The development of an automated nano sampling handling system for nanometre protein crystallography experiments

As the world's synchrotrons and X-FELs endeavour to meet the need to analyse ever-smaller protein crystals, there grows a requirement for a new technique to present nano-dimensional samples to the beam for X-ray diffraction experiments.The work presented here details developmental work to reconfigure the nano tweezer technology developed by Optofluidics (PA, USA) for the trapping of nano dimensional protein crystals for X-ray crystallography experiments. The system in its standard configuration is used to trap nano particles for optical microscopy. It uses silicon nitride laser waveguides that bridge a micro fluidic channel. These waveguides contain 180 nm apertures of enabling the system to use biologically compatible 1.6 micron wavelength laser light to trap nano dimensional biological samples. Using conventional laser tweezers, the wavelength required to trap such nano dimensional samples would destroy them. The system in its optical configuration has trapped protein molecules as small as 10 nanometres.

The development of an automated nano sampling handling system for nanometne protein crystallography experiments

As the world's synchrotrons and X-FELs endeavour to meet the need to analyse ever-smaller protein crystals, there grows a requirement for a new technique to present nano-dimensional samples to the beam for X-ray diffraction experiments.The work presented here details developmental work to reconfigure the nano tweezer technology developed by Optofluidics (PA, USA) for the trapping of nano dimensional protein crystals for X-ray crystallography experiments. The system in its standard configuration is used to trap nano particles for optical microscopy. It uses silicon nitride laser waveguides that bridge a micro fluidic channel. These waveguides contain 180 nm apertures of enabling the system to use biologically compatible 1.6 micron wavelength laser light to trap nano dimensional biological samples. Using conventional laser tweezers, the wavelength required to trap such nano dimensional samples would destroy them. The system in its optical configuration has trapped protein molecules as small as 10 nanometres.

Temporal scaling of optical rogue waves in unidirectional ring fiber laser

A fiber mode-lock laser allows generation of the optical rogue wave (ORW) at different time scales. The criteria for distinguishing between them is a comparison of the event lifetime with the main characteristic time of the system. The characteristic time can be estimated from the decay of an autocorrelation function (AF). Thus, in comparison with AF characteristic time, fast optical rogue wave (FORW) events have duration less than the AF decay time and it appeared due to pulse-pulse interaction and nonlinear pulses dynamics. While slow optical rogue wave (SORW) have a duration much more longer than the decay time of the AF which it papered due to hopping between different attractors. Switching between regimes can be managed by change the artificial birefringence that induced in a laser cavity. For understanding the role playing by the periodical amplification and the resonator, we have performed an unidirectional fiber laser experiments without a saturable absorber. This laser experiment allowed to generate of most of the RW patterns which were either observed experimentally or predicted theoretically. In this way, we have observed the generation of an FORW along with SORW under similar conditions. Most of the patterns were found to be mutually exclusive which means that only one RW mechanism was realized in each regime of generation.

Mode-locked laser pulse sources for wavelength division multiplexing

Recent theoretical investigations have demonstrated that the stability of mode-locked solution of multiple frequency channels depends on the degree of inhomogeneity in gain saturation. In this paper, these results are generalized to determine conditions on each of the system parameters necessary for both the stability and existence of mode-locked pulse solutions for an arbitrary number of frequency channels. In particular, we find that the parameters governing saturable intensity discrimination and gain inhomogeneity in the laser cavity also determine the position of bifurcations of solution types. These bifurcations are completely characterized in terms of these parameters. In addition to influencing the stability of mode-locked solutions, we determine a balance between cubic gain and quintic loss, which is necessary for existence of solutions as well. Furthermore, we determine the critical degree of inhomogeneous gain broadening required to support pulses in multiple frequency channels. © 2010 Copyright SPIE - The International Society for Optical Engineering.

Comparative performance between two photogrammetric systems and a reference laser tracker network for large-volume industrial measurement

This paper determines the capability of two photogrammetric systems in terms of their measurement uncertainty in an industrial context. The first system – V-STARS inca3 from Geodetic Systems Inc. – is a commercially available measurement solution. The second system comprises an off-the-shelf Nikon D700 digital camera fitted with a 28 mm Nikkor lens and the research-based Vision Measurement Software (VMS). The uncertainty estimate of these two systems is determined with reference to a calibrated constellation of points determined by a Leica AT401 laser tracker. The calibrated points have an average associated standard uncertainty of 12·4 μm, spanning a maximum distance of approximately 14·5 m. Subsequently, the two systems’ uncertainty was determined. V-STARS inca3 had an estimated standard uncertainty of 43·1 μm, thus outperforming its manufacturer's specification; the D700/VMS combination achieved a standard uncertainty of 187 μm.

The framework of the virtual laser tracker - A systematic approach to the assessment of error sources and uncertainty in laser tracker measurement

Laser trackers have been widely used in many industries to meet increasingly high accuracy requirements. In laser tracker measurement, it is complex and difficult to perform an accurate error analysis and uncertainty evaluation. This paper firstly reviews the working principle of single beam laser trackers and state-of- The- Art of key technologies from both industrial and academic efforts, followed by a comprehensive analysis of uncertainty sources. A generic laser tracker modelling method is formulated and the framework of the virtual tracker is proposed. The VLS can be used for measurement planning, measurement accuracy optimization and uncertainty evaluation. The completed virtual laser tracking system should take all the uncertainty sources affecting coordinate measurement into consideration and establish an uncertainty model which will behave in an identical way to the real system. © Springer-Verlag Berlin Heidelberg 2010.

Development of Swept Source Optical Coherence Tomography and Adaptive Optics Scanning Laser Ophthalmoscopy: Improved Imaging Speed and Handheld Applications

Optical coherence tomography (OCT) is a noninvasive three-dimensional interferometric imaging technique capable of achieving micrometer scale resolution. It is now a standard of care in ophthalmology, where it is used to improve the accuracy of early diagnosis, to better understand the source of pathophysiology, and to monitor disease progression and response to therapy. In particular, retinal imaging has been the most prevalent clinical application of OCT, but researchers and companies alike are developing OCT systems for cardiology, dermatology, dentistry, and many other medical and industrial applications.

Adaptive optics (AO) is a technique used to reduce monochromatic aberrations in optical instruments. It is used in astronomical telescopes, laser communications, high-power lasers, retinal imaging, optical fabrication and microscopy to improve system performance. Scanning laser ophthalmoscopy (SLO) is a noninvasive confocal imaging technique that produces high contrast two-dimensional retinal images. AO is combined with SLO (AOSLO) to compensate for the wavefront distortions caused by the optics of the eye, providing the ability to visualize the living retina with cellular resolution. AOSLO has shown great promise to advance the understanding of the etiology of retinal diseases on a cellular level.

Broadly, we endeavor to enhance the vision outcome of ophthalmic patients through improved diagnostics and personalized therapy. Toward this end, the objective of the work presented herein was the development of advanced techniques for increasing the imaging speed, reducing the form factor, and broadening the versatility of OCT and AOSLO. Despite our focus on applications in ophthalmology, the techniques developed could be applied to other medical and industrial applications. In this dissertation, a technique to quadruple the imaging speed of OCT was developed. This technique was demonstrated by imaging the retinas of healthy human subjects. A handheld, dual depth OCT system was developed. This system enabled sequential imaging of the anterior segment and retina of human eyes. Finally, handheld SLO/OCT systems were developed, culminating in the design of a handheld AOSLO system. This system has the potential to provide cellular level imaging of the human retina, resolving even the most densely packed foveal cones.

Integrated System Technologies for Modular Trapped Ion Quantum Information Processing

Although trapped ion technology is well-suited for quantum information science, scalability of the system remains one of the main challenges. One of the challenges associated with scaling the ion trap quantum computer is the ability to individually manipulate the increasing number of qubits. Using micro-mirrors fabricated with micro-electromechanical systems (MEMS) technology, laser beams are focused on individual ions in a linear chain and steer the focal point in two dimensions. Multiple single qubit gates are demonstrated on trapped 171Yb+ qubits and the gate performance is characterized using quantum state tomography. The system features negligible crosstalk to neighboring ions (< 3e-4), and switching speeds comparable to typical single qubit gate times (< 2 us). In a separate experiment, photons scattered from the 171Yb+ ion are coupled into an optical fiber with 63% efficiency using a high numerical aperture lens (0.6 NA). The coupled photons are directed to superconducting nanowire single photon detectors (SNSPD), which provide a higher detector efficiency (69%) compared to traditional photomultiplier tubes (35%). The total system photon collection efficiency is increased from 2.2% to 3.4%, which allows for fast state detection of the qubit. For a detection beam intensity of 11 mW/cm2, the average detection time is 23.7 us with 99.885(7)% detection fidelity. The technologies demonstrated in this thesis can be integrated to form a single quantum register with all of the necessary resources to perform local gates as well as high fidelity readout and provide a photon link to other systems.

Experimental Study of Storage Ring Free-Electron Laser with Novel Capabilities

The Duke Free-electron laser (FEL) system, driven by the Duke electron storage ring, has been at the forefront of developing new light source capabilities over the past two decades. In 1999, the Duke FEL demonstrated the first lasing of a storage ring FEL in the vacuum ultraviolet (VUV) region at $194$ nm using two planar OK-4 undulators. With two helical undulators added to the outboard sides of the planar undulators, in 2005 the highest FEL gain ($47.8\%$) of a storage ring FEL was achieved using the Duke FEL system with a four-undulator configuration. In addition, the Duke FEL has been used as the photon source to drive the High Intensity $\gamma$-ray Source (HIGS) via Compton scattering of the FEL beam and electron beam inside the FEL cavity. Taking advantage of FEL's wavelength tunability as well as the adjustability of the energy of the electron beam in the storage ring, the nearly monochromatic $\gamma$-ray beam has been produced in a wide energy range from $1$ to $100$ MeV at the HIGS. To further push the FEL short wavelength limit and enhance the FEL gain in the VUV regime for high energy $\gamma$-ray production, two additional helical undulators were installed in 2012 using an undulator switchyard system to allow switching between the two planar and two helical undulators in the middle section of the FEL system. Using different undulator configurations made possible by the switchyard, a number of novel capabilities of the storage ring FEL have been developed and exploited for a wide FEL wavelength range from infrared (IR) to VUV. These new capabilities will eventually be made available to the $\gamma$-ray operation, which will greatly enhance the $\gamma$-ray user research program, creating new opportunities for certain types of nuclear physics research.

With the wide wavelength tuning range, the FEL is an intrinsically well-suited device to produce lasing with multiple colors. Taking advantage of the availability of an undulator system with multiple undulators, we have demonstrated the first two-color lasing of a storage ring FEL. Using either a three- or four-undulator configuration with a pair of dual-band high reflectivity mirrors, we have achieved simultaneous lasing in the IR and UV spectral regions. With the low-gain feature of the storage ring FEL, the power generated at the two wavelengths can be equally built up and precisely balanced to reach FEL saturation. A systematic experimental program to characterize this two-color FEL has been carried out, including precise power control, a study of the power stability of two-color lasing, wavelength tuning, and the impact of the FEL mirror degradation. Using this two-color laser, we have started to develop a new two-color $\gamma$-ray beam for scientific research at the HIGS.

Using the undulator switchyard, four helical undulators installed in the beamline can be configured to not only enhance the FEL gain in the VUV regime, but also allow for the full polarization control of the FEL beams. For the accelerator operation, the use of helical undulators is essential to extend the FEL mirror lifetime by reducing radiation damage from harmonic undulator radiation. Using a pair of helical undulators with opposite helicities, we have realized (1) fast helicity switching between left- and right-circular polarizations, and (2) the generation of fully controllable linear polarization. In order to extend these new capabilities of polarization control to the $\gamma$-ray operation in a wide energy range at the HIGS, a set of FEL polarization diagnostic systems need to be developed to cover the entire FEL wavelength range. The preliminary development of the polarization diagnostics for the wavelength range from IR to UV has been carried out.

Elemental Analysis of Biological Matrices by Laser Ablation High Resolution Inductively Coupled Plasma Mass Spectrometry (LA-HR-ICP-MS) and High Resolution Inductively Coupled Plasma Mass Spectrometry (HR-ICP-MS)

The need for elemental analysis of biological matrices such as bone, teeth, and plant matter for sourcing purposes has emerged within the forensic and geochemical laboratories. Trace elemental analyses for the comparison of aterials such as glass by inductively coupled plasma mass spectrometry (ICP-MS) and laser ablation ICP-MS has been shown to offer a high degree of discrimination between different manufacturing sources. Unit resolution ICP-MS instruments may suffer from some polyatomic interferences including 40Ar16O+, 40Ar16O1H+, and 40Ca16O+ that affect iron measurement at trace levels. Iron is an important element in the analysis of glass and also of interest for the analysis of several biological matrices. A comparison of the nalytical performance of two different ICP-MS systems for iron analysis in glass for determining the method detection limits (MDLs), accuracy, and precision of the measurement is presented. Acid digestion and laser ablation methods are also compared. Iron polyatomic interferences were reduced or resolved by using dynamic reaction cell and high resolution ICP-MS. MDLs as low as 0.03 ìg g-1 and 0.14 ìg g-1 for laser ablation and solution based analyses respectively were achieved. The use of helium as a carrier gas demonstrated improvement in the detection limits of both iron isotopes (56Fe and 57Fe) in medium resolution for the HR-ICP-MS and with a dynamic reaction cell (DRC) coupled to a quadrupole ICP-MS system. The development and application of robust analytical methods for the quantification of trace elements in biological matrices has lead to a better understanding of the potential utility of these measurements in forensic chemical analyses. Standard reference materials (SRMs) were used in the development of an analytical method using HR-ICP-MS and LA-HR-ICP-MS that was subsequently applied on the analysis of real samples. Bone, teeth and ashed marijuana samples were analyzed with the developed method. Elemental analysis of bone samples from 12 different individuals provided discrimination between individuals, when femur and humerus bones were considered separately. Discrimination of 14 teeth samples based on elemental composition was achieved with the exception of one case where samples from the same individual were not associated with each other. The discrimination of 49 different ashed plant (cannabis)samples was achieved using the developed method.

San Francisco Coastal System grain size and geochemical data for sand provenance study

Over 150 million cubic meter of sand-sized sediment has disappeared from the central region of the San Francisco Bay Coastal System during the last half century. This enormous loss may reflect numerous anthropogenic influences, such as watershed damming, bay-fill development, aggregate mining, and dredging. The reduction in Bay sediment also appears to be linked to a reduction in sediment supply and recent widespread erosion of adjacent beaches, wetlands, and submarine environments. A unique, multi-faceted provenance study was performed to definitively establish the primary sources, sinks, and transport pathways of beach sized-sand in the region, thereby identifying the activities and processes that directly limit supply to the outer coast. This integrative program is based on comprehensive surficial sediment sampling of the San Francisco Bay Coastal System, including the seabed, Bay floor, area beaches, adjacent rock units, and major drainages. Analyses of sample morphometrics and biological composition (e.g., Foraminifera) were then integrated with a suite of tracers including 87Sr/86Sr and 143Nd/144Nd isotopes, rare earth elements, semi-quantitative X-ray diffraction mineralogy, and heavy minerals, and with process-based numerical modeling, in situ current measurements, and bedform asymmetry to robustly determine the provenance of beach-sized sand in the region.

High volume fabrication of laser targets using MEMS techniques

The latest techniques for the fabrication of high power laser targets, using processes developed for the manufacture of Micro-Electro-Mechanical System (MEMS) devices are discussed. These laser targets are designed to meet the needs of the increased shot numbers that are available in the latest design of laser facilities. Traditionally laser targets have been fabricated using conventional machining or coarse etching processes and have been produced in quantities of 10s to low 100s. Such targets can be used for high complexity experiments such as Inertial Fusion Energy (IFE) studies and can have many complex components that need assembling and characterisation with high precision. Using the techniques that are common to MEMS devices and integrating these with an existing target fabrication capability we are able to manufacture and deliver targets to these systems. It also enables us to manufacture novel targets that have not been possible using other techniques. In addition, developments in the positioning systems that are required to deliver these targets to the laser focus are also required and a system to deliver the target to a focus of an F2 beam at 0.1Hz is discussed.

Population inversion between the sup(3)Hsub(4) and the sup(3)Fsub(4) excited states of Tmsup(3+) investigated by means of numerical solutions of the rate equations system in Tmsup(3+)-doped and Tmsup(3+), Hosup(3+)-codoped fluoride glasses

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Energy transfer rates and population inversion of sup(4)Isub(11/2) excited state of Ersup(3+) investigated by means of numerical solutions of the rate equations system in Er:LiYFsub(4) crystal

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Pilot Study on Improving the Efficiency of Transportation Projects Using Laser Scanning, 2003

Laser scanning is a terrestrial laser-imaging system that creates highly accurate three-dimensional images of objects for use in standard computer-aided design software packages. This report describes results of a pilot study to investigate the use of laser scanning for transportation applications in Iowa. After an initial training period on the use of the scanner and Cyclone software, pilot tests were performed on the following projects: intersection and railroad bridge for training purposes; section of highway to determine elevation accuracy and pair of bridges to determine level of detail that can be captured; new concrete pavement to determine smoothness; bridge beams to determine camber for deck-loading calculations; stockpile to determine volume; and borrow pit to determine volume. Results show that it is possible to obtain 2-6 mm precision with the laser scanner as claimed by the manufacturer compared to approximately one-inch precision with aerial photogrammetry using a helicopter. A cost comparison between helicopter photogrammetry and laser scanning showed that laser scanning was approximately 30 percent higher in cost depending on assumptions. Laser scanning can become more competitive to helicopter photogrammetry by elevating the scanner on a boom truck and capturing both sides of a divided roadway at the same time. Two- and three-dimensional drawings were created in MicroStation for one of the scanned highway bridges. It was demonstrated that it is possible to create such drawings within the accuracy of this technology. It was discovered that a significant amount of time is necessary to convert point cloud images into drawings. As this technology matures, this task should become less time consuming. It appears that laser scanning technology does indeed have a place in the Iowa Department of Transportation design and construction toolbox. Based on results from this study, laser scanning can be used cost effectively for preliminary surveys to develop TIN meshes of roadway surfaces. It also appears that this technique can be used quite effectively to measure bridge beam camber in a safer and quicker fashion compared to conventional approaches. Volume calculations are also possible using laser scanning. It seems that measuring quantities of rock could be an area where this technology would be quite beneficial since accuracy is more important with this material compared to soil. Other applications for laser scanning could include developing as-built drawings of historical structures such as the bridges of Madison County. This technology could also be useful where safety is a concern such as accurately measuring the surface of a highway active with traffic or scanning the underside of a bridge damaged by a truck. It is recommended that the Iowa Department of Transportation initially rent the scanner when it is needed and purchase the software. With time, it may be cost justifiable to purchase the scanner as well. Laser scanning consultants can be hired as well but at a higher cost.