Polymer capsules as building blocks for soft, connected mesostructures

We show that polymer capsules can serve as soft building blocks for creating a range of mesoscale (0.1 to 10 mm) structures. The central innovation is a new approach for connecting spherical capsules by exploiting electrostatic complexation. Using this approach, connected structures with complex shapes can be easily assembled, and more importantly, a single connected structure can be made to have a diverse array of functions. The modular approach to shape and function is very much like using Lego bricks of different colors. The connected structures can be made responsive (capable of being actuated) by magnetic fields by including magnetic capsules within them. One motivation for creating these structures is to mimic the mechanics and motility of small creatures such as the earthworm or ant - this could eventually enable the design of autonomous biomimetic robots. In addition, soft connected structures could be employed to transport cargo such as drugs or proteins in blood vessels, or to construct valves, rotors, or mixers in microfluidic or lab-on-a-chip devices

Chiral active fluids: Odd viscosity, active turbulence, and directed flows of hydrodynamic microrotors

While the number of publications on rotating active matter has rapidly increased in recent years, studies on purely hydrodynamically interacting rotors on the microscale are still rare, especially from the perspective of particle based hydrodynamic simulations. The work presented here targets to fill this gap. By means of high-performance computer simulations, performed in a highly parallelised fashion on graphics processing units, the dynamics of ensembles of up to 70,000 rotating colloids immersed in an explicit mesoscopic solvent consisting out of up to 30 million fluid particles, are investigated. Some of the results presented in this thesis have been worked out in collaboration with experimentalists, such that the theoretical considerations developed in this thesis are supported by experiments, and vice versa. The studied system, modelled in order to resemble the essential physics of the experimentally realisable system, consists out of rotating magnetic colloidal particles, i.e., (micro-)rotors, rotating in sync to an externally applied magnetic field, where the rotors solely interact via hydrodynamic and steric interactions. Overall, the agreement between simulations and experiments is very good, proving that hydrodynamic interactions play a key role in this and related systems. While already an isolated rotating colloid is driven out of equilibrium, only collections of two or more rotors have experimentally shown to be able to convert the rotational energy input into translational dynamics in an orbital rotating fashion. The rotating colloids inject circular flows into the fluid, such that detailed balance is broken, and it is not a priori known whether equilibrium properties of colloids can be extended to isolated rotating colloids. A joint theoretical and experimental analysis of isolated, pairs, and small groups of hydrodynamically interacting rotors is given in chapter 2. While the translational dynamics of isolated rotors effectively resemble the dynamics of non-rotating colloids, the orbital rotation of pairs of rotors can be described with leading order hydrodynamics and a two-dimensional analogy of Faxén’s law is derived. In chapter 3, a homogeneously distributed ensemble of rotors (bulk) as a realisation of a chiral active fluid is studied and it is explicitly shown computationally and experimentally that it carries odd viscosity. The mutual orbital translation of rotors and an increase of the effective solvent viscosity with rotor density lead to a non-monotonous behaviour of the average translational velocity. Meanwhile, the rotor suspension bears a finite osmotic compressibility resulting from the long-ranged nature of hydrody- namic interactions such that rotational and odd stresses are transmitted through the solvent also at small and intermediate rotor densities. Consequently, density inhomogeneities predicted for chiral active fluids with odd viscosity can be found and allow for an explicit measurement of odd viscosity in simulations and experiments. At intermediate densities, the collective dynamics shows the emergence of multi-scale vortices and chaotic motion which is identified as active turbulence with a self-similar power-law decay in the energy spectrum, showing that the injected energy on the rotor scale is transported to larger scales, similar to the inverse energy cascade of clas- sical two-dimensional turbulence. While either odd viscosity or active turbulence have been reported in chiral active matter previously, the system studied here shows that the emergence of both simultaneously is possible resulting from the osmotic compressibility and hydrodynamic mediation of odd and active stresses. The collective dynamics of colloids rotating out of phase, i.e., where a constant torque instead of a constant angular velocity is applied, is shown to be qualitatively very similar. However, at smaller densities, local density inhomogeneities imply position dependent angular velocities of the rotors resulting from inter-rotor friction. While the friction of a quasi-2D layer of active colloids with the substrate is often not easily modifiable in experiments, the incorporation of substrate friction into the simulation models typically implies a considerable increase in computational effort. In chapter 4, a very efficient way of incorporating the friction with a substrate into a two-dimensional multiparticle collision dynamics solvent is introduced, allowing for an explicit investigation of the influences of substrate on active dynamics. For the rotor fluid, it is explicitly shown that the influence of the substrate friction results in a cutoff of the hydrodynamic interaction length, such that the maximum size of the formed vortices is controlled by the substrate friction, also resulting in a cutoff in the energy spectrum, because energy is taken out of the system at the respective length. These findings are in agreement with the experiments. Since active particles in confinement are known to organise in states of collective dynamics, ensembles of rotationally actuated colloids are studied in circular confinement and in the presence of periodic obstacle lattices in chapters 5 and 6, respectively. The results show that the chaotic active turbulent transport of rotors in suspension can be enhanced and guided resulting from edge flows generated at the boundaries, as has recently been reported for a related chiral active system. The consequent collective rotor dynamics can be regarded as a superposition of active turbulent and imposed flows, leading to on average stationary flows. In contrast to the bulk dynamics, the imposed flows inject additional energy into the system on the long length scales, and the same scaling behaviour of the energy spectrum as in bulk is only obtained if the energy injection scales, due to the mutual generation of rotor translational dynamics throughout the system and the edge flows, are well separated. The combination of edge flow and entropic layering at the boundaries leads to oscillating hydrodynamic stresses and consequently to an oscillating vorticity profile. In the presence of odd viscosity, this consequently leads to non-trivial steady-state density modulations at the boundary, resulting from a balance of osmotic pressure and odd stresses. Relevant for the efficient dispersion and mixing of inert particles on the mesoscale by means of active turbulent mixing powered by rotors, a study of the dynamics of a binary mixture consisting out of rotors and passive particles is presented in chapter 7. Because the rotors are not self-propelled, but the translational dynamics is induced by the surrounding rotors, the passive particles, which do not inject further energy into the system, are transported according to the same mechanism as the rotors. The collective dynamics thus resembles the pure rotor bulk dynamics at the respective density of only rotors. However, since no odd stresses act between the passive particles, only mutual rotor interactions lead to odd stresses leading to the accumulation of rotors in the regions of positive vorticity. This density increase is associated with a pressure increase, which balances the odd stresses acting on the rotors. However, the passive particles are only subject to the accumulation induced pressure increase such that these particles are transported into the areas of low rotor concentration, i.e., the regions of negative vorticity. Under conditions of sustained vortex flow, this results in segregation of both particle types. Since local symmetry breaking can convert injected rotational into translational energy, microswimmers can be constructed out of rotor materials when a suitable breaking of symmetry is kept in the vicinity of a rotor. One hypothetical realisation, i.e., a coupled rotor pair consisting out of two rotors of opposite angular velocity and of fixed distance, termed a birotor, are studied in chapter 8. The birotor pumps the fluid into one direction and consequently translates into the opposite direction, and creates a flow field reminiscent of a source doublet, or sliplet flow field. Fixed in space the birotor might be an interesting realisation of a microfluidic pump. The trans- lational dynamics of a birotor can be mapped onto the active Brownian particle model for single swimmers. However, due to the hydrodynamic interactions among the rotors, the birotor ensemble dynamics do not show the emergence of stable motility induced clustering. The reason for this is the flow created by birotor in small aggregates which effectively pushes further arriving birotors away from small aggregates, which eventually are all dispersed by thermal fluctuations

Nano scale devices: fabrication, actuation, and related fluidic dynamics

Using external actuating magnetic fields to manipulate magnetic parts is an efficient method to manipulate mesoscopic actable devices. Extensive researches have explored the potentials of self-assembly techniques based on capillary force, static charge force, drying, surface tension, and even dynamic fields as a low cost method for ordered 2D or 3D superlattice structures for new materials and devices. But the ability of tunable patterning nanoparticles for designed actable devices is still a requirement yet to be met. Utilizing anodized aluminum oxide (AAO) membranes as templates, soft-magnetic nanowires around 200 nm in diameter, 10 microns long have been fabricated. In this thesis, I describe a method to assemble these magnetic nanowires into a two dimension Wigner structure, of which the wire-wire distance is conveniently adjustable during the fabrication procedure. Using geometric tailored magnetic fields, we can plant these self-assembled magnetic nanowires with desired patterns into a thin soft polymer support layer. The final devices may be readily actuated by an external actuating magnetic field (a self-designed magnetic system, 3-dimensional force microscope (3DFM)) with precise patterns and frequencies in a micro-fluidic system. This method offers a general method to fabricate mesoscopic devices from a wide range of materials with magnetic dipoles to desired structures. And the actable devices themselves can find direct usage in low Re number flow mixing and bio-physical fluidic dynamic researches. The beating of cilia and flagella, slender cylinders 250 nanometers in diameter with lengths from 7 to 50 microns, is responsible for many important biological functions such as organism feeding, propulsion, for bacterial clearance in the lungs and for the right-left asymmetry in vertebrates. The hydrodynamics produced by these beating structures, including mixing, shear and extensional flows, is not understood. We developed an experimental model system for cilia beating through the use of magnetic nanowires. We apply our custom magnetic system, 3DFM, to drive these magnetic nanowires rotating with desired patterns and frequencies in a liquid chamber. High speed movies of passive tracers in the oscillating 3-D flow fields reveal the spatio-temporal structure of the induced fluid motion. Complementing these experimental studies, we have developed a family of exact solutions of the Stoke's equations for a spheroid sweeping a double cone in free space, and an asymptotic solution for a spinning slender rod sweeping an upright cone above a flat, infinite no-slip plane. We are using these solutions to develop a mathematical package to quantitatively model, and predict the tracer motion induced by the spinning nano-rods with and without Brownian noise. To understand the effect of these epicyclical flows on molecular conformations, we have studied the conformation of fluorescently labeled, single DNA molecules (_-DNA) in the flow produced by a precessing nanowire. The flow patterns in a viscoelastic medium about a precessing nanowire are also presented to reveal the epicyclical flows in a more biorelated environment

Efficient tools for the design and simulation of microelectromechanical and microfluidic systems

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2007.Includes bibliographical references (p. 131-136).In air-packaged surface micromachined devices and microfluidic devices the surface to volume ratio is such that drag forces play a very important role in device behavior and performance. Especially for surface micromachined devices, the amount of drag is greatly influenced by the presence of the nearby substrate. In this thesis a precorrected FFT accelerated boundary element method specialized for calculating the drag force on structures above a substrate is presented. The method uses the Green's function for Stokes flow bounded by an infinite plane to implicitly represent the device substrate, requiring a number of modifications to the precorrected FFT algorithm. To calculate the velocity due to force distribution on a panel near a substrate an analytical panel integration algorithm was also developed. Computational results demonstrate that the use of the implicit representation of the substrate reduces computation time and memory while increasing the solution accuracy. The results also demonstrate that surprisingly, and unfortunately, even though representing the substrate implicitly has many benefits it does not completely decouple discretization fineness from distance to the substrate. To simulate the time dependent behavior of micromechanical and microfluidic systems, a stable velocity implicit time stepping scheme coupling the precorrected FFT solver with rigid body dynamics was introduced and demonstrated. The ODE library was integrated with the solver to enable the simulation of systems with collisions, contacts and friction. Several techniques for speeding up the calculation of each time step were presented and tested. The time integration algorithm was successfully used to simulate the behavior of several real-world microfluidic devices.by Carlos Pinto Coelho.Ph.D

Microbioreactors for bioprocess development

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2006.Includes bibliographical references (leaves 109-113).This thesis presents the design, fabrication, and characterization of a microbioreactor integrated with automated sensors and actuators as a step towards high-throughput bioprocess development. In particular, this thesis demonstrates the feasibility of culturing microbial cells in microliter-volume reactors in batch, continuous, fed-batch operations. The microbioreactor is fabricated out of poly(methylmethacrylate) and poly(dimethylsiloxane). Active mixing is made possible by a miniature magnetic stir bar. Online optical measurements for optical density, pH, and dissolved oxygen are integrated. Oxygenation in the microbioreactor is characterized and reproducible batch fermentation of Escherichia coli and Saccharomyces cerevisiae are demonstrated and benchmarked with benchscale bioreactors. Global gene expression analysis of S. cerevisiae exhibits physiological and molecular characteristics which parallel those of large-scales. A microchemostat, continuous culture of microbial cells, is realized in the microbioreactor. E. coli cells are fed by pressure-driven single phase flow of fresh medium through a microchannel. Chemotaxis, the back growth of bacterial cells into the medium feed channel, is prevented by local heating.(cont.) Using poly(ethylene glycol) -grafted poly(acrylic acid) copolymer films, PMMA and PDMS surfaces are modified to generate bio-inert surfaces resistant to nonspecific protein adsorption and cell adhesion. These advances enable cell growth kinetics and stoichoimetry to be obtained in the microchemostat consistent with reported phenomena from conventional stirred-tank bioreactors, as indicated by the time profiles of OD600nm, pH, and DO measurements at steady states. Water evaporation from the microbioreactor allows feeding of base and glucose solutions into the small reactor to realize fed-batch operations. Commercial microvalves are integrated to obtain closed-loop pH control. pH value in the microbioreactor is successfully maintained within a physiological scale during the time course of E. coli cell cultivation in rich media. One key issue for high-throughput bioprocessing is the parallel operation of multiple microbial fermentations while keeping each single microbioreactor disposable. Plug-in-and-flow microfluidic connectors and fabricated polymer micro-optical lenses/connectors are integrated in the microbioreactor "cassettes" for fast set-up and easy operation.(cont.) A protocol multiplexed system for the parallel operation of four microbioreactors is demonstrated. The demonstrated functionality of the microbioreactor with integrated measurements and flexible operations could potentially have a large impact in bioprocess developments.by Zhiyu Zhang.Ph.D