Interfacing optics with biology--Optical sensors, actuators and protein lithography

In the present thesis, the applications of optics in biotechnology were extensively investigated, including optical biosensing, optical bioactuation and optical lithography for defining microenvironments for cell development.;The fabrication and characterization of nano-plasmonic resonators was explored for use as optical biosensors, in particular for applications in mapping protein secretions from individual live cells. The high throughput fabrication of nano-plasmonic resonator array biosensors by Nanolmprint Lithography (NIL) was achieved and the fluorescence enhancement was characterized. High spatial resolution mapping of lnterleukin-2 (TL-2) secreted from individual live Jurkat T cells was successfully demonstrated using these resonators. These results demonstrate that nano-plasmonic-resonator arrays enhance the fluorescence signal, which drastically improves the signal to noise ratio and avoids the need of large area integration for biological sensing. Thus, we are able to achieve high resolution mapping of secreted signaling molecules. This technique can be extended to the simultaneous local mapping the combinations of several types of signaling molecules secreted from multiple types of cells in sub-cellular resolution, and enable applications in decoding cell communications.;Design of the nano-plasmonic-resonator array for label free biosensing was further explored. In order to optimize the signal from surface enhanced Raman scattering (SERS), we designed and fabricated a high-aspect ratio nano-pin arrays by a single-step electron-beam lithography process. These nano-pin arrays were designed to maximize the plasmonic field enhancement of these nano-scale structures by increasing the enhancement volume. Each nano-pin is comprised of a metal capped dielectric pillar upon a ring shaped metallic disc. Highly tunable optical properties and the electromagnetic interplay between the metallic components were studied by experiment and simulation. The two metallic components have asymmetric roles in their coupling to each other due to their drastic size and plasmonic energy difference. These structures can be used for ultra-sensitive SERS detection, as well as chemical and biological sensor arrays.;In order to address one of the key technical barriers to furthering our understanding of complex neural networks, which is the lack of tools for the simultaneous spatiotemporal control and detection of activity in a large number of neurons, we created an all-optical system for achieving this kind of parallel and selective control and detection. We do this by delivering spatiotemporally complex optical stimuli through a digital micromirror light modulator to cells expressing a light-activated ionotropic glutamate receptor (LiGluR), which have been labeled with a calcium dye to provide a fluorescent report of activity. Reliable and accurate spatiotemporal stimulation was obtained using HEK293 cells and cultured rat hippocampal neurons. This technique could be adaptable to in vivo applications and can serve as an optical interface for communicating with complex neural circuits.;Optical lithography for defining cell development microenvironments was obtained by combining projection dynamic mask lithography and protein engineering with non-canonical photosensitive amino acids. We demonstrated a simple, scalable, strategy to fabricate any user-defined 2D or 3D stable gradient pattern with complex geometries from an artificial extracellular matrix (aECM) protein. Our fabrication method enables the construction of protein patterns that closely mimic native microenvironments, such as gradient protein distributions with desirable mechanical properties. Furthermore, the elastic modulus and chemical nature of these gradient profiles are biocompatible and enable useful applications in cell biological research.