<p>Through thousands of years of evolution, natural biological systems have optimized their structures to thrive in diverse ecological conditions. Extracting and leveraging the inherent design principles of these biological systems can provide inspiration for the development of advanced lightweight structural materials. To effectively facilitate this transition, it is crucial to understand the specific mechanisms by which the microstructure of biological materials influences their mechanical properties. This dissertation focuses on understanding microstructure-property correlations in three biological systems: Venus flower basket, Cholla cactus, and Organ pipe coral.</p> <p>The Venus flower basket exhibits a cylindrical cage-like structure made from a complex network of silica fibers which exhibit a core-shell like layered architectures. A novel multimodal approach involving nanoindentation, ex situ and in situ fiber testing, and post-failure fractography was utilized to precisely understand the impact of the layered structure on the tensile and fracture behavior of fibers. The observation of fibers in real-time revealed, for the first time, that the initiation of failure occurs at the fiber's surface and progressively advances towards the core, traversing multiple layers. The concentric layers encompassing the central core act sacrificially, employing various toughening mechanisms to protect the core. Furthermore, nanoindentation experiments performed in situ in water shed light on the significance of the layered fiber structure in a marine environment. Another interesting system is the Cholla cactus. In arid environments, Cholla cactus produces porous wood with a mesh-like structure. To comprehensively understand the structure, properties, and designs of Cholla cactus wood, various techniques such as x-ray tomography, scanning electron microscopy, nanoindentation, and finite element simulations were employed. The structure and function of different wood components was investigated from both biological and mechanical behavior perspectives. The impact of the unique structure of wood components on the design of engineering materials is discussed. Finally, the dissertation focuses on the Organ pipe coral, which exhibits a hierarchical structure comprising vertical tubes and horizontal platforms at the macrostructure level. At the microstructure level, cells are formed through a unique arrangement of micrometer-sized plates made of calcium carbonate. Nanoindentation was used to assess the impact of this hierarchical structure on micromechanical properties. The results unveiled distinct toughening mechanisms operating at different length scales within the coral.</p> <p>17</p> <p>By gaining a precise understanding of the correlations between microstructure and properties in various biological materials, this research provides valuable insights for the design of advanced architected structural materials. The unique interplay between microstructure, function, and properties is discussed.</p>

<p>  </p> <p>Many engineering structures are designed to withstand a critical mechanical load before failure. When a load greater than the critical load is encountered, the manner of structural failure is important. Nature has been a source of technical inspiration for centuries, and the power of modern scientific investigative techniques has enhanced engineers’ abilities to learn from millennia of evolutionary mechanical refinement. </p> <p>Chitons, a family of marine mollusks, feed on algae attached to rocky substrates, and parts of their feeding organs are subjected to varied loads in the process. In this work, the manner of failure of a chiton’s tooth and supporting structure is investigated, and it is suggested that mechanical details of the structure enable load-limiting and fail-safe performance that protects the animal from potentially dangerous overloading.</p>

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Bioinspiration and biomimetics are two increasingly important fields in applied science and mechanics that seek to imitate systems or processes in nature to design improved engineering devices. Here, we are inspired and motivated by microscale internal flow transport phenomena in insect tracheal networks, which are observed to be induced by the rhythmic tracheal wall contractions. These networks have been shown to mange fluid very efficiently compared to current state-of-the-art microfluidic devises. This dissertation presents two versions of a novel bioinspired pumping mechanism that is neither peristaltic nor belongs to impedance mismatch class of pumping mechanisms. The insect-inspired pumping models presented here are expected to function efficiently in the microscale flow regime in a simple channel/tube geometries or a complex network of channels. The first pumping approach shows the ability of inducing a unidirectional net flow by using an inelastic tube or channel with at least two moving contractions. The second pumping approach presents a new concept for directional pumping, namely ``selective pumping in a network.". The results presented here might help in mimicking features of physiological systems in insects and guide efforts to fabricate novel microfluidic devices with improved efficiency. In this study, both theoretical analysis and Stokeslets-meshfree computational methods are used to solve for the 2D and 3D viscous flow transport in several micro-geometries (tubes, channels and networks) with prescribed moving wall contractions. The derived theoretical analysis is based on both lubrication theory and quasi-steady approximations at low Reynolds numbers. The meshfree numerical method is based on the method of fundamental solutions (MFS) that uses a set of singularized force elements ``Stokeslets'' to induce the flow motions. Moreover, the passive particle tracking simulation approach in the Lagrangian frame of reference is also used to strengthen and support our pumping paradigm developed in this dissertation. / Ph. D.

Many animal species are known for their unparalleled abilities to encode sensory information that supports fast, reliable action in complex environments, but the mechanisms remain often unclear. Through fast ear motions, bats can encode information on target direction into time-frequency Doppler signatures. These species were thought to be evolutionarily tuned to Doppler shifts generated by a prey's wing beat. Self-generated Doppler shifts from the bat's own flight motion were for the most part considered a nuisance that the bats compensate for. My findings indicate that these Doppler-based biosonar systems may be more complicated than previously thought because the animals can actively inject Doppler shifts into their input signals. The work in this dissertation presents a novel nonlinear principle for sensory information encoding in bats. Up to now, sound-direction finding has required either multiple signal frequencies or multiple pressure receivers. Inspired by bat species that add Doppler shifts to their biosonar echoes through fast ear motions, I present a source-direction finding paradigm based on a single frequency and a single pressure receiver. Non-rigid ear motions produce complex Doppler signatures that depend on source direction but are difficult to interpret. To demonstrate that deep learning can solve this problem, I have combined a soft-robotic microphone baffle that mimics a deforming bat ear with a CNN for regression. With this integrated cyber-physical setup, I have able to achieve a direction-finding accuracy of 1 degree based on a single baffle motion. / Doctor of Philosophy / Bats are well-known for their intricate biosonar system that allow the animals to navigate even the most complex natural environments. While the mechanism behind most of these abilities remains unknown, an interesting observation is that some bat species produce fast movements of their ears when actively exploring their surroundings. By moving their pinna, the bats create a time-variant reception characteristic and very little research has been directed at exploring the potential benefits of such behavior so far. One hypothesis is that the speed of the pinna motions modulates the received biosonar echoes with Doppler-shift patterns that could convey sensory information that is useful for navigation. This dissertation intends to explore this hypothetical dynamic sensing mechanism by building a soft-robotic biomimetic receiver to replicate the dynamics of the bat pinna. The experiments with this biomimetic pinna robot demonstrate that the non-rigid ear motions produce Doppler signatures that contain information about the direction of a sound source. However, these patterns are difficult to interpret because of their complexity. By combining the soft-robotic pinna with a convolutional neural network for processing the Doppler signatures in the time-frequency domain, I have been able to accurately estimate the source direction with an error margin of less than one degree. This working system, composed of a soft-robotic biomimetic ear integrated with a deep neural net, demonstrates that the use of Doppler signatures as a source of sensory information is a viable hypothesis for explaining the sensory skills of bats.

Tails are frequently utilized by animals to enhance their motion agility, dexterity, and versatility, such as a cheetah using its tail to change its body orientation while its legs are all off the ground and a monkey using its tail to stabilize its locomotion on branches. However, limited by technology and application scenarios, most existing legged robots do not include a robotic tail on board. This research aims to explore the possibilities of adding this missing part on legged robots and investigate the tail's functionalities on enhancing the agility, dexterity, and versatility of legged locomotion. In particular, this research focuses on animal-like serpentine tail structure, due to its larger workspace and higher dexterity. The overall research approach consists of two branches: a theoretical branch that focuses on dynamic modeling, analysis, and control of the legged robots with a serpentine robotic tail; and an empirical branch that focuses on hardware development and experiments of novel serpentine robotic tails and novel legged robots with tail. More specifically, the theoretical work includes modeling and control of a general quadruped platform and a general biped platform, equipped with one of the two general serpentine tail structures: an articulated-structure tail or a continuum-structure tail. Virtual work principle-based formulation was used to formulate the dynamic model. Both classic feedback linearization-based control and optimization-based control were used to coordinate the leg motions and the tail motion. Comparative studies on different tail structures as well as numerical analyses on robotic locomotion were performed to investigate the dynamic effects of serpentine robotic tails. The empirical work includes the developments and experiments of two novel serpentine robotic tail mechanisms and one first-of-its-kind quadruped robot ("VT Lemur") equipped with a serpentine robotic tail. To develop these novel robots, a systematic approach based on dynamic analysis was used. Various experiments were then conducted using the robot hardware. Both the theoretical and empirical results showed that the serpentine robotic tail has significant effects on enhancing the agility, dexterity, and versatility of legged robot motion. / Doctor of Philosophy / Quadruped robots have made impressive progresses over the past decade and now can easily achieve complicated, highly dynamic motions, such as the backflip of the MIT Mini Cheetah robot and the gymnastic parkour motions of the Atlas robot from Boston Dynamics, Inc. However, by looking at nature, many animals use tails to achieve highly agile and dexterous motions. For instance, monkeys are observed to use their tails to grasp branches and to balance their bodies during walking. Kangaroos are found to use their tails as additional limbs to propel and assist their locomotion. Cheetahs and kangaroo rats are thought to use their tails to help maneuvering. Therefore, this research aims to understand the fundamental principles behind these biological observations and develop novel legged robots equipped with a serpentine robotic tail. More specifically, this research aims to answer three key questions: (1) what are the functional benefits of adding a serpentine robotic tail to assist legged locomotion, (2) how do animals control their tail motion, and (3) how could we learn from these findings and enhance the agility, dexterity, and versatility of existing legged robots. To answer these questions, both theoretical investigations and experimental hardware testing were performed. The theoretical work establishes general dynamic models of legged robots with either an articulated tail or a continuum tail. A corresponding motion control framework was also developed to coordinate the leg and tail motions. To verify the proposed theoretical framework, a novel quadruped robot with a serpentine robotic tail was developed and tested.

Nous avons cherché dans ce travail à élaborer un biofilm artificiel électroactif dans le but de promouvoir les réactions de transfert extracellulaire d’électrons (EET) en reconstituant artificiellement un biofilm en présence de matériaux exogènes. Un matériau composite auto-assemblé constitué de cellules bactériennes (Shewanella oneidensis), de nanotubes de carbone et de cytochromes c exogènes (issue de cellules de cœur de bœuf) a été tout d’abord proposé. Le processus d’auto-assemblage a été étudié par diffusion de lumière dynamique, microscopie électronique à balayage et spectroscopie Raman. Ces analyses ont mis en évidence l’importance du cytochrome exogène dans l’assemblage et l’organisation du matériau. La viabilité bactérienne a été étudiée et l’activité métabolique a été caractérisée par électrochimie. Les courants à l’anode étaient 10 et 4 fois plus importants avec ce biofilm artificiel (0,027 A m-2) qu’avec les électrodes modifiées par les bactéries seules (0,003 A m-2) ou associées au cytochrome c (0,007 A m-2). Le biofilm artificiel a été testé en substituant S. oneidensis par Pseudomonas fluorescens, produisant un courant d’oxydation lors de l’ajout de 1,5 mM de glucose. Le cytochrome c possède, outre son rôle structurant, une activité de navette à électrons. Son potentiel redox, 254 mV (vs NHE), était adapté à l’oxydation du formiate mais inadapté à la réduction du fumarate. Pour cette raison, il a été substitué par d’autres cytochromes (c3DvH, c7Da, c553DvH, c3DdN ou c3Dg) possédant des potentiels redox plus bas, de 20 mV à -400 mV. Ces cytochromes variaient aussi au niveau de leur charge à pH neutre, permettant de valider l’importance des forces électrostatiques dans l’assemblage du biocomposite. Les résultats optimaux obtenus avec c3DvH et c7Da ont montré l’importance du potentiel redox des éléments exogènes pour l’EET. Nous avons ensuite remplacé le cytochrome c par la protamine. Cette protéine non électroactive a permis l’assemblage du biocomposite tout en maintenant les transferts directs d’électrons entre les bactéries et les différents nanomatériaux testés. Les optimisations ont permis d’atteindre des courants cathodiques de plus de 12 A m-2 en présence de 50 mM de fumarate. Les expériences de stabilité ont montré la présence d’un courant biotique de 1,75 A m-2 après 24 h de réduction de 50 mM de fumarate / The aim of this PhD work was to design an artificial electroactive biofilm in order to optimize extracellular electron transfers (EET) by artificially reconstituting the biofilm in the presence of exogenous materials. A biocomposite material was proposed from the self-assembly of the bacteria Shewanella oneidensis with carbon nanotubes and cytochrome c (extract from bovine heart). The self-assembly was first studied by diffusion light scattering, scanning electron microscopy and Raman spectroscopy. These analyzes showed the importance of the cytochrome c in the assembly and organization of the biocomposite. Bacterial viability was studied and metabolic activity was characterized with the help of electrochemistry. The current at the anode was 10 and 4 times higher with the artificial biofilm (0.027 A m2) than with film composed with bacteria alone (0.003 A m2) or associated with cytochrome c (0.007 A m2). Artificial biofilm was also tested with Pseudomonas fluorescens instead of S. oneidensis, producing an oxidative current upon the addition of 1.5 mM glucose. That indicates cytochrome c has, in addition to its structuring role, an electron shuttle activity. Its redox potential, +254 mV (vs. NHE), was adapted to the oxidation of formate but was unsuitable for the reduction of fumarate. For this reason, it has been substituted by other cytochromes, c3DvH, c7Da, c553DvH, c3DdN, and c3Dg, possessing lower redox potentials, in the range of 20 mV to -400 mV. These cytochromes also varied at the level of their charge at neutral pH and allowed to validate the importance of the electrostatic forces in the assembly of the biocomposite. The optimal results obtained with c3DvH and c7Da showed the importance of the redox potential of the exogenous elements for the EET. We then replaced the cytochrome c with protamine. This non-electroactive protein allowed the assembly of the biocomposite by promoting direct electrons transfer between the bacteria and the different nanomaterials tested. The optimizations made it possible to reach cathodic currents of more than 12 A m2 in the presence of 50 mM of fumarate. The stability experiments showed the presence of a biotic current of 1.75 A m2 after 24 h of reduction of 50 mM of fumarate

Snakes are one of the world’s most versatile organisms, at ease slithering through rubble or climbing vertical tree trunks. Their adaptations for conquering complex terrain thus serve naturally as inspirations for search and rescue robotics. In a combined experimental and theoretical investigation, we elucidate the propulsion mechanisms of snakes on both hard and granular substrates. The focus of this study is on physics of snake interactions with its environment. Snakes use one of several modes of locomotion, such as slithering on flat surfaces, sidewinding on sand, or accordion-like concertina and worm-like rectilinear motion to traverse crevices. We present a series of experiments and supporting mathematical models demonstrating how snakes optimize their speed and efficiency by adjusting their frictional properties as a function of position and time. Particular attention is paid to a novel paradigm in locomotion, a snake’s active control of its scales, which enables it to modify its frictional interactions with the ground. We use this discovery to build bio-inspired limbless robots that have improved sensitivity to the current state of the art: Scalybot has individually controlled sets of belly scales enabling it to climb slopes of 55 degrees. These findings will result in developing new functional materials and control algorithms that will guide roboticists as they endeavor towards building more effective all-terrain search and rescue robots.

Fire ants link their legs and jaws together to form functional structures called self- assemblages. Examples include floating rafts, towers, bridges, and bivouacs. We investigate these self-assemblages of fire ants. Our studies are motivated in part by the vision of providing guidance for programmable robot swarms. The goal for such systems is to develop a simple programmable element from which complex patterns or behaviors emerge on the collective level. Intelligence is decentralized, as is the case with social insects such as fire ants. In this combined experimental and theoretical study, we investigate the construction of two fire ant self-assemblages that are critical to the colony’s survival: the raft and the tower. Using time-lapse photography, we record the construction processes of rafts and towers in the laboratory. We identify and characterize individual ant behaviors that we consistently observe during assembly, and incorporate these behaviors into mathematical models of the assembly process. Our models accurately predict both the assemblages’ shapes and growth patterns, thus providing evidence that we have identified and analyzed the key mechanisms for these fire ant self-assemblages. We also develop novel techniques using scanning electron microscopy and micro-computed tomography scans to visualize and quantify the internal structure and packing properties of live linked fire ants. We compare our findings to packings of dead ants and similarly shaped granular material packings to understand how active arranging affects ant spacing and orientation. We find that ants use their legs to increase neighbor spacing and hence reduce their packing density by one-third compared to packings of dead ants. Also, we find that live ants do not align themselves in parallel with nearest neighbors as much as dead ants passively do. Our main contribution is the development of parsimonious mathematical models of how the behaviors of individuals result in the collective construction of fire ant assemblages. The models posit only simple observed behaviors based on local information, yet their mathe- matical analysis yields accurate predictions of assemblage shapes and construction rates for a wide range of ant colony sizes.

This work explores the representations and mathematical modeling of biologically-inspired robotic muscles called Cellular Actuator Arrays. These actuator arrays are made of many small interconnected actuation units which work together to provide force, displacement, robustness and other properties beyond the original actuator's capability. The arrays can also exhibit properties generally associated with biological muscle and can thus provide test bed for research into the interrelated nature of the nervous system and muscles, kinematics/dynamics experiments to understand balance and synergies, and building full-strength, safe muscles for prosthesis, rehabilitation, human force amplification, and humanoid robotics. This thesis focuses on the mathematical tools needed bridge the gap between the conceptual idea of the cellular actuator array and the engineering design processes needed to build physical robotic muscles. The work explores the representation and notation needed to express complex actuator array typologies, the mathematical modeling needed to represent the complex dynamics of the arrays, and properties to guide the selection of arrays for engineering purposes. The approach is designed to aid automation and simulation of actuator arrays and provide an intuitive base for future controls and physiology work. The work is validated through numerical results using MatLab's SimMechanics dynamic modeling system and with three physical actuator arrays built using solenoids and shape memory alloy actuators.