UC Merced

Active matter is a growing interdisciplinary field of science that studies the collective motion of different species of particles and living organisms. This field of research is often bio-inspired as collective motion of fish, birds and insects are ubiquitous throughout nature. Such behavior is not just limited to the macroscopic world but is also found in the micro- and nanoscopic realms as well. Under the microscope, it can be observed that bacterial and protein assemblies are subject to the same group motion serving as the inner machines vital to the functions of life and natural forces of the world. In this thesis, I focus attention to the interesting method of an actively driven bundled microtubule network in a lyotropic liquid crystal phase.

The active nematic bundled microtubule system has gained substantial international exposure in the field of soft matter. Several groups across the world have not only reproduced this novel system, but also developed new methods to measure and probe its properties and kinematics. These actively driven protein networks have become a useful framework to study energy driven particles in complex structured fluids. An interesting method to probe the behavior of this system is the the implementation of boundaries serving as a useful strategy to control defect flow, morphology and dynamics. In this thesis, I study the behavior of an active nematic microtubule system confined to several different geometries. I was initially motivated from our preliminary work, when I observed that submerged 3D structures can influence defect dynamics by organizing their flows and pinning defects at specific locations. This prompted me to investigate active nematic flows in microfluidic devices in different confining conditions, which will be covered in this work.

For my first project, I engineered micropatterned surfaces using photolithography to control local orientation directors to take advantage of the interplay between surface curvatures and topological defects. Epoxy-based lithography represents a simple approach to develop lab-on-a-chip methods to probe active materials. In this dissertation, I will discuss optimized fabrication methods using negative tone epoxy-based photoresists to create microfluidic devices for active matter systems. I demonstrate that arrays of circular structures and submerged topographies can generate a variety of liquid crystal defect configurations, not typically observed on unconfined planar surfaces. I then build on these observations by considering the creation of new interfaces not limited to hard boundaries.

For my second project, I demonstrated that soft or virtual boundaries can be generated by submerged structures. With the assistance of micro patterned surfaces, different submersed geometrical patterns were created for my analysis: trenches, pillars, stairways, and undulated sinusoidal structures. I investigated the spontaneous flows of this novel system as pillar dimensions influenced active material flow due to abrupt changes in oil depth. This created virtual boundaries because of the change in the effective viscosity in proximity to the boundary. In this study, I collaborated with several groups to develop simulations and other micro-milled patterns.

Finally, my third project was to confine active material but by curving the oil-active layer interface, creating a two-tiered elevated system. The geometry for this work was submersed pillars impinging on the interface, creating a two-tier continuous active layer in which material is partially confined. Active flows above the pillars were influenced by the circular geometry and the thin oil layer resulting in physical changes of the material i.e., depletion. Building from the second project, the thin oil layer beneath the active material was thinner in the region above the pillars relative to outside the encircled area, consequently producing an area of higher effective friction. This was confirm using 3D reconstructions of the curvature of the active layer and auto-fluorescent pillar using confocal microscopy. This resulted in changes of velocity fields, defect densities and active length scales.

Overall, I have investigated new methods for probing a living liquid crystal system capable of generating internal flows using microfluidic devices. This new way to confine active material opens many opportunities to control and organize topological defects and materials at nanoscales using simple micro-fabricated structures. I hope that we can move this method and platform to other active or even passive liquid crystal systems for biomedical and electronic devices. Such methods can be invaluable to pursue the integration of liquid crystal phase to nanoelectronics. The work presented in this dissertation has demonstrated the adaptability of this active protein assembly and open new possibilities to organize structured fluids.