Development of experimental and instrumental systems to study biological systems

Chapters 1-4 of this thesis describes the development of an experimental system to measure diffusion-limited reaction kinetics in a biological environment. About 100 years ago, the relationship between reaction rate and diffusion in homogenous solution, ie water or buffer, was described as a linear relationship by Smoluchowski. Applying this theory naively would suggest that since the diffusion coefficients drop by factors of 4-100 then the rates of reaction would drop by the same amount. However, recent theory and simulations suggest that this does not hold. Even though biological diffusion coefficients drop to 0.1-20% of that in buffer, these recent studies show that the reaction kinetics are much more weakly affected by the biological environment. Due to the lack of experimental evidence for biological diffusion, there is a great need for information in this area. Here, I describe a protein system, exogenous to E. coli¸ that will form a dimer in the presence of a small molecule. ^ I also describe the development of a new type of multivariate hyperspectral Raman instrument (MHI); the instrument is developed for use to study biological tissues and for high speed cell sorting applications. The new instrument design has a large speed advantage over traditional Raman instrumentation for rapid chemical imaging. While the MHI can reproduce the functionality of a traditional Raman spectrometer, its true speed advantage is realized after pre-training on known sample components. The MHI makes use of a spatial light modulator as a programmable optical filter that can be programmed with filters based on multivariate signal processing algorithms, such as PLS, in order to rapidly detect chemical components and create chemical maps. Chapters 5-8 of this thesis describe the development and construction of the MHI, as well as provide proof-of-concept experimental results demonstrating its functionality

High-speed surface profilometry based on an adaptive microscope with axial chromatic encoding

An adaptive microscope with axial chromatic encoding is designed and developed, namely the AdaScope. With the ability to confocally address any locations within the measurement volume, the AdaScope provides the hardware foundation for a cascade measurement strategy to be developed, dramatically accelerating the speed of 3D confocal microscopy

Optical MEMS

Optical microelectromechanical systems (MEMS), microoptoelectromechanical systems (MOEMS), or optical microsystems are devices or systems that interact with light through actuation or sensing at a micro- or millimeter scale. Optical MEMS have had enormous commercial success in projectors, displays, and fiberoptic communications. The best-known example is Texas Instruments’ digital micromirror devices (DMDs). The development of optical MEMS was impeded seriously by the Telecom Bubble in 2000. Fortunately, DMDs grew their market size even in that economy downturn. Meanwhile, in the last one and half decade, the optical MEMS market has been slowly but steadily recovering. During this time, the major technological change was the shift of thin-film polysilicon microstructures to single-crystal–silicon microsructures. Especially in the last few years, cloud data centers are demanding large-port optical cross connects (OXCs) and autonomous driving looks for miniature LiDAR, and virtual reality/augmented reality (VR/AR) demands tiny optical scanners. This is a new wave of opportunities for optical MEMS. Furthermore, several research institutes around the world have been developing MOEMS devices for extreme applications (very fine tailoring of light beam in terms of phase, intensity, or wavelength) and/or extreme environments (vacuum, cryogenic temperatures) for many years. Accordingly, this Special Issue seeks to showcase research papers, short communications, and review articles that focus on (1) novel design, fabrication, control, and modeling of optical MEMS devices based on all kinds of actuation/sensing mechanisms; and (2) new developments of applying optical MEMS devices of any kind in consumer electronics, optical communications, industry, biology, medicine, agriculture, physics, astronomy, space, or defense

Small business innovation research. Abstracts of completed 1987 phase 1 projects

Non-proprietary summaries of Phase 1 Small Business Innovation Research (SBIR) projects supported by NASA in the 1987 program year are given. Work in the areas of aeronautical propulsion, aerodynamics, acoustics, aircraft systems, materials and structures, teleoperators and robotics, computer sciences, information systems, spacecraft systems, spacecraft power supplies, spacecraft propulsion, bioastronautics, satellite communication, and space processing are covered

Assessing the performance of Digital Micromirror Devices for use in space-based multi-object spectrometers

A current need in space-based instrumentation is a reconfigurable slit mask. Several techniques for slit masks have been employed for ground-based astronomical spectrographs. These ground-based instruments have used large discrete components, which are impractical for remote operation in space-based deployment. The Texas Instruments\u27 Digital Micromirror Device (DMD) was originally conceived purely for display purposes, but is a viable candidate to be use as a slit mask in a space-based multi-object spectrograph (MOS). The Integrated Circuit (IC) manufacturing industry has enabled the robust integration of both silicon transistors and Micro-Electrical Mechanical Systems (MEMS) optical components into a very reliable monolithic chip (the DMD). The focus of this work was in three areas that addressed the suitability of proposing DMDs for future space missions. The DMDs were optically characterized to assess their utility in a spectrograph. The DMDs were also cooled in a liquid nitrogen dewar to determine their minimum operating temperature. The low temperature tests indicated that the DMD can operate to temperatures as low as 130 K. In addition, several DMDs were irradiated with high-energy protons at the LBNL 88 Cyclotron to determine how robust the devices are to ionizing radiation (protons). The radiation testing results indicate that DMDs would survive medium to long duration space missions with full operability. Based on preliminary tests in these three areas, the DMD should be considered as an excellent candidate for deployment in future space missions

Use of acousto-Optic Filters in imaging applications. A contribution to the SmartSpectra project

This Thesis analyses the use of an acousto-optic tunable filter (AOTF) for the realisation of spectral imaging systems. An AOTF is an electronically tunable spectral bandpass optical filter. It consists on a crystal that, excited with acoustic waves, diffracts and then separates a single wavelength of light from a broadband source. The wavelength of selected light is a function of the frequency of the signal applied to the crystal. We have implemented a spectral imaging instrument called Autonomous Tunable Filtering System (ATFS) that includes an AOTF in order to acquire multispectral images with a monochrome digital camera. Careful design and calibration permits its use in spectroscopic applications. By using a convenient radio-frequency source, it is possible to configure the spectral filtering performance of the AOTF. This Thesis presents two different excitation techniques: the use of a Direct Digital Synthesiser, and the use of a high-speed Digital- to-Analog Converter. Both methods achieve a configurable broadening of the spectral bandwidth characteristic of the AOTF. In this Thesis we evaluate the use of AOTF’s in spectral imaging applications by means of the implemented instrument. We present a methodology to fully characterise the spectral performance of the AOTF’s respect to the parameters of the driving signal (frequency and power), and we apply this methodology for the characterisation of three different AOTF models from different manufacturers. Imaging performance of the AOTF’s presents some problems due to their low efficiency and chromatic aberration. However, we propose a methodology to overcome the drawbacks of this filtering technology. Finally, the Thesis demonstrates this spectral imaging technology in several applications, including the mapping of the spectral reflectance and transmittance indexes of plant leaves, and the multispectral imaging of different objects. This Thesis concludes that AOTF technology can be successfully applied to spectral imaging systems. Imaging performance of such systems is good, but a proper image processing is needed. Spectral performance of AOTF’s is accurate, allowing their use in quantitative measuring applications, although they require a careful calibration process.Esta Tesis analiza el uso de los filtros ajustables acusto-ópticos (Acousto-Optic Tunable Filter, AOTF) en la implementación de sistemas de visión espectral. Un AOTF es un filtro espectral pasabanda ajustable electrónicamente. Está formado por un cristal que, al ser excitado con una onda acústica, difracta una determinada longitud de onda y por tanto la separa del resto del espectro lumínico. La longitud de onda de la luz separada es función de la frecuencia de la señal acústica aplicada al cristal. Para la realización de esta Tesis Doctoral hemos diseñado un instrumento de visión industrial denominado Sistema de Filtrado Ajustable Autónomo, el cual incluye un AOTF para la adquisición de imágenes multiespectrales a través de una cámara de video monocroma. El sistema ha sido diseñado y calibrado específicamente para permitir su uso en aplicaciones de espectroscopía. El uso de una fuente adecuada de señales de radio frecuencia (RF) para excitar el AOTF permite configurar dinámicamente el funcionamiento del filtrado espectral. En esta Tesis presentamos dos nuevas técnicas de excitación por RF: una basada en un Sintetizador Digital Directo y otra basada en un Conversor Digital-Analógico de alta velocidad. Ambas técnicas presentan la novedosa característica de que se pueden utilizar para ajustar dinámicamente el ancho de banda de filtrado del AOTF. El instrumento diseñado se ha utilizado en la presente Tesis para evaluar el uso de los AOTF en aplicaciones de visión espectral. Para ello, presentamos una metodología de caracterización del comportamiento espectral del AOTF respecto a su señal de excitación. Hemos aplicado esta metodología para la caracterización de tres modelos distintos de AOTF suministrados por diferentes fabricantes. El comportamiento en imagen de los AOTF presenta ciertos problemas, debido a su baja eficiencia espectral y a la existencia de aberraciones cromáticas. Sin embargo, proponemos una metodología de procesado que soluciona estos inconvenientes. Por último, esta Tesis demuestra el uso de esta tecnología de imagen espectral en varias aplicaciones. Entre otras, mostramos el mapa de reflectancia y transmitancia espectral de las hojas de diversas especies vegetales, y la adquisición de imágenes multiespectrales de diversos objetos

Programmable optics for ultrashort pulse management: devices and applications

The contribution of the present report to the field of ultrashort optics has several aspects: from the development of new optical devices for ultrashort pulse management, to the application of those devices for triggering laser-matter interaction processes. In this sense, the key point of this Thesis is the use of reconfigurable phase-only SLMs based on LCOS technology for spatial and temporal shaping of femtosecond pulses. The management of femtosecond pulses demands specific strategies to obtain the desired output response while preventing undesirable distortions. Our results show that programmable diffractive optics encoded in SLMs is a powerful tool for ultrashort (~30 fs) beam management. The reconfigurable nature of SLMs allows wavefront control of an input pulsed beam at a micro scale level. In this way, we have developed devices for transferring amplitude and/or phase maps onto the spatial and temporal profile of an ultrashort pulse. Moreover, our proposals result in very compact optical devices, allowing easy-to-align setups especially suitable for non-expert users. We believe that this fact may promote the use of ultrafast technology in many different scientific fields that demands user-friendly devices for ultrashort pulse control

Optical Gas Sensing: Media, Mechanisms and Applications

Optical gas sensing is one of the fastest developing research areas in laser spectroscopy. Continuous development of new coherent light sources operating especially in the Mid-IR spectral band (QCL—Quantum Cascade Lasers, ICL—Interband Cascade Lasers, OPO—Optical Parametric Oscillator, DFG—Difference Frequency Generation, optical frequency combs, etc.) stimulates new, sophisticated methods and technological solutions in this area. The development of clever techniques in gas detection based on new mechanisms of sensing (photoacoustic, photothermal, dispersion, etc.) supported by advanced applied electronics and huge progress in signal processing allows us to introduce more sensitive, broader-band and miniaturized optical sensors. Additionally, the substantial development of fast and sensitive photodetectors in MIR and FIR is of great support to progress in gas sensing. Recent material and technological progress in the development of hollow-core optical fibers allowing low-loss transmission of light in both Near- and Mid-IR has opened a new route for obtaining the low-volume, long optical paths that are so strongly required in laser-based gas sensors, leading to the development of a novel branch of laser-based gas detectors. This Special Issue summarizes the most recent progress in the development of optical sensors utilizing novel materials and laser-based gas sensing techniques