Crystal growth, characterization and point contact spectroscopy on CuxTiSe₂

Various s e t s of single c rys t a l s and poly c rys t a l s of Cux TiSe2 were grown. X- r ay diffraction and ene rgy dispersive spe c t ros copy r e sul t s verified tha t the c rys t a l s were the cor r e c t compos i t ion and c rys t a l s t ruc tur e . Re s i s t ivi ty me a sur ement s and magne t i c sus c ept ibi l i ty me a sur ement s de t e rmined the supe r conduc t ing t r ans i t ion t empe r a tur e s for the c rys t a l s . The c rys t a l s in each growth had various supe r conduc t ing t r ans i t ion t empe r a tur e s . Also, the me a sur ement s indi c a t ed tha t the c rys t a l s were inhomogeneous. Point cont a c t spe c t ros copy expe r iment s were employed on various single c rys t a l s . Inspe c t ion of the da t a indi c a t ed tha t the ma t e r i a l ha s a single ene rgy gap . A progr am was bui l t ut i l i z ing the Levenbe rg-Ma rqua rdt me thod and theory on point cont a c t spe c t ros copy to de t e rmine the supe r conduc t ing ene rgy gap. Plot s of the supe r conduc t ing ene rgy gap a t various t empe r a tur e s were in di s agr e ement wi th wha t was expe c t ed for a convent iona l supe r conduc tor .

Infrared Spectroscopy of Gadolinium

Measurements of the optical reflectivity of the normal incident light along c-axis [0001] have been made on a Gadolinium single crystal, for temperatures between 50 K and room temperature just above the Curie temperature of Gd, which is 293 K. And covering the spectrum range between 100 -11000 cm-I . This work is the first study of Gd in the far infrared range. In fact it fills the gap below 0.2 eV which has never been measured before. Extreme attention was paid to the fact that Gadolinium is a very reactive metal with air. Thus, the sample was mechanically polished and carefully handled during the measurement. However, temperature dependent optical measurements have been made in the same frequency range for a sample of Gd2O3. For comparison, both samples of Gd and Gd2O3 were examined by X-Ray diffraction. XRD analysis showed that the sample was pure gadolinium and the oxide layer either does not exist, or is very thin. Furthermore, this fact was supported by the absence of any of Gd2O3 features in the Gd sample reflectivity. Kramers Kronig analysis was applied to extract the optical functions from the reflectance data. The optical conductivity shows a strong temperature dependence feature in the mid-infrared. This feature disappears completely at room temperature which supports a magnetic origin.

Improving Short DNA Sequence Alignment with Parallel Computing

Variations in different types of genomes have been found to be responsible for a large degree of physical diversity such as appearance and susceptibility to disease. Identification of genomic variations is difficult and can be facilitated through computational analysis of DNA sequences. Newly available technologies are able to sequence billions of DNA base pairs relatively quickly. These sequences can be used to identify variations within their specific genome but must be mapped to a reference sequence first. In order to align these sequences to a reference sequence, we require mapping algorithms that make use of approximate string matching and string indexing methods. To date, few mapping algorithms have been tailored to handle the massive amounts of output generated by newly available sequencing technologies. In otrder to handle this large amount of data, we modified the popular mapping software BWA to run in parallel using OpenMPI. Parallel BWA matches the efficiency of multithreaded BWA functions while providing efficient parallelism for BWA functions that do not currently support multithreading. Parallel BWA shows significant wall time speedup in comparison to multithreaded BWA on high-performance computing clusters, and will thus facilitate the analysis of genome sequencing data.

Transient and Pulsed Electron Paramagnetic Resonance Spectroscopy on Type I Photosynthetic Reaction Centers

Two time-resolved EPR techniques, have been used to study the light induced electron transfer(ET) in Type I photosynthetic reaction centers(RCs). First, pulsed EPR was used to compare PsaA-M688H and PsaB-M668H mutants of Chlamydomonas reinhardtii and Synechosystis sp. PCC 6803.The out-of-phase echo modulation curves combined with other EPR and optical data show that the effect of the mutations is species dependent. Second, transient and pulsed EPR data are presented which show that PsaA-A660N and PsaB-A640N mutations in C. reinhardtii alter the relative quantum yield of ET in the A- and B-branches of PS I. Third, transient EPR studies on RCs from Heliobacillus mobilis that have been exposed to oxygen show partial inhibition of ET. In the RCs in which ET still occurs, the ET kinetics and EPR spectra show evidence of oxidation of some but not all of the, BChl g and BChl g' to Chl a.

Electron Transfer Involving the Phylloquinone (A1) Cofactor of Photosystem I Examined with Time Resolved Absorbance and Electron Paramagnetic Resonance Spectroscopy

The dependence of the electron transfer (ET) rate on the Photosystem I (PSI) cofactor phylloquinone (A1) is studied by time-resolved absorbance and electron paramagnetic resonance (EPR) spectroscopy. Two active branches (A and B) of electron transfer converge to the FX cofactor from the A1A and A1B quinone. The work described in Chapter 5 investigates the single hydrogen bond from the amino acid residue PsaA-L722 backbone nitrogen to A1A for its effect on the electron transfer rate to FX. Room temperature transient EPR measurements show an increase in the rate for the A1A- to FX for the PsaA-L722T mutant and an increased hyperfine coupling to the 2-methyl group of A1A when compared to wild type. The Arrhenius plot of the A1A- to FX ET in the PsaA-L722T mutant suggests that the increased rate is probably the result of a slight change in the electronic coupling between A1A- and FX. The reasons for the non-Arrhenius behavior are discussed. The work discussed in Chapter 6 investigates the directionality of ET at low temperature by blocking ET to the iron-sulfur clusters FX, FA and FB in the menB deletion mutant strain of Synechocyctis sp. PCC 6803, which is unable to synthesize phylloquinone, by incorporating the high midpoint potential (49 mV vs SHE) 2,3-dichloro-1,4-naphthoquinone (Cl2NQ) into the A1A and A1B binding sites. Various EPR spectroscopic techniques were implemented to differentiate between the spectral features created from A and B- branch electron transfer. The implications of this result for the directionality of electron transfer in PS I are discussed. The work discussed in Chapter 7 was done to study the dependence of the heterogeneous ET at low temperature on A1 midpoint potential. The menB PSI mutant contains plastiquinone-9 in the A1 binding site. The solution midpoint potential of the quinone measures 100 mV more positive then wild-type phylloquinone. The irreversible ET to the terminal acceptors FA and FB at low temperature is not controlled by the forward step from A1 to FX as expected due to the thermodynamic differences of the A1 cofactor in the two active branches A and B. Alternatives for the ET heterogeneity are discussed.

Study of the diffusion in polymer solutions and hydrogels by NMR spectroscopy and NMR imaging

Afin d'étudier la diffusion et la libération de molécules de tailles inférieures dans un gel polymère, les coefficients d'auto-diffusion d'une série de polymères en étoile avec un noyau d'acide cholique et quatre branches de poly(éthylène glycol) (PEG) ont été déterminés par spectroscopie RMN à gradient de champ pulsé dans des solutions aqueuses et des gels de poly(alcool vinylique). Les coefficients de diffusion obtenus ont été comparés avec ceux des PEGs linéaires et dendritiques pour étudier l'effet de l'architecture des polymères. Les polymères en étoile amphiphiles ont des profils de diffusion en fonction de la concentration similaires à leurs homologues linéaires dans le régime dilué. Ils diffusent plus lentement dans le régime semi-dilué en raison de leur noyau hydrophobe. Leurs conformations en solution ont été étudiées par des mesures de temps de relaxation spin-réseau T1 du noyau et des branches. L'imagerie RMN a été utilisée pour étudier le gonflement des comprimés polymères et la diffusion dans la matrice polymère. Les comprimés étaient constitués d'amidon à haute teneur en amylose et chargés avec de l'acétaminophène (de 10 à 40% en poids). Le gonflement des comprimés, ainsi que l'absorption et la diffusion de l'eau, augmentent avec la teneur en médicament, tandis que le pourcentage de libération du médicament est similaire pour tous les comprimés. Le gonflement in vitro des comprimés d'un complexe polyélectrolyte à base d'amidon carboxyméthylé et de chitosane a également été étudié par imagerie RMN. Ces comprimés sont sensibles au pH : ils gonflent beaucoup plus dans les milieux acides que dans les milieux neutres en raison de la dissociation des deux composants et de la protonation des chaînes du chitosane. La comparaison des résultats avec ceux d'amidon à haute teneur en amylose indique que les deux matrices ont des gonflements et des profils de libération du médicament semblables dans les milieux neutres, alors que les comprimés complexes gonflent plus dans les milieux acides en raison de la dissociation du chitosane et de l'amidon.

In vivo phosphorus spectroscopy in human subjects on a clinical 3T MRI system

Alors que l’Imagerie par résonance magnétique (IRM) permet d’obtenir un large éventail de données anatomiques et fonctionnelles, les scanneurs cliniques sont généralement restreints à l’utilisation du proton pour leurs images et leurs applications spectroscopiques. Le phosphore jouant un rôle prépondérant dans le métabolisme énergétique, l’utilisation de cet atome en spectroscopie RM présente un énorme avantage dans l’observation du corps humain. Cela représente un certain nombre de déEis techniques à relever dus à la faible concentration de phosphore et sa fréquence de résonance différente. L’objectif de ce projet a été de développer la capacité à réaliser des expériences de spectroscopie phosphore sur un scanneur IRM clinique de 3 Tesla. Nous présentons ici les différentes étapes nécessaires à la conception et la validation d’une antenne IRM syntonisée à la fréquence du phosphore. Nous présentons aussi l’information relative à réalisation de fantômes utilisés dans les tests de validation et la calibration. Finalement, nous présentons les résultats préliminaires d’acquisitions spectroscopiques sur un muscle humain permettant d’identiEier les différents métabolites phosphorylés à haute énergie. Ces résultats s’inscrivent dans un projet de plus grande envergure où les impacts des changements du métabolisme énergétique sont étudiés en relation avec l’âge et les pathologies.

Dynamic magnetic resonance spectroscopy of phosphate energetics during muscle exercise and recovery

Entailing of phosphorus exchanges in most bio-chemicals as a key factor in disease, increases researcher’s interest to develop the technologies capable of detecting this metabolite. Phosphorus magnetic resonance spectroscopy is able to detect key metabolites in a non-invasive manner. Particularly, it offers the ability to measure the dynamic rate of phosphocreatine(PCr) degeneration through the exercise and recovery. This metric as a valid indication of mitochondrial oxidative metabolism in muscle, differentiate between normal and pathological state. To do magnetic resonance imaging and spectroscopy, clinical research tools provide a wide variety of anatomical and functional contrasts, however they are typically restricted to the tissues containing water or hydrogen atoms and they are still blind to the biochemicals of other atoms of interests. Through this project we intended to obtain the phosphorus spectrum in human body – specificadenerativelly in muscle – using 31P spectroscopy. To do so a double loop RF surface coil, tuned to phosphorus frequency, is designed and fabricated using bench work facilities and then validated through in vitro spectroscopy using 3 Tesla Siemens scanner. We acquired in vitro as well as in vivo phosphorus spectrum in a 100 mM potassium phosphate phantom and human calf muscle in rest-exercise-recovery phase in a 3T MR scanner. The spectrum demonstrates the main constituent in high-energy phosphate metabolism. We also observed the dynamic variation of PCr for five young healthy subjects who performed planter flexions using resistance band during exercise and recovery. The took steps in this project pave the way for future application of spectroscopic quantification of phosphate metabolism in patients affected by carotid artery disease as well as in age-matched control subjects.

Non-Destructive Evaluation of Ion-Implanted Semiconductor Thin Films Using Photothermal Deflections Spectroscopy

Materials and equipment which fail to achieve the design requirements or projected life due to undetected defects may require expensive repair or early replacement. Such defects may also be the cause of unsafe conditions or catastrophic unexpected failure, and will lead to loss of revenue due to plant shutdown. Non-Destructive Evaluation (NDE) / Non Destructive Testing (NDT) is used for the examination of materials and components without changing or destroying their usefulness. NDT can be applied to each stage of a system’s construction, to monitor the integrity of the system or structure throughout its life.

Characterization of radio frequency plasma using Langmuir probe and optical emission spectroscopy

The radio frequency plasma generated during the sputtering of Indium Tin Oxide target using Argon was analyzed by Langmuir probe and optical-emission spectroscopy. The basic plasma parameters such as electron temperature and ion density were evaluated. These studies were carried out by varying the RF power from 20 to 50 W. A linear increase in ion density and an exponential decrease in electron temperature with rf power were observed. The measured plasma parameters were then correlated with the properties of ITO thin films deposited under similar plasma conditions.

Tunable diode Laser Absorption Spectroscopy ,Nir Overtone and Life Studies of Some Organic Compound

The present work is mainly concentrated on setting up a NIR tunable diode laser absorption (TDLA) spectrometer for high-resolution molecular spectroscopic studies. For successfully recording the high-resolution tunable diode laser spectrum, various experimental considerations are to be taken into account like the setup should be free from mechanical vibrations, sample should be kept at a low pressure, laser should be in a single mode operation etc. The present experimental set up considers all these factors. It is to be mentioned here that the setting up of a high resolution NIR TDLA spectrometer is a novel experiment requiring much effort and patience. The analysis of near infrared (NIR) vibrational overtone spectra of some substituted benzene compounds using local mode model forms another part of the present work. An attempt is made to record the pulsed laser induced fluorescence/Raman spectra of some organic compounds. A Q-switched Nd:YAG laser is used as the excitation source. A TRIAX monochromator and CCD detector is used for the spectral recording. The observed fluorescence emission for carbon disulphide is centered at 680 nm; this is assigned as due to the n, p* transition. Aniline also shows a broad fluorescence emission centered at 725 nm, which is due to the p,p* transition. The pulsed laser Raman spectra of some organic compounds are also recorded using the same experimental setup. The calibration of the set up is done using the laser Raman spectra of carbon tetrachloride and carbon disulphide. The observed laser Raman spectra for aniline, o-chloroaniline and m-chlorotoluene show peaks characteristics of the aromatic ring in common and the characteristics peaks due to the substitutuent groups. Some new peaks corresponding to low-lying vibrations of these molecules are also assigned

Photodiagnosis of Oral Malignancy using Laser-Induced Fluorescence and Diffuse Reflectance Spectroscopy

Biophotonics Laboratory,Centre for Earth Science Studies

Characterization of Photonic Materials Using Thermal Lens Technique

The subject of Photonics is concerned with the generation,control and utilization of photons for performing a variety of tasks.It came to existence as a consequence of the harmonious fusion of optical methods with electronic technology.Wide spread use of laser based methods in electronics is slowly replacing elecrtons with photons in the field of Communication,Control and Computing .Therefore,there is a need to promote the R & D activities in the area of Photonics and to generate well trained manpower in laser related fields.Development and characterization of photonic materials is an important subject of research in the field of Photonics.Optical and thermal characterization of photonic materials using thermal lens technique is a PhD thesis in the field of Photonics in which the author describes how thermal lens effect can be used to characterize themal and optical properties of photonic materials.Plausibility of thermal lens based logic gates is also presented in this thesis.

Dynamics of laser produced silver plasma under film deposition conditions studied using optical emission spectroscopy

Laser produced plasma from silver is generated using a Q-switched Nd:YAG laser. Optical emission spectroscopy is used to carry out time of flight (TOF) analysis of atomic particles. An anomalous double peak profile in the TOF distribution is observed at low pressure. A collection of slower species emerge at reduced pressure below 4 X lO-3 mbar and this species has a greater velocity spread. At high pressure the plasma expansion follows the shockwave model with cylindrical symmetry whereas at reduced pressure it shows unsteady adiabatic expansion (UAE). During UAE the species show a parabolic increases in the expansion time with radial distance whereas during shock wave expansion the exponent is less than one. The angular distribution of the ablated species in the plume is obtained from the measurement of optical density of thin films deposited on to glass substrates kept perpendicular to the plume. There is a sharp variation in the film thickness away from the film centre due to asymmetries in the plume.