PLANNING FOR AUTOMATED OPTICAL MICROMANIPULATION OF BIOLOGICAL CELLS

Optical tweezers (OT) can be viewed as a robot that uses a highly focused laser beam for precise manipulation of biological objects and dielectric beads at micro-scale. Using holographic optical tweezers (HOT) multiple optical traps can be created to allow several operations in parallel. Moreover, due to the non-contact nature of manipulation OT can be potentially integrated with other manipulation techniques (e.g. microfluidics, acoustics, magnetics etc.) to ensure its high throughput. However, biological manipulation using OT suffers from two serious drawbacks: (1) slow manipulation due to manual operation and (2) severe effects on cell viability due to direct exposure of laser. This dissertation explores the problem of autonomous OT based cell manipulation in the light of addressing the two aforementioned limitations. Microfluidic devices are well suited for the study of biological objects because of their high throughput. Integrating microfluidics with OT provides precise position control as well as high throughput. An automated, physics-aware, planning approach is developed for fast transport of cells in OT assisted microfluidic chambers. The heuristic based planner employs a specific cost function for searching over a novel state-action space representation. The effectiveness of the planning algorithm is demonstrated using both simulation and physical experiments in microfluidic-optical tweezers hybrid manipulation setup. An indirect manipulation approach is developed for preventing cells from high intensity laser. Optically trapped inert microspheres are used for manipulating cells indirectly either by gripping or pushing. A novel planning and control approach is devised to automate the indirect manipulation of cells. The planning algorithm takes the motion constraints of the gripper or pushing formation into account to minimize the manipulation time. Two different types of cells (Saccharomyces cerevisiae and Dictyostelium discoideum) are manipulated to demonstrate the effectiveness of the indirect manipulation approach

Chirality in optical trapping and optical binding

Optical trapping is a well-established technique that is increasingly used on biological substances and nanostructures. Chirality, the property of objects that differ from their mirror image, is also of significance in such fields, and a subject of much current interest. This review offers insight into the intertwining of these topics with a focus on the latest theory. Optical trapping of nanoscale objects involves forward Rayleigh scattering of light involving transition dipole moments; usually these dipoles are assumed to be electric although, in chiral studies, magnetic dipoles must also be considered. It is shown that a system combining optical trapping and chirality could be used to separate enantiomers. Attention is also given to optical binding, which involves light induced interactions between trapped particles. Interesting effects also arise when binding is combined with chirality

Direct imaging of a digital-micromirror device for configurable microscopic optical potentials

Programable spatial light modulators (SLMs) have significantly advanced the configurable optical trapping of particles. Typically, these devices are utilized in the Fourier plane of an optical system, but direct imaging of an amplitude pattern can potentially result in increased simplicity and computational speed. Here we demonstrate high-resolution direct imaging of a digital micromirror device (DMD) at high numerical apertures (NA), which we apply to the optical trapping of a Bose-Einstein condensate (BEC). We utilise a (1200 x 1920) pixel DMD and commercially available 0.45 NA microscope objectives, finding that atoms confined in a hybrid optical/magnetic or all-optical potential can be patterned using repulsive blue-detuned (532 nm) light with 630(10) nm full-width at half-maximum (FWHM) resolution, within 5% of the diffraction limit. The result is near arbitrary control of the density the BEC without the need for expensive custom optics. We also introduce the technique of time-averaged DMD potentials, demonstrating the ability to produce multiple grayscale levels with minimal heating of the atomic cloud, by utilising the high switching speed (20 kHz maximum) of the DMD. These techniques will enable the realization and control of diverse optical potentials for superfluid dynamics and atomtronics applications with quantum gases. The performance of this system in a direct imaging configuration has wider application for optical trapping at non-trivial NAs.Comment: 9 page

Visual Computing Tools for Studying Micro-scale Diffusion

In this dissertation, we present novel visual computing tools and techniques to facilitate the exploration, simulation, and visualization of micro-scale diffusion. Our research builds upon the latest advances in visualization, high-performance computing, medical imaging, and human perception. We validate our research using the driving applications of nano-assembly and diffusion kurtosis imaging (DKI). In both of these applications, diffusion plays a central role. In the former it mediates the process of transporting micron-sized particles through moving lasers, and in the latter it conveys brain micro-geometry. Nanocomponent-based devices, such as bio-sensors, electronic components, photonic devices, solar cells, and batteries, are expected to revolutionize health care, energy, communications, and the computing industry. However, in order to build such useful devices, nanoscale components need to be properly assembled together. We have developed a hybrid CPU/GPU-based computing tool to understand complex interactions between lasers, optical beads, and the suspension medium. We demonstrate how a high-performance visual computing tool can be used to accelerate an optical tweezers simulation to compute the force applied by a laser onto micro particles and study shadowing (refraction) behavior. This represents the first steps toward building a real-time nano-assembly planning system. A challenge in building such a system, however, is that optical tweezers systems typically lack stereo depth cues. We have developed a visual tool to provide an enhanced perception of a scene's 3D structure using the kinetic depth effect. The design of our tool has been informed by user studies of stereo perception using the kinetic-depth effect on monocular displays. Diffusion kurtosis imaging is gaining rapid adoption in the medical imaging community due to its ability to measure the non-Gaussian property of water diffusion in biological tissues. Compared with the traditional diffusion tensor imaging (DTI), DKI can provide additional details about the underlying microstructural characteristics of neural tissues. It has shown promising results in studies on changes in gray matter and mild traumatic brain injuries, where DTI is often found to be inadequate. However, the highly detailed spatio-angular fields in DKI datasets present a special challenge for visualization. Traditional techniques that use glyphs are often inadequate for expressing subtle changes in the DKI fields. In this dissertation, we outline a systematic way to manage, analyze, and visualize spatio-angular fields using spherical harmonics lighting functions to facilitate insights into the micro-structural properties of the brain

REGULATION OF SHAPE DYNAMICS AND ACTIN POLYMERIZATION DURING COLLECTIVE CELL MIGRATION

This thesis aims to understand how cells coordinate their motion during collective migration. As previously shown, the motion of individually migrating cells is governed by wave-like cell shape dynamics. The mechanisms that regulate these dynamic behaviors in response to extracellular environment remain largely unclear. I applied shape dynamics analysis to Dictyostelium cells migrating in pairs and in multicellular streams and found that wave-like membrane protrusions are highly coupled between touching cells. I further characterized cell motion by using principle component analysis (PCA) to decompose complex cell shape changes into a serial shape change modes, from which I found that streaming cells exhibit localized anterior protrusion, termed front narrowing, to facilitate cell-cell coupling. I next explored cytoskeleton-based mechanisms of cell-cell coupling by measuring the dynamics of actin polymerization. Actin polymerization waves observed in individual cells were significantly suppressed in multicellular streams. Streaming cells exclusively produced F-actin at cell-cell contact regions, especially at cell fronts. I demonstrated that such restricted actin polymerization is associated with cell-cell coupling, as reducing actin polymerization with Latrunculin A leads to the assembly of F-actin at the side of streams, the decrease of front narrowing, and the decoupling of protrusion waves. My studies also suggest that collective migration is guided by cell-surface interactions. I examined the aggregation of Dictyostelim cells under distinct conditions and found that both chemical compositions of surfaces and surface-adhesion defects in cells result in altered collective migration patterns. I also investigated the shape dynamics of cells suspended on PEG-coated surfaces, which showed that coupling of protrusion waves disappears on touching suspended cells. These observations indicate that collective migration requires a balance between cell-cell and cell-surface adhesions. I hypothesized such a balance is reached via the regulation of cytoskeleton. Indeed, I found cells actively regulate cytoskeleton to retain optimal cell-surface adhesions on varying surfaces, and cells lacking the link between actin and surfaces (talin A) could not retain the optimal adhesions. On the other hand, suspended cells exhibited enhanced actin filament assembly on the periphery of cell groups instead of in cell-cell contact regions, which facilitates their aggregation in a clumping fashion

Design of three degrees-of-freedom motion stage for micro manipulation

A miniaturized translational motion stage has potentials to provide not only performances equivalent to conventional motion stages, but also additional features from its small form factor and low cost. These properties can be utilized in applications requiring a small space such as a vacuum chamber in a scanning electron microscopy (SEM), where hidden surface can decrease by manipulating objects to measure. However, existing miniaturized motion stages still have several cm3 level volumes and provide simple operations. In this dissertation, Micro-electro-mechanical systems (MEMS)-based motion stages are utilized to replace a miniaturized motion stage for micro-scale manipulation and possible applications. However, most MEMS fabrication methods remain in monolithic fabrication methods and a lot of MEMS based multiple degrees-of-freedom (DOFs) motion stage also remain for in-plane motions. In this dissertation, a nested structure based on a serial kinematic mechanism is implemented in order to overcome these constraints and implement out-of-plane motion, where one independent stage is embedded into the other individual stage with additional features for structurally and electrically isolations among the engaged stages. MEMS actuators and displacement amplifiers are also investigated for reasonable performance. 3-axis motions are divided into two in-plane motions and one out-of-plane motion; an in-plane 1 DOF motion stage (called an X-stage) and one out-of-plane 1 DOF motion stage (called a Z-stage) are designed and characterized experimentally. Based on the two stages, the XY-stage is designed by merging one X-stage into the motion platform of the other X-stage with a different orientation (called an XY-stage). With this nested approach, the fabricated XY-stage demonstrated in-plane motions larger than 50 µm with ignorable coupled motion errors. Based on this nested approach, the 3-axis motion stage is also implemented by utilizing the nested structure twice; integrating the Z-stage with the motion platform of the XY-stage (called an XYZ-stage). The XYZ-stage demonstrated out-of-plane motions about 23 µm as well as the in-plane motions. Two presented motion stages have been utilized in the manipulation of micro-scale object by the cooperation of the two XY-stages inside a SEM chamber. The large motion platform of the X-stage is also utilized in a parallel plate type rheometer to measure the material properties of viscoelastic materials

3 dimensional proton beam writing for micro electromechanical systems applications.

Proton beam writing is a direct write lithographic technique that uses finely focused MeV proton beams to create structures in a target material. The depth the protons travel in a material is dependent on its energy, this unique property of proton beams allow multi level structures to be created in materials. PBW has been demonstrated successfully on semiconductor materials, glass and polymers. This thesis is a study of the application of PBW in creating Micro Electro-Mechanical Systems (MEMS) in a polymer SU 8 and SU 8 polymer nano composite with silver, and shows experimental steps, theory and computer simulations involved in creating an electrostatic actuated micro-gripping device. Proton beam writing in silver SU 8 composite results in the creation of electrically conducting microstructures. The unique predictability of the range of protons in materials is leveraged in the creating of free standing conducting cantilevers structures which are used as the building blocks for a micro gripping device. The electrostatic actuation has been modelled using a finite element modelling software Sugar 3.1, and the results are comparable with actual actuations in a realized micro-gripping device

Magnetic Levitation of Polymeric Photo-thermal Microgrippers

Precise manipulation of micro objects became great interest in engineering and science with the advancements in microengineering and microfabrication. In this thesis, a magnetically levitated microgripper is presented for microhandling tasks. The use of magnetic levitation for positioning reveals the problems associated with modeling of complex surface forces and the use of jointed parts or wires. The power required for the levitation of the microgripper is generated by an external drive unit that makes further minimization of the gripper possible. The gripper is made of a biocompatible material and can be activated remotely. These key features make the microgripper a great candidate for manipulation of micro components and biomanipulation. In order to achieve magnetic levitation of microrobots, the magnetic field generated by the magnetic levitation setup is simulated. The magnetic flux density in the air gap region is improved by the integration of permanent magnets and an additional electromagnet to the magnetic loop assembly. The levitation performance is evaluated with millimeter size permanent magnets. An eddy current damping method is implemented and the levitation accuracy is doubled by reducing the positioning error to 20.3 µm. For a MEMS-compatible microrobot design, the electrodeposition of Co-Ni-Mn-P magnetic thin films is demonstrated. Magnetic films are deposited on silicon substrate to form the magnetic portion of the microrobot. The electrodeposited films are extensively characterized. The relationship between the deposition parameters and structural properties is discussed leading to an understanding of the effect of deposition parameters on the magnetic properties. It is shown that both in-plane and out-of-plane magnetized films can be obtained using electrodeposition with slightly differentiated deposition parameters. The levitation of the electrodeposited magnetic samples shows a great promise toward the fabrication of levitating MEMS devices. The end-effector tool of the levitating microrobot is selected as a microgripper that can achieve various manipulation operations such as pulling, pushing, tapping, grasping and repositioning. The microgripper is designed based on a bent-beam actuation technique. The motion of the gripper fingers is achieved by thermal expansion through laser heat absorption. This technique provided non-contact actuation for the levitating microgripper. The analytical model of the displacement of the bent-beam actuator is developed. Different designs of microgripper are fabricated and thoroughly characterized experimentally and numerically. The two microgripper designs that lead to the maximum gripper deflection are adapted for the levitating microrobot. The experimental results show that the levitating microrobot can be positioned in a volume of 3 x 3 x 2 cm^3. The positioning error is measured as 34.3 µm and 13.2 µm when electrodeposited magnets and commercial permanent magnets are used, respectively. The gripper fingers are successfully operated on-the-fly by aligning a visible wavelength laser beam on the gripper. Micromanipulation of 100 µm diameter electrical wire, 125 µm diameter optical fiber and 1 mm diameter cable strip is demonstrated. The microgripper is also positioned in a closed chamber without sacrificing the positioning accuracy