Active Emulsions: Physicochemical Hydrodynamics and Collective Behavior

Active matter is a collection of constituent elements that constantly consume energy, convert it to mechanical work, and interact with their counterparts. These materials operate out of equilibrium and exhibit fascinating collective dynamics such as spontaneous pattern formation. Self-organization of bio-polymers within a cell, collective migration of bacteria in search of nutrition, and the bird flocks are paragons of active living matter and the primary source of our knowledge on it. To understand the overarching physical principles of active matter, it is desirable to build artificial systems that are capable of imitating living active matter while ruling out the biological complexities. The goal of this thesis is to study active micro-droplets as a paradigm for biomimetic artificial active particles, using fundamental principles of fluid dynamics and statistical physics. The Marangoni-driven motility in these droplets is reminiscent of the locomotion of some protozoal organisms, known as squirmers. The main scientific objectives of this research are to (i) investigate the potential biomimetic features of active droplets including compartmentalization, adaptability (e.g. multi-gait motility), and information processing (signaling and sensing) and (ii) study the implications of those features in the collective dynamics of active emulsions governed by hydrodynamic and autochemotactic interactions. These objectives are addressed experimentally using microfluidics and microscopy, integrated with quantitative image analysis. The quantitative experimental results are then compared with the predictions from theory or simulations. The findings of this thesis are presented in five chapters. First, we address the challenge of compartmentalizing active droplets. We use microfluidics to generate liquid shells (double emulsions). We propose and successfully prove the use of a nematic liquid crystal oil to stabilize the liquid shells, which are otherwise susceptible to break up during motility. We investigate the propulsion dynamics and use that insight to put forward routes to control shell motion via topology, chemical signaling, and topography. In the second results chapter, we establish the bimodal dynamics of chaotic motility in active droplets; a regime that emerges as a response to the increase of viscosity in the swimming medium. To establish the physical mechanism of this dynamical transition, we developed a novel technique to simultaneously visualize the hydrodynamic and chemical fields around the droplet. The results are rationalized by quantitative comparison to established advection-diffusion models. We further observe that the droplets undergo self-avoiding random walks as a result of interaction with the self-generated products of their activity, secreted in the environment. The third results chapter presents a review of the dynamics of chemotactic droplets in complex environments, highlighting the effects of self-generated chemical interactions on the droplet dynamics. In the fourth results chapter, we investigate how active droplets sense and react to the chemical gradients generated by their counterparts--- a behavior known as autochemotaxis. Then, we study the collective dynamics governed by these autochemotactic interactions, in two and three dimensions. For the first time, we report the observation of ‘history caging’, where swimmers are temporarily trapped in an evolving network of repulsive chemical trails. The caging results in a plateau in the mean squared displacement profiles as observed for dense colloidal systems near the glass transition. In the last results chapter, we investigate the collective dynamics in active emulsions, governed by hydrodynamic interactions. We report the emergence of spontaneously rotating clusters. We show that the rotational dynamics originates from a novel symmetry breaking mechanism for single isotropic droplets. By extending our understanding to the collective scale, we show how the stability and dynamics of the clusters can be controlled by droplet activity and cluster size. The experimental advancements and the findings presented in this thesis lay the groundwork for future investigations of emergent dynamics in active emulsions as a model system for active matter. In the outlook section, we present some of the new questions that have developed in the course of this research work and discuss a perspective on the future directions of the research on active droplets.2022-01-1

Aerospace medicine and biology: A cumulative index to a continuing bibliography (supplement 384)

This publication is a cumulative index to the abstracts contained in Supplements 372 through 383 of Aerospace Medicine and Biology: A Continuing Bibliography. It includes seven indexes: subject, personal author, corporate source, foreign technology, contract number, report number, and accession number

The Functional, Ecological, and Evolutionary Morphology of Sea Lampreys (Petromyzon marinus)

Lampreys (Petromyzontiformes) are jawless vertebrates with an evolutionary history lasting at least 360 million years and are often used in comparisons with jawed vertebrates because some of their morphological aspects, such as the segmented trunk musculature with curved myosepta and a non-mineralized skeleton fibrous skeleton, are thought to resemble the condition of early vertebrates before the evolution of jaws. Although earlier authors studied the morphology of the skeleto-muscular system of the trunk of lampreys, their studies are not detailed and complete enough to allow a functional and biomechanical analysis that is needed as a basis for modeling the mechanics of lamprey locomotion and for understanding the causal roles played by the anatomical structures within the trunk. Questions remain, such as what is the architecture of the trunk fibroskeleton, and how does it function with the musculature to bend the trunk? This dissertation studied the functional, ecological and evolutionary morphology of the trunk of Sea Lampreys (Petromyzon marinus) as well as its relevance in understanding the environmental history of landlocked lamprey populations. Functional morphology revealed that the fibroskeleton of the trunk is a self-supporting concatenated system of fibers, which creates a scaffold for the musculature and transmits forces to bend the trunk during swimming. Ecological morphology demonstrated the adaptive advantage of the fibroskeleton’s architecture, which enables the movements that are performed during migration and spawning and gives lampreys the capacity to colonize upstream realms. These results help explain the evolutionary morphology of lampreys, which likely originated in freshwater as algal feeders and evolved into parasites after going through an intermediary scavenging stage. When these insights are applied to the evolution of landlocked Sea Lampreys, it becomes evident that their entry into freshwater lakes occurred as soon as they were able to reach them and that populations likely became established in Lake Ontario, Lake Champlain, and the Finger Lakes thousands of years ago. This insight undermines the current status of landlocked Sea Lampreys as invasive species in these lakes and the case for their eradication. Hence, this dissertation provides a comprehensive and integrative analysis of lamprey biology from their anatomy to environmental policy

Roadmap on emerging concepts in the physical biology of bacterial biofilms: from surface sensing to community formation

Bacterial biofilms are communities of bacteria that exist as aggregates that can adhere to surfaces or be free-standing. This complex, social mode of cellular organization is fundamental to the physiology of microbes and often exhibits surprising behavior. Bacterial biofilms are more than the sum of their parts: single-cell behavior has a complex relation to collective community behavior, in a manner perhaps cognate to the complex relation between atomic physics and condensed matter physics. Biofilm microbiology is a relatively young field by biology standards, but it has already attracted intense attention from physicists. Sometimes, this attention takes the form of seeing biofilms as inspiration for new physics. In this roadmap, we highlight the work of those who have taken the opposite strategy: we highlight the work of physicists and physical scientists who use physics to engage fundamental concepts in bacterial biofilm microbiology, including adhesion, sensing, motility, signaling, memory, energy flow, community formation and cooperativity. These contributions are juxtaposed with microbiologists who have made recent important discoveries on bacterial biofilms using state-of-the-art physical methods. The contributions to this roadmap exemplify how well physics and biology can be combined to achieve a new synthesis, rather than just a division of labor

MicroBioRobots for Single Cell Manipulation

One of the great challenges in nano and micro scale science and engineering is the independent manipulation of biological cells and small man-made objects with active sensing. For such biomedical applications as single cell manipulation, telemetry, and localized targeted delivery of chemicals, it is important to fabricate microstructures that can be powered and controlled without a tether in fluidic environments. These microstructures can be used to develop microrobots that have the potential to make existing therapeutic and diagnostic procedures less invasive. Actuation can be realized using various different organic and inorganic methods. Previous studies explored different forms of actuation and control with microorganisms. Bacteria, in particular, offer several advantages as controllable micro actuators: they draw chemical energy directly from their environment, they are genetically modifiable, and they are scalable and configurable in the sense that any number of bacteria can be selectively patterned. Additionally, the study of bacteria inspires inorganic schemes of actuation and control. For these reasons, we chose to employ bacteria while controlling their motility using optical and electrical stimuli. In the first part of the thesis, we demonstrate a bio-integrated approach by introducing MicroBioRobots (MBRs). MBRs are negative photosensitive epoxy (SU8) microfabricated structures with typical feature sizes ranging from 1-100 μm coated with a monolayer of the swarming Serratia marcescens. The adherent bacterial cells naturally coordinate to propel the microstructures in fluidic environments, which we call Self-Actuation. First, we demonstrate the control of MBRs using self-actuation, DC electric fields and ultra-violet radiation and develop an experimentally-validated mathematical model for the MBRs. This model allows us to to steer the MBR to any position and orientation in a planar micro channel using visual feedback and an inverted microscope. Examples of sub-micron scale transport and assembly as well as computer-based closed-loop control of MBRs are presented. We demonstrate experimentally that vision-based feedback control allows a four-electrode experimental device to steer MBRs along arbitrary paths with micrometer precision. At each time instant, the system identifies the current location of the robot, a control algorithm determines the power supply voltages that will move the charged robot from its current location toward its next desired position, and the necessary electric field is then created. Second, we develop biosensors for the MBRs. Microscopic devices with sensing capabilities could significantly improve single cell analysis, especially in high-resolution detection of patterns of chemicals released from cells in vitro. Two different types of sensing mechanisms are employed. The first method is based on harnessing bacterial power, and in the second method we use genetically engineered bacteria. The small size of the devices gives them access to individual cells, and their large numbers permit simultaneous monitoring of many cells. In the second part, we describe the construction and operation of truly micron-sized, biocompatible ferromagnetic micro transporters driven by external magnetic fields capable of exerting forces at the pico Newton scale. We develop micro transporters using a simple, single step micro fabrication technique that allows us to produce large numbers in the same step. We also fabricate microgels to deliver drugs. We demonstrate that the micro transporters can be navigated to separate single cells with micron-size precision and localize microgels without disturbing the local environment