Modeling and design of heterogeneous hierarchical bioinspired spider web structures using generative deep learning and additive manufacturing

Spider webs are incredible biological structures, comprising thin but strong silk filament and arranged into complex hierarchical architectures with striking mechanical properties (e.g., lightweight but high strength, achieving diverse mechanical responses). While simple 2D orb webs can easily be mimicked, the modeling and synthesis of 3D-based web structures remain challenging, partly due to the rich set of design features. Here we provide a detailed analysis of the heterogenous graph structures of spider webs, and use deep learning as a way to model and then synthesize artificial, bio-inspired 3D web structures. The generative AI models are conditioned based on key geometric parameters (including average edge length, number of nodes, average node degree, and others). To identify graph construction principles, we use inductive representation sampling of large experimentally determined spider web graphs, to yield a dataset that is used to train three conditional generative models: 1) An analog diffusion model inspired by nonequilibrium thermodynamics, with sparse neighbor representation, 2) a discrete diffusion model with full neighbor representation, and 3) an autoregressive transformer architecture with full neighbor representation. All three models are scalable, produce complex, de novo bio-inspired spider web mimics, and successfully construct graphs that meet the design objectives. We further propose algorithm that assembles web samples produced by the generative models into larger-scale structures based on a series of geometric design targets, including helical and parametric shapes, mimicking, and extending natural design principles towards integration with diverging engineering objectives. Several webs are manufactured using 3D printing and tested to assess mechanical properties

The drivers of heuristic optimization in insect object manufacture and use

Insects have small brains and heuristics or ‘rules of thumb’ are proposed here to be a good model for how insects optimize the objects they make and use. Generally, heuristics are thought to increase the speed of decision making by reducing the computational resources needed for making decisions. By corollary, heuristic decisions are also deemed to impose a compromise in decision accuracy. Using examples from object optimization behavior in insects, we will argue that heuristics do not inevitably imply a lower computational burden or lower decision accuracy. We also show that heuristic optimization may be driven by certain features of the optimization problem itself: the properties of the object being optimized, the biology of the insect, and the properties of the function being optimized. We also delineate the structural conditions under which heuristic optimization may achieve accuracy equivalent to or better than more fine-grained and onerous optimization methods

Le treuil élasto-capillaire : de la soie d'araignée aux actionneurs intelligents

For more details about my past and current research projects, find me at herveelettro.wordpress.com.The goal of this PhD thesis was to understand and recreate artificially a self-assembling mechanism involving capillarity and elasticity present in natural spider silk. The primary function of the micronic glue droplets that exist on spider capture silk is to provide the spider web with adhesive properties, crucial in attaining efficiency as a food trap. These droplets play yet another role: the dramatic enhancement of silk mechanical properties, as well as the preservation of the integrity of the web structure. This is due to the localization of the buckling instability within the liquid glue droplets, site of over-compression due to the capillary meniscii. This leads to local coiling of the fibre, and retightening of the overall system. In effect, this is a micronic automatic coiling system that is powered by capillarity, and is thus coined elasto-capillary windlass. The first part of my thesis aimed to the characterization of natural samples and visualization of the natural windlass. This required adjustements of environmental parameters (especially relative humidity), microscopic observations and sub-micronewton force measurements both in compression and in tension, as well as image analysis and technical problem solving. We have found that the local shape of the fibre is intimately linked to the mechanical properties of the overall sample. The existence of the windlass mechanism implies that under compression this special drop-on-fibre system behaves like a liquid, whereas under tension it has a classical elastic spring regime. Spiders have thus found a way to create liquid-solid mechanical hybrids using shape-induced functionalisation.We use a fully mechanical model to explain this unique behaviour, as well as an analogy with phase transition formalism. Using a drop-on-deformable-fibre system, we show that if the wetting energy is higher than the bending energy, the system “activates” and in-drop coiling begins. Numerical simulations of 3D elastica under local soft confinement potential reproduce the observed link between local fibre shape and mechanical response. We then fabricate centimeter-long micronic soft fibres, by melt spinning or wet spinning of thermoplastic polymers, and show that the simple addition of a wetting liquid droplet makes for an effective system with mechanical properties quantitatively close to that of spider capture silk. Further experimental characterization of the created drop-on-coilable-fibre systems was found to agree with predictions from numerical simulations and theory, especially for properties such as the threshold for activation, the existence of an hysteresis, the fine details of the stress-strain curve, or the influence of gravity and of the deformability of the droplet interface.We further showed that the drop-on-coilable-fibre systems can be enriched by the addition of new degrees of freedom, such as using several fibres, temperature changes or evaporation. This led to the design of actuators and sensors, as well as a new technique for 3D microfabrication, showing the potential of increasingly complex cases of drop-on-coilable-fibre systems, both technologically and academically.For more details about my past and current research projects, find me at herveelettro.wordpress.com.Le but de cette thèse était de comprendre et recréer artificiellement un mécanisme d’autoassemblage faisant appel aux notions de capillarité et d’élasticité dans la soie d’araignée. La fonction première des gouttes de glue microniques qui existent sur la soie d’araignée dîte de capture est de fournir à la toile sespropriétés adhésives, cruciales pour atteindre une efficacité digne d’un piège. Ces gouttes jouent pourtant un autre rôle : elles améliorent de façon spectaculaire les propriétés mécaniques de la soie, et permettent par la même occasion de préserver l’intégrité structurelle de la toile. Ceci est dû à la localisation de l’instabilité de flambage au sein des gouttes de glue, qui sont le site d’une surcompression de la part des ménisques capillaires, ce qui provoque un enroulement local de la fibre, et la retension du système entier. Ceci constitue un microsystème d’enroulement automatique qui tire son énergie de la capillarité, qui sera appelé treuil élasto-capillaire.La première partie de ma thèse fut dédiée à la caractérisation d’échantillons naturels et à la visualisation du treuil naturel, à travers le réglage de paramètres d’environnement, des observations microscopiques, des mesures de forces sub-micronewtons en compression et en tension, mais aussi de l’analyse d’image et la résolution de problèmes techniques. Les mesures indiquent qu’il y a un rapport intime entre la forme locale de la fibre et les propriétés mécaniques de l’ensemble de l’échantillon.L’existence du phénomène de treuil implique que ce système spécial de gouttes sur fibre se comporte sous compression comme un liquide, alors que sous tension il possède un régime de ressort élastique classique. Les araignées ont donc trouvé un moyen de construire des hybrides mécaniques liquide-solidegrâce à une technique de functionalisation induite par forme. Nous avons utilisé un modèle n'incluant que des arguments mécaniques pour expliquer ce comportement unique, ainsi qu’une analogie avec le formalisme des transitions de phases. Nous modélisons ce système comme une goutte sur une fibre déformable, et montrons que si l’énergie de mouillage est supérieure à l’énergie de courbure, le système “s’active” et l’enroulement en goutte commence. Des simulations numériques du problème de l’elastica 3D sous compression locale dans un potentiel de confinement mou reproduit le lien observé entre la forme locale de la fibre et la réponse mécanique. Nous fabriquons ensuite des fibres flexibles de taille micronique et longues de plusieurs centimètres par extrusion de polymères thermoplastiques, et montrons que le simple dépôt d’une goutte de liquide mouillant permet par la suite la création efficace d’un système ayant des propriétés mécaniques proches de celles de la soie d’araignée de capture. La caractérisation expérimentale des systèmes de goutte sur fibre enroulable est en accord avec les simulations numériques et la théorie, notamment pour des propriétés telles que le seuil d’activation, l’existence d’un hystérésis, les détails subtils de la courbe contrainte-déformation, ou encore l’influence de la gravité et de la déformabilité de la surface de la goutte. Nous montrons ensuite que les systèmes de goutte sur fibre enroulable peuvent être enrichi par de nouveaux degrés de liberté, tels que l’utilisation de plusieurs fibres, les changements de température ou la possibilité d’évaporation. Ceci a mené à la conception d’actionneurs et de capteurs, ainsi qu’à une nouvelle technique de microfabrication 3D, révélant le potential de situations de plus en plus complexes, tant technologiquement qu’académiquement

Diversity and Structure of Spider Assemblages in Terai Conservation Area

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Molecular dynamics analysis of supercontraction in spider dragline silk

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2013.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student-submitted PDF version of thesis.Includes bibliographical references (p. 67-73).Spider dragline silk is a material that has evolved over millions of years to develop finely tuned mechanical properties. It is a protein-based fiber, used as the main structural component in spider webs and as a lifeline for the spider, and it combines strength and extensibility to give it toughness currently unmatched by synthetic materials. Dragline silk has the unusual tendency of shrinking by up to 50% when exposed to high humidity, a phenomenon called supercontraction. Supercontraction is thought to occur due to the association of water molecules with the amorphous region of silk proteins. The water molecules are believed to break the hydrogen bonds that connect the protein strands, causing a fundamental reorganization of molecular structure, which is manifested at the macro scale by a large retraction in length. However, the details of these mechanisms remain unknown and have not been directly demonstrated in prior research. Here we use full-scale atomic modeling of spider silk using molecular dynamics to investigate the structure and properties of this material at a length scale that is not yet accessible by experimental methods. A model of spider silk protein is used to explore the phenomenon of supercontraction. Two classes of simulations with different models are performed, and in both cases the models show a reorganization of the molecular structure consistent with the theory of supercontraction, yet fail to show the dramatic change in size that is observed on the macro scale.by Laura Batty.M.Eng

Tunable silk: using microfluidics to investigate sequence-structure-property relationships

Thesis (Ph.D.)--Boston UniversitySilk is an ancient material that is produced in nature by both silkworms and spiders and has been used in textiles for thousands o·f years. Stronger than steel and tougher than Kevlar, silk fibers possess a unique combination of strength and elasticity. Silk is also biodegradable and biocompatible, and has been the focus of research areas ranging from fiber optics to tissue regeneration. While textile applications utilize raw silkworm silk, biomedical applications rely primarily on regenerated silk, which is derived from silkworm cocoons and reprocessed into the desired material. Additionally, there has been much progress in the area of recombinant silk technology, where genetically engineered proteins are inspired by or mimic: native silk sequences. However, despite major advancements in silk engineering, native silk spinning - a remarkable process that takes place at ambient temperature and pressure- is still not completely understood. Given these gaps in knowledge, it remains a challenge in the field to fabricate a regenerated or recombinant material that can mimic the outstanding properties of native silks. We have developed a novel microfluidic silk processing technique that mimics aspects of silkworm spinning to transform aqueous silk solution into fibers in a highly controlled manner. By altering flow parameters within the device and utilizing post-spin processing, we can tune properties such as fiber diameter and Young's modulus across a broad range for tailored applications. Unlike alternative processing methods, we can fabricate a fiber from as little as 50 micro-liters of silk solution or spin continuously for up to two hours to produce a non-woven mesh from a single fiber approximately 6.5 meters long. Using this device we have fabricated regenerated silk fibers to investigate cell behavior, incorporated silk fibers into cell sheets to provide structural support, and fabricated non-woven silk meshes for use as structural support layers for multi-layer tissue constructs. We have also spun multiple variants of recombinant silk-like sequences. We have optimized this device for use as a low-volume sequence screening tool as part of a combined computational and experimental approach to further the understanding of both native and recombinant silk protein folding and hierarchical assembly

Elucidating Complex Animal Interactions in the Modern World: Determining the occurrence and effects of intraguild predation within food webs

Animal interactions structure food webs with stability being contingent on the presence and strength of multi-species interactions. Intraguild predation (IGP) is a complex interaction that can impact species at the individual, population and community levels, ultimately determining the strength, direction and linearity of trophic cascades and species abundance across trophic levels. IGP occurs among a minimum of three species; a predator (IGpredator) that kills and consumes a prey (IGprey) with which it competes for a common resource. Through a systematic literature search, I determined traditional to modern approaches to measure the occurrence and effect of IGP and then identified the research effort afforded to the different implication levels and IGP effects characterized by Polis et al. (1989). I highlighted IGP effects that require focused attention and provided recommendations on methods that could be used to address knowledge gaps. To understand the role of IGP in higher order predators, I focused on the large shark assemblage given their largely unknown role in top down control and limited IGP studies to date. The large shark assemblage exhibits high phenotypic plasticity that results in varied functional roles (e.g. secondary vs. tertiary piscivores) suggesting complex IGP interactions occur. Stable isotope analysis (SIA) provides an approach to reconstruct consumer diet to examine IGP, however, a detailed understanding of tissue preparation techniques is first required to ensure accurate interpretation of results. Elasmobranch liver is a useful high turnover tissue for IGP studies, but it contains high lipid levels and is expected to retain urea and TMAO for osmotic balance which can bias isotopic values. I found that deionized water washing for urea and TMAO removal was not required as δ15N values were not modified following treatment. Residual lipid within lipid extracted liver samples, however, required the development of C:N thresholds to derive ecologically relevant liver isotopic values. A preliminary comparison between muscle and liver tissue highlighted the value of liver for understanding short vs. long term movements and its application for IGP studies. The occurrence, class and consistency of IGP among large sharks was examined using published stomach content data and prey contributions from stable isotope mixing models. IGP was present among all sharks with the strength and class varying by species, ontogeny and over time (i.e. daily vs. annually). Understanding shark functional roles within marine food webs can improve management practices through the lens of multi-species interactions; targeted conservation on shark species involved in moderate levels of IGP with high connectance among species may enhance food web stability