We simulate ultrashort pulse propagation through water by numerical methods, which is a kind of optical communication research. Ultrashort pulses have been known to have non Beer-Lambert behavior, whereas continuous waves (CW) obey the Beer-Lambert law. People have expected that the ultrashort pulse loses less intensity for a given distance in water than CW which implies that the pulse can travel over longer distances. In order to understand this characteristic of the pulse, we model numerically its spectral and temporal evolution as a function of traveling distance through water. We achieve the pulse intensity attenuation with traveling distance, obtain the temporal envelope of the pulse and compare them with experimental data. This research proves that the spectral and temporal profile of a pulse can be predicted knowing only the intensity spectrum of the input pulse and the refractive index spectrum of water in the linear regime. The real feasibility and the advantage of using an ultrashort pulse as a communication carrier will also be discussed.

Functional Near Infrared Spectroscopy (fNIRS) is a safe, low-cost, non-invasive opti-cal technique to monitor focal changes in brain activity using neurovascular coupling and measurements of local tissue oxygenation, i.e., changes in concentrations of oxygenated hemoglobin (HbO) and deoxygenated hemoglobin (HbR)[42]. This thesis utilizes two fNIRS approaches to measure hemodynamic changes associated with functional stimulation of the human auditory cortex. The first approach, single-distance continuous wave NIRS (CW-NIRS) utilizes relatively simple instrumentation and the Modified-Beer Lambert (MBL) law to estimate activation induced changes in tissue oxygenation (∆CHbO and ∆CHbR)[17]. The second more complex approach, frequency domain NIRS (FD-NIRS), employs a photon diffusion model of light propagation through tissue to measure both baseline (CHbO and CHbR), and stimulus induced changes in oxygenated and deoxygenated hemoglobin[10]. FD-NIRS is more quantitative, but requires measurements at multiple light source-detector separations and thus its use in measuring focal changes in cerebral hemodynamics have been limited. A commercial FD-NIRS instrument was used to measure the cerebral hemodynamics from the right auditory cortex of 9 adults (21 ± 35 years) with normal hearing, while presented with two types of auditory stimuli: a 1000 Hz Pure tone, and Broad band noise. Measured optical intensities were analyzed using both MBL and photon diffusion approaches. Oxygenated hemoglobin was found to increase by 0.351 ± 0.116 µM and 0.060 ± 0.084 µM for Pure tone and Broad band noise stimuli, when analyzed by the MBL method at the ‘best’ source-detector separation. On average (across all sources), MBL analysis estimated an increase in CHbO of 0.100±0.075 µM and 0.099±0.084 µM respectively for Pure tone and Broad band noise stimulation. In contrast, the frequency domain analysis method estimated CHbO to increase by −0.401 ± 0.384 µM and −0.031 ± 0.358 µM for Pure tone and Broad band noise stimulation respectively. These results suggest that although more quantitative, multi-distance FD-NIRS may underestimate focal changes in cerebral hemodynamics that occur due to functional activation. Potential reasons for this discrepancy, including the partial volume effect, are discussed.

Τα τελευταία χρόνια, οι μη επεμβατικές μέθοδοι διάγνωσης αλλά και θεραπείας κερδίζουν συνεχώς έδαφος έναντι των παραδοσιακών επεμβατικών μεθόδων. Σκοπός της διπλωματικής αυτής εργασίας είναι η μελέτη της μετάδοσης του φωτός μέσα στο ανθρώπινο δέρμα και κυρίως η μελέτη της απορρόφησης που υφίσταται από αυτό, με σκοπό την μέτρηση βιολογικών συντελεστών, όπως οι συγκεντρώσεις κάποιων ουσιών στον οργανισμό, ο υπολογισμός των οποίων μπορεί να οδηγήσει σε χρήσιμα διαγνωστικά συμπεράσματα. Επίσης, αναλύεται η μέθοδος της παλμικής οξυμετρίας, που χρησιμοποιείται ευρύτατα για την παρακολούθηση του αρτηριακού κορεσμού οξυγόνου και του καρδιακού παλμού. Μετρώντας την απορρόφηση του φωτός σε δύο διαφορετικά μήκη κύματος, ένα στο ερυθρό (660 nm) και ένα στο εγγύς υπέρυθρο (940 nm), και απομονώνοντας το μεταβαλλόμενο μέρος αυτής, που οφείλεται στις διακυμάνσεις στον όγκο του αρτηριακού αίματος, μπορούμε να υπολογίσουμε με τη χρήση του νόμου των Beer-Lambert τον κορεσμό του αίματος σε οξυγόνο μέσω του υπολογισμού των συγκεντρώσεων του σε μειωμένη αιμογλοβίνη και σε οξυαιμογλοβίνη. Τέλος, περιγράφεται η υλοποίηση της μεθόδου και ο σχεδιασμός ενός παλμικού οξυμέτρου ενός chip με τη χρήση του μικροεπεξεργαστή MSP430. / Over recent years, non-invasive methods of diagnosis and treatment are gaining ground against the traditional invasive methods. In this thesis, an integrated review of the transfer of optical radiation into human skin and primarily light absorption through human skin is presented, aiming at measuring biological information, such as concentrations of certain substances in the human body, whose calculation can lead to useful diagnostic conclusions. The method of Pulse Oximetry, which is widely used for monitoring arterial oxygen saturation and heart rate of a patient, is also presented. By measuring the absorption of light at two different wavelengths, one red (660 nm) and one near-infrared (940 nm), and isolating its AC component, which is a result of the variations in the volume of arterial blood, we can calculate the oxygen saturation using the Beer-Lambert law, by estimating the concentrations of oxyhemoglobin and reduced hemoglobin. Moreover, the implementation of a single chip portable pulse oximeter using the ultra low power capability of the MSP430 is demonstrated.

Submitted by Renata Lopes (renatasil82@gmail.com) on 2017-06-09T15:24:44Z No. of bitstreams: 1 danielgustavomesquitadasilva.pdf: 1286713 bytes, checksum: 02c113ea7352199324c4ee67f18311bf (MD5) / Approved for entry into archive by Adriana Oliveira (adriana.oliveira@ufjf.edu.br) on 2017-06-29T12:06:17Z (GMT) No. of bitstreams: 1 danielgustavomesquitadasilva.pdf: 1286713 bytes, checksum: 02c113ea7352199324c4ee67f18311bf (MD5) / Made available in DSpace on 2017-06-29T12:06:17Z (GMT). No. of bitstreams: 1 danielgustavomesquitadasilva.pdf: 1286713 bytes, checksum: 02c113ea7352199324c4ee67f18311bf (MD5) Previous issue date: 2009-04-06 / Neste trabalho foram obtidas Secções de Choque Totais Absolutas (SCTA) para moléculas de Etanol e Metanol utilizando um aparelho desenvolvido no Laboratório de Espectroscopia Atômica e Molecular do DF/UFJF, que emprega a técnica de transmissão linear. As medidas foram realizadas para o Metanol e Etanol cobrindo as energias de impacto de 70, 80, 90, 100, 150, 200, 250, 300, 350, 400 e 500 eV e também de 60 eV para o Etanol. A resolução de energia em todas as medidas foi de 0,6 eV (FWHM) e a incerteza no cálculo das SCTs foi estimada em 5%. A faixa de pressão na célula de espalhamento foi mantida entre 1 a 4mTorr. Os elétrons que sofreram processos de colisões inelásticas podem ser descriminados daqueles que não sofreram nenhum processo de interação com o alvo por um analisador cilíndrico dispersivo 127º, que tem a finalidade de selecionar os elétrons que serão detectados pelo Coletor de Faraday. Medindo a intensidade do feixe de elétrons atenuados, a SCTA pode ser obtida aplicando a Lei de Lambert Beer. Os dados foram obtidos através de um procedimento estatístico envolvendo uma série de 4 a 7 sessões de medidas, os valores obtidos foram utilizados para encontrar a SCT para uma determinada energia definida. Além das medidas experimentais, nós determinamos SCT utilizando a Regra da Aditividade. Nós também avaliamos nossos dados experimentais usando uma fórmula de dois parâmetros (Curva de Born) para cada gás. Nossos dados experimentais concordam com a maioria dos dados publicados na literatura. Não existem dados reportados na literatura de SCT para a molécula do Etanol (C2H5OH). / We have measured the absolute Total Cross Section (TCS) for methanol and ethanol molecules using an apparatus manufactured at the Molecular Spectroscopy Laboratory at DF/UFJF, which employ the linear transmission technique. The experimental data were taken at incident electron energies of 70, 80, 90, 100, 150, 200, 250, 300, 350, 400 and 500 eV for methanol and ethanol and also of 60 eV for ethanol. The energy resolution in all measurements was 0,6 eV (FWHM) and the overall systematic uncertainty at the TCS were evaluated to be less than 5%. The pressure range in the scattering cell was chosen between 1 and 4mTorr. Those electrons which passed the exit orifice of the chamber were discriminated with a 127o cylindrical energy selector coupled with an entrance set of electrostatic lenses and detected by a Faraday cup. Measuring the attenuation of intensity of the projectile-particle beam transmitted through the target volume, the absolute TCS for a given impact energy was derived from the Beer-Lambert law. The measurements were carried out for a given energy in a series of alt least 4 runs, each one taking at least 7 values and an averaging procedure was applied to derive the final total cross section at a particular energy. Besides the experimental measurements, we have additionally determined TCS using the Additivity Rule. We have also evaluated our experimental data using a fitting procedure with the Born-like formula containing two parameters for each gas. Our experimental data are in good agreement with the majority of previous measurements published in the literature. There are no previous reports of experimental electron scattering Total Cross Section C2H5OH in the literature.

Near Infrared (NIR) and Photoacoustic (PA) Imaging are promising imaging modalities that provides functional information of the soft biological tissues in-vivo, with applica-tions in breast and brain tissue imaging. These techniques use near infrared light in the wavelength range of (600 nm - 900 nm), giving an advantage of being non-ionizing imaging modality. This makes the prolong bed-side monitoring of tissue feasible, making them highly desirable medical imaging modalities in the clinic. The computation models that are deployed in these imaging scenarios are computationally demanding and often require a high performance computing systems to deploy them in real-time. This the-sis presents three computationally e cient models for near-infrared and photoacoustic imaging, without compromising the quality of measured functional properties, to make them more appealing in clinical scenarios. The attenuation of near-infrared (NIR) light intensity as it propagates in a turbid medium like biological tissue is described by modi ed the BeerLambert law (MBLL). The MBLL is generally used to quantify the changes in tissue chromophore concen-trations for NIR spectroscopic data analysis. Even though MBLL is e ective in terms of providing qualitative comparison, it su ers from its applicability across tissue types and tissue dimensions. A Lambert-W function-based modeling for light propagation in biological tissues is proposed and introduced, which is a generalized version of the Beer-Lambert model. The proposed modeling provides parametrization of tissue properties, which includes two attenuation coe cients o and . The model is validated against the Monte Carlo simulation, which is the gold standard for modeling NIR light propagation in biological tissue. Numerous human and animal tissues are included to validate the proposed empirical model, including an inhomogeneous adult human head model. The proposed model, which has a closed form (analytical), is rst of its kind in providing accurate modeling of NIR light propagation in biological tissues. Model based image reconstruction techniques yield better quantitative accuracy in photoacoustic (PA) image reconstruction, especially in limited data cases. An exponen-tial ltering of singular values is proposed for carrying out the image reconstruction in photoacoustic tomography. The results were compared with widely popular Tikhonov regularization, time reversal, and the state of the art least-squares QR based reconstruc-tion algorithms for three digital phantom cases with varying signal-to-noise ratios of data. The exponential ltering provided superior photoacoustic images of better quanti-tative accuracy. Moreover, the proposed ltering approach was observed to be less biased towards regularization parameter and did not come with any additional computational burden as it was implemented within the Tikhonov ltering framework. It was also shown that the standard Tikhonov ltering becomes an approximation to the proposed exponential ltering. The model based image reconstruction techniques for photoacoustic tomography re-quire an explicit regularization. An error estimate minimization based approach was proposed and developed for the determination of regularization parameter for PA imag-ing. The regularization was used within Lanczos bidiagonalization framework, which provides the advantage of dimensionality reduction for a large system of equations. The proposed method was computationally faster than the state of the art techniques and provided similar performance in terms of quantitative accuracy in reconstructed im-ages.The estimate can also be utilized in determining suitable regularization parameter for other popular techniques such as Tikhonov,exponential ltering and `1 norm based regularization methods.

The identification and quantification of atoms, molecules, or ions concentrations in gaseous samples are in great demand for medical, environmental, industrial, law enforcement and national security applications. These applications require in situ, high-resolution, non-destructive, sensitive, miniature, inexpensive, rapid detection, remotely accessed, real time and continuously operating chemical sensing devices. The aim of this work is to design a miniature optical sensing device that is capable of detecting and measuring chemical species, compatible with being integrated into a large variety of monitoring systems, and durable enough to be used under extreme conditions. The miniature optical sensor has been realized by employing technologies from the optical communication industry and spectroscopic methods and techniques. Fused silica capillary tubing along with standard communication optical fibers have been utilized to make miniature gas sensor based on near-infrared spectroscopy for acetylene gas detection. In this work, the basic principles of infrared spectroscopy are reviewed. Also, the principle of operation, fabrication, testing, and analysis of the proposed sensor are discussed in details. / Master of Science

No / Sedimentation of non-homogeneous systems is the typical phenomenon indicating the physical instability as a key measure to the quality control of the preparation products. Currently, the determination methods for the sedimentation of non-homogeneous preparations are based on manual measurement or semi-quantitative observation, lacking of either automation or quantitative dynamic analysis. The purpose of this research was to realize automatic and quantitative monitoring of the sedimentation dynamics for non-homogenous systems as suspension, emulsions at laboratory level. Non-contact measurement method has been established to determine the sedimentation behaviors in a standard quartz tube for sedimentation, with internal diameter and height 23 mm and 215 mm, respectively, with controlled temperature and light intensity. As high performance camera has been equipped, the sedimentation images with high spatial and temporal resolution could be acquired, which can continuously capture sedimentation images with the resolution of 2048 x 2048 pixel at a maximum rate of 60 slides/s. All the pictures were processed to extract the luminance matrix top-down along the fixed vertical midline of each picture, which implied sedimentation characteristics of the system at the moment the picture was taken. Combining all the luminance matrixes along vertical middle lines of the pictures, a time-luminance matrix profile was obtained. Digital image processing techniques were used to eliminate interference and establish a three-dimensional surface model of the sedimentation dynamics. Then, the derivative mutation algorithm has been developed for the intelligent identification of sedimentation interface with threshold optimization so as to quantitatively analyze the sedimentation dynamics with visualization. The sedimentation curve and sedimentation dynamic equation of the non-homogeneous system were finally outputted by numerical fitting. The methodology was validated for great significance in determinations of small volume samples, parallel control multiple batches, and long period of time automatic measurement. (C) 2015 Elsevier B.V. All rights reserved.

Cryo-electron microscopy (cryo-EM) has been established as the leading imaging technique for structural studies from small proteins to whole cells at a molecular level. The great advances in cryo-EM have led to the ability to provide unique insights into a wide variety of biological processes in a close to native, hydrated state at near-atomic resolutions. The developments of computational approaches have significantly contributed to the exciting achievements of cryo-EM. This dissertation emphasizes new approaches to address image processing problems in cryo-EM, including tilt series alignment evaluation, simultaneous determination of sample thickness, tilt, and electron mean free path based on Beer-Lambert law, Model-Based Iterative Reconstruction (MBIR) on tomographic data, minimization of objective lens astigmatism in instrument alignment and defocus and magnification dependent astigmatism of TEM images. The final goal of these methodological developments is to improve the 3D reconstruction of cryo-EM and visualize more detailed characterization.