Emergence in artificial life

Even when concepts similar to emergence have been used since antiquity, we lack an agreed definition. However, emergence has been identified as one of the main features of complex systems. Most would agree on the statement ``life is complex''. Thus, understanding emergence and complexity should benefit the study of living systems. It can be said that life emerges from the interactions of complex molecules. But how useful is this to understand living systems? Artificial life (ALife) has been developed in recent decades to study life using a synthetic approach: build it to understand it. ALife systems are not so complex, be them soft (simulations), hard (robots), or wet (protocells). Then, we can aim at first understanding emergence in ALife, for then using this knowledge in biology. I argue that to understand emergence and life, it becomes useful to use information as a framework. In a general sense, I define emergence as information that is not present at one scale but is present at another scale. This perspective avoids problems of studying emergence from a materialist framework, and can be also useful in the study of self-organization and complexity.Comment: 28 pages, 1 figur

Designing parametric matter:Exploring adaptive material scale self-assembly through tuneable environments

3D designs can be created using generative processes, which can be transformed and adapted almost infinitely if they remain within their digital design software. For example, it is easy to alter a 3D object's colour, size, transparency, topology and geometry by adjusting values associated with those attributes. Significantly, these design processes can be seen as morphogenetic, where form is grown out of bottom-up logic’s and processes. However, when the designs created using these processes are fabricated using traditional manufacturing processes and materials they lose all of these abilities. For example, even the basic ability to change a shapes' size or colour is lost. This is partly because the relationships that govern the changes of a digital design are no longer present once fabricated. The motivating aim is: how can structures be grown and adapted throughout the fabrication processes using programmable self-assembly? In comparison the highly desirable attribute of physical adaptation and change is universally present within animals and biological processes. Various biological organisms and their systems (muscular or skeletal) can continually adapt to the world around them to meet changing demands across different ranges of time and to varying degrees. For example, a cuttlefish changes its skin colour and texture almost immediately to hide from predators. Muscles grow in response to exercise, and over longer time periods bones remodel and heal when broken, meaning biological structures can adapt to become more efficient at meeting regularly imposed demands. Emerging research is rethinking how digital designs are fabricated and the materials they are made from, leading to physically responsive and reconfigurable structures. This research establishes an interdisciplinary and novel methodology for building towards an adaptive design and fabrication system when utilising material scale computation process (e.g. self-assembly) within the fabrication process, which are guided by stimuli. In this context, adaption is the ability of a physical design (shape, pattern) to change its local material and or global properties, such as: shape, composition, texture and volume. Any changes to these properties are not predefined or constrained to set limits when subjected to environmental stimulus, (temperature, pH, magnetism, electrical current). Here, the stimulus is the fabrication mechanisms, which are governed and monitored by digital design tools. In doing so digital design tools will guide processes of material scale self-assembly and the resultant physical properties. The fabrication system is created through multiple experiments based on various material processes and platforms, from paint and additives, to ink diffusion and the mineral accretion process. A research through design methodology is used to develop the experiments, although the experiments by nature are explorative and incremental. Collectively they are a mixture of analogue and digital explorations, which establish principles and a method of how to grow physical designs, which can adapt based on digital augmentations by guiding material scale self-assembly. The results demonstrate that it is possible to grow physical 2D and 3D designs (shapes and patterns) that could have their properties tuned and adapted by creating tuneable environments to guide the mineral accretion process. Meaning, the desirable and dynamic traits of digital computational designs can be leveraged and extended the as they are made physical. Tuneable environments are developed and defined thought the series experiments within this thesis. Tuneable environments are not restricted to the mineral accretion process, as it is demonstrated how they can manipulate ink cloud patterns (liquid diffusion), which are less constrained in comparison to the mineral accretion process. This is possible due to the use of support mediums that dissipate energy and also contrast materially (they do not diffuse). Combining contrasting conditions (support mediums, resultant material effects) with the idea of tuneable environments reveals how: 1) material growth and properties can be monitored and 2) the possibilities of growing 3D designs using material scale self-assembly, which is not confined to a scaffold framework. The results and methodology highlight how tuneable environments can be applied to advance other areas of emerging research, such as altering environmental conditions during methods of additive manufacturing, such as, suspended deposition, rapid liquid printing, computed axial lithography or even some strategies of bioprinting. During the process, deposited materials and global properties could adapt because of changing conditions. Going further and combining it with the idea of contrasting mediums, this could lead to new types 3D holographic displays, which are grown and not restricted to scaffold frameworks. The results also point towards a potential future where buildings and infrastructure are part of a material ecosystem, which can share resources to meet fluctuating demands, such as, solar shading, traffic congestion, live loading

Designing parametric matter:Exploring adaptive self-assembly through tuneable environments

3D digital models can be created using generative processes, which can be transformed and adapted almost infinitely if they remain within their digital design software. For example, it is easy to alter a 3D structure’s/object's colour, size, geometry and topology by adjusting values associated with those attributes. However, when these digital models are fabricated using traditional, highly deterministic fabrication processes, where form is imposed upon materials, the physical structure typically loses all of these adaptive abilities. These reduced physical abilities are primarily a result of how design representations are fabricated and if they can maintain relationships with the physical counterpart/materials post-fabrication. If relationships between design representations and physical materials are removed it can lead to redundancy and significant material waste as the material make-up of a physical structure can’t accommodate fluctuating design demands (e.g. aesthetics, structural, programmatic). This raises the question: how can structures be grown and adapted throughout fabrication processes using programmable self-assembly? This research explores and documents the development of an adaptive design and fabrication system through a series of ‘material probes’, which begin to address this aim. The series of material probes have been carried out using research through design as an approach, which enables an exploration and highlights challenges, developments and reflections of the design process as well as, the potentials of rethinking design and fabrication processes and their relationships with materials. Importantly, the material probes engage with material computation (e.g. self-assembly/autonomous-assembly) and demonstrate that various patterns, shapes and structures can have various material properties (e.g. volume, composition, texture, shape) tuned and adapted throughout the fabrication process by inducing stimuli (e.g. temperature, magnetism, electrical current) and altering parameters of stimuli (e.g. duration, magnitude, location). As a result, the structures created can tune and adapt their material properties across length scales and time scales. These adaptive capacities are enabled by creating what is termed ‘tuneable environments. Significantly, tuneable environments fundamentally rethink design and fabrication processes and their relationships with materials, since inducing stimuli and controlling their parameters can be used as an approach to creating programmable self-assembly. Consequently, the material platforms’ units of matter do not have to have pre-design properties (e.g. geometries, interfaces) This research points towards future potentials of structures that can physically evolve and lead to the decarbonising of urban contexts where they could behave like ‘living material eco-systems’, and resources are shared to meet fluctuating demands through passive means

Algae Textile: A Lightweight Photobioreactor for Urban Buildings

By innovating the photobioreactor, the growth of algae can be deployed as a performative and ecological layer within contemporary building systems. Proposed is an algae textile: a building–integrated photobioreactor organized as a flexible membrane, whose form can be adjusted according to given programmatic and environmental conditions. This organization translates functions from industrial photobioreactors into forms that can operate at the lightweight scale of an enclosure or partition, demonstrating how algae might be integrated within the layers of a building as an alternative ecology. A typical curtain wall is used as an example to test new standards of geometry and materiality using the membrane, where parametrically–controlled quasiperiodic and conformal geometries are studied. These offer geometric plasticity when generating the reactor’s organization, refining its ability to modulate light and view by varying porosity, and tailoring it to the characteristics of a given space. When paired with the minimal dimensions of transparent thin–film polymers, this method of forming enclosures shows how renewable resources such as algae can be positioned within buildings without an expansion in the wall assembly and easily retrofitted into existing ones to create performative next-generation building skins. To support these qualities, design principles addressing both qualitative and quantitative measures are emphasized, aiming to define a photobioreactor’s required behaviours when used specifically as a component within urban buildings. This direct integration of biology in architecture asserts that building material can be seen as a productive entity, contributing to the discourse surrounding postnatural urban ecology, and drawing from research exploring articulated material systems, including Achim Menges’ composite membranes and Neri Oxman’s use of digital morphogenesis. In this way, the industrial process of algae cultivation can be translated into complimentary building systems which acknowledge both the productivity and the aesthetic of algae: as agile components of a larger renewable resource network, and as icons for a self–sufficient urban lifestyle

Accumulation, gelation, and crystallization of prebiotic molecules in a thermal gradient and deep UV circular dichroism

Der Ort an dem das Leben entstanden ist hat die physikalischen Randbedingungen, unter denen sich die ersten replizierenden Systeme entwickelten, definiert. Dabei waren Nichtgleichgewichtssysteme notwendig, welche die Energie lieferten um diese anzutreiben. Eine solche Form von Nichtgleichgewicht stellen beispielsweise Temperaturgradienten dar, wie sie in porösem Gestein in hydrothermalen Quellen am Meeresboden möglich sind. Diese Arbeit behandelt die Auswirkungen von solchen Temperaturgradienten auf Moleküle in Lösung und die Frage wie man diese analysieren kann. Im ersten Teil wird dabei die Akkumulation von selbstkomplementären Oligonukleotiden in einer thermischen Falle demonstriert. Die dabei stattfindende längenselektive Akkumulation führt zur Entstehung von Hydrogelen aus DNA in Lösung, ohne dabei Kondensationsmittel oder multivalente Ionen zu benötigen. Dieser Gelierungsprozess wird für DNA mit zwei oder drei selbstkomplementären Bindungsstellen und einer Länge von lediglich 24 Basen gezeigt. Kontrollversuche zeigen dabei, dass nicht-komplementäre DNA in Lösung bleibt und dass der Prozess nicht von der Interaktion der DNA mit Fluoreszenzfarbstoffen dominiert wird. Zwei selbstkomplementäre Stränge mit zueinander orthogonalen Sequenzen, also einer minimalen Komplementarität, bilden im Experiment sequenzreine Hydrogele Im zweiten Teil wird die Akkumulation von Molekülen an Gas-Wasser-Grenzflächen in einem Temperaturgradienten gezeigt. In diesem System führt die lokale Verdunstung von Wasser an der warmen Seite der Grenzfläche zu einer Kapillarströmung hin zum Meniskus. Dies führt zu einer Akkumulation von Molekülen, welche eine mehr als 1000-fache Konzentration erreichen. Dieser Mechanismus akkumuliert größere Moleküle und daher auch längere Polymere besser. An dieser Grenzfläche kommt es zu einer stark erhöhten Aktivität des Hammerhead Ribozyms, da sowohl Oligonukleotide als auch das für die Aktivität wichtige Magnesium akkumuliert werden. Außerdem kommt es auch hier zur Gelierung selbstkomplementärer RNA sowie zum Einschluss von Molekülen in Vesikelclustern, zur Kristallisation von Ribose Aminooxazolin und zu einer gesteigerten Phosphorylierung von Nukleotiden. Eine vollständige Simulation des Akkumulationsmechanismus bestätigt die Ergebnisse. Der dritte Teil beschreibt den Aufbau eines Circulardichroismus-Mikroskops (CDIM) im UV-Bereich. Ziel war es, den Circulardichroismus (CD) von präbiotischen Molekülen, wie etwa dem Vorprodukt von RNA Nukleotiden---Ribose Aminooxazolin---zu untersuchen und gleichzeitig dessen Akkumulation und eventuelle Kristallisation zu beobachten. In diesem Kapitel wird dabei die experimentelle Realisierung des CDIM gezeigt. Ein Schwerpunkt liegt dabei auf der Erzeugung von zirkular polarisiertem Licht mittels einem gepulsten UV-Laser und einem photoelastischen Modulator. Messungen von Proben mit einem bekannten CD wurden zur Kalibrierung des Systems verwendet. Die Ergebnisse zeigen, dass das CDIM eingeschränkt verwendet werden kann, um das Vorzeichen des CD einer Probe in Wasser zu bestimmen. Weitere Experimente sind jedoch notwendig um Artefakte auszuschließen und zu zeigen, ob man das System mit thermischen Fallen kombinieren kann.The location at which life emerged on Earth defined the physical boundary conditions under which the first replicating systems evolved. Nonequilibrium systems were necessary to provide the energy driving these processes. One such nonequilibrium system could have been temperature gradients, found for example across porous rock in hydrothermal vents. The work presented here focuses on the effects of temperature gradients on molecules in these water-filled micro-compartments and on methods how they could be analyzed. In the first part of this thesis, the accumulation of self-complementary oligonucleotides in a thermal trap is demonstrated. The length-selective accumulation in this system is used to create hydrogels from DNA in solution without the use of condensing agents or multivalent ions. This gelation process is demonstrated for DNA with two and three self-complementary binding sites and strands as short as 24mers. Control experiments show that non-complementary DNA stays in solution and that the process is not dominated by the interaction of DNA with fluorescent dyes. Two self-complementary strands with orthogonal sequences, i.e. a minimal sequence overlap, form pure hydrogels when accumulated together. In part two, the accumulation of molecules at gas-water interfaces in a temperature gradient is demonstrated. In this system, the local evaporation of water at the warm side of the interface leads to a capillary flow towards the meniscus and therefore an accumulation of molecules in this area, reaching a more than 1000-fold concentration increase. This mechanism is length-dependent, accumulating larger molecules better. At the interface, the activity of the Hammerhead ribozyme strongly increases due to the combined accumulation of oligomers and magnesium. In addition, the accumulation can trigger the gelation of self-complementary RNA, the encapsulation of molecules in vesicle clusters, the crystallization of ribose aminooxazoline, and the enhanced phosphorylation of nucleotides. A full simulation of the accumulation mechanism confirms these results. The third part describes the implementation of a circular dichroism imaging microscope (CDIM) in deep UV. The aim was to study the circular dichroism (CD) of prebiotic molecules such as the RNA precursor ribose aminooxazoline, while simultaneously observing its accumulation and possible crystallization. In this part, the experimental realization of the CDIM is shown, with a focus on the mechanisms to create circularly polarized light from a pulsed UV laser using a photoelastic modulator. Measurements of samples with a known CD were used to calibrate the system. The results show that the system might be used to determine the sign of the CD of a sample in water. However, further experiments are necessary to exclude measurement artifacts and investigate if the system can be combined with thermal traps

Self-assembled proteins for food applications: A review

Background: The development of advanced food materials necessarily involves the building of well-known and oriented micro- and nanoarchitectures, which are obtained through the self-assembly of food grade (edible) polymers.Scope and approachKeeping this in view, proteins have proven to be more versatile building blocks than carbohydrate polymers for the manufacture of multifaceted and advanced systems for food applications.Key findings and conclusionsProteins from different sources (animal, vegetal and microbiological) can be self-assembled in several forms (films, hydrogels, micelles/vesicles and particles) to be targeted and tuned for various food applications such as biosensors, coatings, emulsions, controlled and sustained release of active food additives, development of functional foods, etc. Proteins can be self-assembled with each other, with carbohydrates or other proteins, and includes the use of enzymes and essential oils have achieved this physicochemical phenomenon that occurs between macromolecules via chemical interactions, mainly by hydrogen, hydrophilic and ionic bonding, which are determined by the conditions of ionic strength, mechanical force, pH, salt concentration and type, temperature, among others. This review aims to provide a comprehensive and concise analysis of the state of the art of self-assembled proteins for food applications, which have had a significant boom over the past five years in terms of the development of nanotechnology within the food industry.Fil: Tomadoni, Bárbara María. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones en Ciencia y Tecnología de Materiales. Universidad Nacional de Mar del Plata. Facultad de Ingeniería. Instituto de Investigaciones en Ciencia y Tecnología de Materiales; ArgentinaFil: Capello, Cristiane. Universidade Federal de Santa Catarina; BrasilFil: Ayala Valencia, Germán. Universidade Federal de Santa Catarina; BrasilFil: Gutiérrez Carmona, Tomy José. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones en Ciencia y Tecnología de Materiales. Universidad Nacional de Mar del Plata. Facultad de Ingeniería. Instituto de Investigaciones en Ciencia y Tecnología de Materiales; Argentin