Writing and characterisation methods for UV-photosensitivity based devices and their applications

The underlying work to this thesis focused on the exploitation and investigation of photosensitivity mechanisms in optical fibres and planar waveguides for the fabrication of advanced integrated optical devices for telecoms and sensing applications. One major scope is the improvement of grating fabrication specifications by introducing new writing techniques and the use of advanced characterisation methods for grating testing. For the first time the polarisation control method for advanced grating fabrication has successfully been converted to apodised planar waveguide fabrication and the development of a holographic method for the inscription of chirped gratings at arbitrary wavelength is presented. The latter resulted in the fabrication of gratings for pulse-width suppression and wavelength selection in diode lasers. In co-operation with research partners a number of samples were tested using optical frequency domain and optical low coherence reflectometry for a better insight into the limitations of grating writing techniques. Using a variety of different fabrication methods, custom apodised and chirped fibre Bragg gratings were written for the use as filter elements for multiplexer-demultiplexer devices, as well as for short pulse generation and wavelength selection in telecommunication transmission systems. Long period grating based devices in standard, speciality and tapered fibres are presented, showing great potential for multi-parameter sensing. One particular scope is the development of vectorial curvature and refractive index sensors with potential for medical, chemical and biological sensing. In addition the design of an optically tunable Mach-Zehnder based multiwavelength filter is introduced. The discovery of a Type IA grating type through overexposure of hydrogen loaded standard and Boron-Germanium co-doped fibres strengthened the assumption of UV-photosensitivity being a highly non-linear process. Gratings of this type show a significantly lower thermal sensitivity compared to standard gratings, which makes them useful for sensing applications. An Oxford Lasers copper-vapour laser operating at 255 nm in pulsed mode was used for their inscription, in contrast to previous work using CW-Argon-Ion lasers and contributing to differences in the processes of the photorefractive index chang

The bending and temperature characteristics of long period gratings written in elliptical core step-index fibre

We describe the characterisation of long period gratings written in elliptical core fibre, which yield a discriminatory sensor for curvature and temperature with a resolution ±0.05m-1 for curvature and ±0.9 °C for temperature

Hybrid-type fibre Bragg gratings and their applications

Fiber Bragg gratings (FBGs) have attracted a lot of attention in recent years due to their wide applications in optical telecommunications and smart sensing. They have been used as DWDM filters, dispersion compensators, gain flattening filters, optical switch and connection devices, and temperature/strain sensors. FBGs have been found to exhibit four different type structures according to their different growth mechanisms. Each type of FBG exhibits unique thermal and strain properties. Generally, the Type I gratings in hydrogenated and hydrogen-free fibers are used most for applications. However, some novel devices may be achieved by combinational structure of different types of gratings in the future. In this paper, we propose a novel concept of fabrication and application of FBGs with hybrid grating types. We have observed a complex growth behavior of a hybrid-type grating in the UV exposure to a B/Ge codoped fiber through a phase mask. A new model has been developed to simulate the complex growth behavior of the hybrid-type gratings, giving results in excellent agreement with experiment

Tapered fibre LPG device as a sensing element for refractive index

The fabrication and characterisation of Long Period Gratings in fibre tapers is presented alongside supporting theory. The devices possess a high sensitivity to the index of aqueous solutions due to an observed spectral bifurcation effect

A long period grating directional bend sensor incorporating index modification of the cladding

Long period gratings written into a standard optical fibre were modified by a femtosecond laser, which produced an asymmetric change to the cladding's refractive index resulting in a directional bend sensor

Bending characteristics of fiber long-period gratings with cladding index modified by femtosecond laser

A femtosecond laser has been used to asymmetrically modify the cladding of fiber containing long-period gratings. Following modification, devices in single-mode fiber are shown to be capable of sensing the magnitude and direction of bending in one plane by producing blue and red wavelength shifts depending upon the orientation of the bend. The resulting curvature sensitivities were -1.62 and +3.82 nm·m. Devices have also been produced using an elliptical core fiber to study the effects of the cladding modification on the two polarization eigenstates. A cladding modification applied on the fast axis of the fiber is shown to affect the light in the fast axis much more significantly than the light in the orthogonal state; this behavior may ultimately lead to a sensor capable of detecting the direction of bending in two dimensions for applications in shape sensing. © 2006 IEEE

Micro-fabrication of advanced photonic devices by means of direct point-by-point femtosecond inscription in silica

We present recent results on experimental micro-fabrication and numerical modeling of advanced photonic devices by means of direct writing by femtosecond laser. Transverse inscription geometry was routinely used to inscribe and modify photonic devices based on waveguiding structures. Typically, standard commercially available fibers were used as a template with a pre-fabricated waveguide. Using a direct, point-by-point inscription by infrared femtosecond laser, a range of fiber-based photonic devices was fabricated including Fiber Bragg Gratings (FBG) and Long Period Gratings (LPG). Waveguides with a core of a couple of microns, periodic structures, and couplers have been also fabricated in planar geometry using the same method

Classification of 1D-Signal Types Using Deep Learning

De-novo sastavljanje genoma proces je temeljen na preklapanju i analizi kratkih genetskih očitanja. Uslijed raznolikih tehničkih izazova, određene vrste lažnih očitanja i preklapanja mogu također biti sintetizirane, što uvelike otežava is- pravno sastavljanje originalne sekvence. Jedna od metoda za otkrivanje takvih preklapanja je i pretvorba istih u 1D-signal, pomoću kojih se onda može jed- nostavnije zaključiti koji tip preklapanja predstavlja. U okviru ovog rada, pred- stavljeno je nekoliko metoda duboko učenja za klasifikaciju ovih signala, točnije 1D-konvolucijske mreže, povratne mreže, kao i primjena autoenkodera. Dodatno, prikazana je i njihova primjena na stvarnim podacima, kao i usporedba usp- ješnosti.The de novo genome assembly process is based on overlapping and analyzing short reads of genetic information. Due to various technical challenges, certain types of false overlaps can also be generated, which greatly impedes successful reconstruction. One of the methods for detecting such overlaps is by generating a 1D-signal for each read, which can then be used to determine its exact overlap type. This thesis proposes several deep learning methods for classifying these signals, including 1D-convolutional & recurrent networks, as well as autoencoders. A detailed comparison of their application on real-world data is also included

Manual Detection of False Overlaps Occured During the Genome Assembly Process

Proces sastavljanja genoma temeljen je na analizi preklapanja kratkih očitanja genetskog materijala. Zbog očitanja loše kvalitete, kao i zbog prisutnosti kimernih i ponavljajućih očitanja, osim ispravnih preklapanja pojavljuju se i lažna preklapanja. Detekcija lažnih preklapanja ključna je u postizanju boljeg konačnog rezultata. Jedna od metoda detekcije je generiranje 1D-signala temeljenog na izračunu broja preklapanja svake nukleinske baze pojedinog očitanja, koji se potom prikazuje u obliku grafa. Kroz ovaj rad predstavljeno je aplikacijsko rješenje za Android uređaje, kojim je moguće označiti regije u kojima se pojavljuju lažna preklapanja, kao i sortirati grafove po predefiniranim kategorijama. U radu je data teorijska osnova rješenja, kao i detalji njegove implementacije i konačnog ispitivanja.The genome assembly process is based on overlapping and analyzing short reads of genetic information. False positive overlaps arise in addition to true positive overlaps, as a result of low quality, chimeric and repetitive reads. Detection of these false positive overlaps is key to constructing more accurate and complete genomes. One of the methods for detecting such overlaps is by generating a 1D-signal based on the number of overlaps of each nucleobase in a read, which can then be shown in the form of a chart. This thesis presents an Android application for demarking areas of false overlaps on the aforementioned charts, as well as sorting charts in predefined categories. Both the theoretical and practical solution, as well as the testing process, have been documented inside of this paper

Manual Detection of False Overlaps Occured During the Genome Assembly Process

Proces sastavljanja genoma temeljen je na analizi preklapanja kratkih očitanja genetskog materijala. Zbog očitanja loše kvalitete, kao i zbog prisutnosti kimernih i ponavljajućih očitanja, osim ispravnih preklapanja pojavljuju se i lažna preklapanja. Detekcija lažnih preklapanja ključna je u postizanju boljeg konačnog rezultata. Jedna od metoda detekcije je generiranje 1D-signala temeljenog na izračunu broja preklapanja svake nukleinske baze pojedinog očitanja, koji se potom prikazuje u obliku grafa. Kroz ovaj rad predstavljeno je aplikacijsko rješenje za Android uređaje, kojim je moguće označiti regije u kojima se pojavljuju lažna preklapanja, kao i sortirati grafove po predefiniranim kategorijama. U radu je data teorijska osnova rješenja, kao i detalji njegove implementacije i konačnog ispitivanja.The genome assembly process is based on overlapping and analyzing short reads of genetic information. False positive overlaps arise in addition to true positive overlaps, as a result of low quality, chimeric and repetitive reads. Detection of these false positive overlaps is key to constructing more accurate and complete genomes. One of the methods for detecting such overlaps is by generating a 1D-signal based on the number of overlaps of each nucleobase in a read, which can then be shown in the form of a chart. This thesis presents an Android application for demarking areas of false overlaps on the aforementioned charts, as well as sorting charts in predefined categories. Both the theoretical and practical solution, as well as the testing process, have been documented inside of this paper