step size by allowing all the reactions to fire, from a Poisson or Binomial distribution, within that step. Although the expected value for the different species in the reactive system is maintained with respect to more precise methods, the variance at steady state can suffer from large errors as τ grows. Results: In this paper we extend Poisson τ-leap methods to a general class of Runge-Kutta (RK) τ-leap methods. We show that with the proper selection of the coefficients, the variance of the extended τ-leap can be well-behaved, leading to significantly larger step sizes.Conclusions: The benefit of adapting the extended method to the use of RK frameworks is clear in terms of speed of calculation, as the number of evaluations of the Poisson distribution is still one set per time step, as in the original τ-leap method. The approach paves the way to explore new multiscale methods to simulate (bio)chemical systems.