Novel fluorescence detection technique for non-contact temperature sensing in microchip PCR

DNA amplification using Polymerase Chain Reaction (PCR) in a small volume is used in Lab-on-a-chip systems involving DNA manipulation. For few microliters of volume of liquid, it becomes difficult to measure and monitor the thermal profile accurately and reproducibly, which is an essential requirement for successful amplification. Conventional temperature sensors are either not biocompatible or too large and hence positioned away from the liquid leading to calibration errors. In this work we present a fluorescence based detection technique that is completely biocompatible and measures directly the liquid temperature. PCR is demonstrated in a 3 ILL silicon-glass microfabricated device using non-contact induction heating whose temperature is controlled using fluorescence feedback from SYBR green I dye molecules intercalated within sensor DNA. The performance is compared with temperature feedback using a thermocouple sensor. Melting curve followed by gel electrophoresis is used to confirm product specificity after the PCR cycles. (c) 2007 Elsevier B.V. All rights reserved.

Non-Gaussian Cosmological Perturbations from Hybrid Inflation and Preheating

This thesis consists of four research papers and an introduction providing some background. The structure in the universe is generally considered to originate from quantum fluctuations in the very early universe. The standard lore of cosmology states that the primordial perturbations are almost scale-invariant, adiabatic, and Gaussian. A snapshot of the structure from the time when the universe became transparent can be seen in the cosmic microwave background (CMB). For a long time mainly the power spectrum of the CMB temperature fluctuations has been used to obtain observational constraints, especially on deviations from scale-invariance and pure adiabacity. Non-Gaussian perturbations provide a novel and very promising way to test theoretical predictions. They probe beyond the power spectrum, or two point correlator, since non-Gaussianity involves higher order statistics. The thesis concentrates on the non-Gaussian perturbations arising in several situations involving two scalar fields, namely, hybrid inflation and various forms of preheating. First we go through some basic concepts -- such as the cosmological inflation, reheating and preheating, and the role of scalar fields during inflation -- which are necessary for the understanding of the research papers. We also review the standard linear cosmological perturbation theory. The second order perturbation theory formalism for two scalar fields is developed. We explain what is meant by non-Gaussian perturbations, and discuss some difficulties in parametrisation and observation. In particular, we concentrate on the nonlinearity parameter. The prospects of observing non-Gaussianity are briefly discussed. We apply the formalism and calculate the evolution of the second order curvature perturbation during hybrid inflation. We estimate the amount of non-Gaussianity in the model and find that there is a possibility for an observational effect. The non-Gaussianity arising in preheating is also studied. We find that the level produced by the simplest model of instant preheating is insignificant, whereas standard preheating with parametric resonance as well as tachyonic preheating are prone to easily saturate and even exceed the observational limits. We also mention other approaches to the study of primordial non-Gaussianities, which differ from the perturbation theory method chosen in the thesis work.

Non-Gaussianities and Preheating from N-flation and Magnetogenesis via rotating cosmic string loops

In this thesis we examine multi-field inflationary models of the early Universe. Since non-Gaussianities may allow for the possibility to discriminate between models of inflation, we compute deviations from a Gaussian spectrum of primordial perturbations by extending the delta-N formalism. We use N-flation as a concrete model; our findings show that these models are generically indistinguishable as long as the slow roll approximation is still valid. Besides computing non-Guassinities, we also investigate Preheating after multi-field inflation. Within the framework of N-flation, we find that preheating via parametric resonance is suppressed, an indication that it is the old theory of preheating that is applicable. In addition to studying non-Gaussianities and preheatng in multi-field inflationary models, we study magnetogenesis in the early universe. To this aim, we propose a mechanism to generate primordial magnetic fields via rotating cosmic string loops. Magnetic fields in the micro-Gauss range have been observed in galaxies and clusters, but their origin has remained elusive. We consider a network of strings and find that rotating cosmic string loops, which are continuously produced in such networks, are viable candidates for magnetogenesis with relevant strength and length scales, provided we use a high string tension and an efficient dynamo.

Characterization of non-imaging semiconductor X-ray solar monitors

The first observations of solar X-rays date back to late 1940 s. In order to observe solar X-rays the instruments have to be lifted above the Earth s atmosphere, since all high energy radiation from the space is almost totally attenuated by it. This is a good thing for all living creatures, but bad for X-ray astronomers. Detectors observing X-ray emission from space must be placed on-board satellites, which makes this particular discipline of astronomy technologically and operationally demanding, as well as very expensive. In this thesis, I have focused on detectors dedicated to observing solar X-rays in the energy range 1-20 keV. The purpose of these detectors was to measure solar X-rays simultaneously with another X-ray spectrometer measuring fluorescence X-ray emission from the Moon surface. The X-ray fluorescence emission is induced by the primary solar X-rays. If the elemental abundances on the Moon were to be determined with fluorescence analysis methods, the shape and intensity of the simultaneous solar X-ray spectrum must be known. The aim of this thesis is to describe the characterization and operation of our X-ray instruments on-board two Moon missions, SMART-1 and Chandrayaan-1. Also the independent solar science performance of these two almost similar X-ray spectrometers is described. These detectors have the following two features in common. Firstly, the primary detection element is made of a single crystal silicon diode. Secondly, the field of view is circular and very large. The data obtained from these detectors are spectra with a 16 second time resolution. Before launching an instrument into space, its performance must be characterized by ground calibrations. The basic operation of these detectors and their ground calibrations are described in detail. Two C-flares are analyzed as examples for introducing the spectral fitting process. The first flare analysis shows the fit of a single spectrum of the C1-flare obtained during the peak phase. The other analysis example shows how to derive the time evolution of fluxes, emission measures (EM) and temperatures through the whole single C4 flare with the time resolution of 16 s. The preparatory data analysis procedures are also introduced in detail. These are required in spectral fittings of the data. A new solar monitor design equipped with a concentrator optics and a moderate size of field of view is also introduced.

Context-based assessment: Creating opportunities for resonance between classroom fields and societal fields

There is on-going international interest in the relationships between assessment instruments, students’ understanding of science concepts and context-based curriculum approaches. This study extends earlier research showing that students can develop connections between contexts and concepts – called fluid transitions – when studying context-based courses. We provide an in-depth investigation of one student’s experiences with multiple contextual assessment instruments that were associated with a context-based course. We analyzed the student’s responses to context-based assessment instruments to determine the extent to which contextual tests, reports of field investigations, and extended experimental investigations afforded her opportunities to make connections between contexts and concepts. A system of categorizing student responses was developed that can inform other educators when analyzing student responses to contextual assessment. We also refine the theoretical construct of fluid transitions that informed the study initially. Implications for curriculum and assessment design are provided in light of the findings.

Structure formation in short designed peptides probed by proteolytic cleavage

The formation of local structure, in short peptides has been probed by examining cleavage patterns and rates of proteolysis of designed sequences with a high tendency to form β-hairpin structures. Three model sequences which bear fluorescence donor and acceptor groups have been investigated: Dab-Gaba-Lys-Pro-Leu-Gly-Lys-Val-Xxx-Yyy-Glu-Val-Ala-Ala-Cys-Lys-NH2 ï EDANS Xxx-Yyy: Peptide 1=DPro-LPro, Peptide 2=DPro-Gly, Peptide 3=Leu-Ala Fluorescence resonance energy transfer (FRET) provides a convenient probe for peptide cleavage. MALDI mass spectrometry has been used to probe sites of cleavage and CD spectroscopy to access the overall backbone conformation using analog sequences, which lack strongly absorbing donor and acceptor groups. The proteases trypsin, subtilisin, collagenase, elastase, proteinase K and thermolysin were used for proteolysis and the rates of cleavage determined. Peptide 3 is the most susceptible to cleavage by all the enzymes except thermolysin, which cleaves all three peptides at comparable rates. Peptides 1 and 2 are completely resistant to the action of trypsin, suggesting that β-turn formation acts as a deterrent to proteolytic cleavage.

Manifestation of conical intersections in resonance Raman intensities

This paper deals with the manifestations of conical intersections (CIs), unequivocal spectroscopic signatures of which are still elusive, in the resonance Raman intensities. In particular, the results of our calculations on the `two state-two vibrational mode' and the `two state-three vibrational mode' models are presented. The models comprise two excited states of different spatial symmetry, one bright and one dark, which are coupled by a nontotally symmetric mode while the energy gap between them is tuned by one/two totally symmetric modes. Time dependent theory for vibronically coupled states is employed for the calculation and analysis of Raman excitation profiles (REPs). The manifestation of intersections in REPs is studied by extensive modelm calculations and the results of two specific models are presented. Themfeasibility of using REPs to probe the role of CIs in polyatomic systems is ascertained by multimode calculations on two polyatomic systems viz., pyrazine and trans-azobenzene. The study also notes the importance of the pump excitation wavelength dependence in a femtosecond time-resolved experiment probing the intersection-induced nonadiabatic dynamics. Copyright (C) 2009 John Wiley & Sons, Ltd.

Search for a Fermiophobic Higgs Boson Decaying into Diphotons in p p-bar Collisions at sqrt{s} = 1.96 TeV

A search for a narrow diphoton mass resonance is presented based on data from 3.0 fb^{-1} of integrated luminosity from p-bar p collisions at sqrt{s} = 1.96 TeV collected by the CDF experiment. No evidence of a resonance in the diphoton mass spectrum is observed, and upper limits are set on the cross section times branching fraction of the resonant state as a function of Higgs boson mass. The resulting limits exclude Higgs bosons with masses below 106 GeV at a 95% Bayesian credibility level (C.L.) for one fermiophobic benchmark model.

Genetic Mechanisms Underlying Autism Spectrum Disorders

Autism is a childhood-onset developmental disorder characterized by deficits in reciprocal social interaction, verbal and non-verbal communication, and dependence on routines and rituals. It belongs to a spectrum of disorders (autism spectrum disorders, ASDs) which share core symptoms but show considerable variation in severity. The whole spectrum affects 0.6-0.7% of children worldwide, inducing a substantial public health burden and causing suffering to the affected families. Despite having a very high heritability, ASDs have shown exceptional genetic heterogeneity, which has complicated the identification of risk variants and left the etiology largely unknown. However, recent studies suggest that rare, family-specific factors contribute significantly to the genetic basis of ASDs. In this study, we investigated the role of DISC1 (Disrupted-in-schizophrenia-1) in ASDs, and identified association with markers and haplotypes previously associated with psychiatric phenotypes. We identified four polymorphic micro-RNA target sites in the 3 UTR of DISC1, and showed that hsa-miR-559 regulates DISC1 expression in vitro in an allele-specific manner. We also analyzed an extended autism pedigree with genealogical roots in Central Finland reaching back to the 17th century. To take advantage of the beneficial characteristics of population isolates to gene mapping and reduced genetic heterogeneity observed in distantly related individuals, we performed a microsatellite-based genome-wide screen for linkage and linkage disequilibrium in this pedigree. We identified a putative autism susceptibility locus on chromosome 19p13.3 and obtained further support for previously reported loci at 1q23 and 15q11-q13. To follow-up these findings, we extended our study sample from the same sub-isolate and initiated a genome-wide analysis of homozygosity and allelic sharing using high-density SNP markers. We identified a small number of haplotypes shared by different subsets of the genealogically connected cases, along with convergent biological pathways from SNP and gene expression data, which highlighted axon guidance molecules in the pathogenesis of ASDs. In conclusion, the results obtained in this thesis show that multiple distinct genetic variants are responsible for the ASD phenotype even within single pedigrees from an isolated population. We suggest that targeted resequencing of the shared haplotypes, linkage regions, and other susceptibility loci is essential to identify the causal variants. We also report a possible micro-RNA mediated regulatory mechanism, which might partially explain the wide-range neurobiological effects of the DISC1 gene.

Instability of Coupled Longitudinal and Transverse Electromagnetic Modes of Wave‐Propagation in Bounded Streaming Plasmas

The instability of coupled longitudinal and transverse electromagnetic modes associated with long wavelengths is studied in bounded streaming plasmas. The main conclusions are as follows: (i) For long waves for which O (k 2)=0, in the absence of relative streaming motion of electrons and ions and aωp/c<0.66, the whole spectrum of harmonic waves is excited due to finite temperature and boundary effects consisting of two subseries. One of these subseries can be identified with Tonks-Dattner resonance oscillations for the electrons, and arises primarily due to the electrons with frequencies greater than the electrostatic plasma frequency corresponding to the electron density in the midplane in the undisturbed state. The other series arises primarily due to ion motion. When aωp/c>0.66, in addition to the above spectrum of harmonic waves, the system admits an infinite number of growing and decaying waves. The instability associated with these modes is found to arise due to the interaction of the waves inside the plasma with the external electromagnetic field. (ii) For modes with comparatively shorter wavelengths for which O (k3)=0, the coupling due to finite temperature sets in, and it is found that the two series of harmonic waves obtained in (i) deriving energy from the transverse modes also become unstable. Thus, for these wavelengths the system admits three sets of growing and decaying modes, first two for all values of aωp/c and the third for (aωp/c) > 0.66. (iii) The presence of streaming velocities introduces various other coupling mechanisms, and we find that even for the wavelengths for which O (k2)=0, we get three sets of growing and decaying waves. The numerical values for the growth rates show that the streaming velocities enhance the growth rates of instability significantly.