Surface plasmon fluorescence spectroscopy and microscopy studies for biomolecular interaction studies

ABSTARCT Biotechnology has enabled the modification of agricultural materials in a very precise way. Crops have been modified through the insertion of new traits or the inhibition of existing gene functions, named Genetically Modified Organism (GMO), and resulted in improved tolerance of herbicide and/or increased resistance against pests, viruses and fungi. Commercial cultivation of GMO started in 1996 and increased rapidly in 2003 according to a recently released report by the International Service for the Acquisition of Agri-Biotech Applications (ISAAA), depicted continuing consumer resistance in Europe and other part of the world. Upon these developments, the European Union regulations mandated labeling of GMOs containing food and as a consequence, the labeling of GMO containing product in the case of exceeding the1% threshold of alien DNA is required. The aim of the study is to be able to detect and quantify the GMO from the mixture of natural food components. The surface plasmon resonance (SPR) technique combined with fluorescence was used for this purpose. During the presented studies, two key issues are addressed and tried to solve; what is the best strategy to design and built an interfacial architecture of a probe oligonucletide layer either on a two dimensional surface or on an array platform; and what is the best detection method allowing for a sensitive monitoring of the hybridisation events. The study includes two parts: first part includes characterization of different PNAs on a 2D planar surface by defining affinity constants using the very well established optical method “Surface Plasmon Fluorescence Spectroscopy”(SPFS) and on the array platform by “Surface Plasmon Fluorescence Microscopy” (SPFM), and at the end comparison of the sensitivity of these two techniques. The second part is composed of detection of alien DNA in food components by using DNA and PNA catcher probes on the array platform in real-time by SPFM.

Feasibility studies of the pp pi 0 e + e - electromagnetic channel at PANDA

Among all possible realizations of quark and antiquark assembly, the nucleon (the proton and the neutron) is the most stable of all hadrons and consequently has been the subject of intensive studies. Mass, shape, radius and more complex representations of its internal structure are measured since several decades using different probes. The proton (spin 1/2) is described by the electric GE and magnetic GM form factors which characterise its internal structure. The simplest way to measure the proton form factors consists in measuring the angular distribution of the electron-proton elastic scattering accessing the so-called Space-Like region where q2 < 0. Using the crossed channel antiproton proton <--> e+e-, one accesses another kinematical region, the so-called Time-Like region where q2 > 0. However, due to the antiproton proton <--> e+e- threshold q2th, only the kinematical domain q2 > q2th > 0 is available. To access the unphysical region, one may use the antiproton proton --> pi0 e+ e- reaction where the pi0 takes away a part of the system energy allowing q2 to be varied between q2th and almost 0. This thesis aims to show the feasibility of such measurements with the PANDA detector which will be installed on the new high intensity antiproton ring at the FAIR facility at Darmstadt. To describe the antiproton proton --> pi0 e+ e- reaction, a Lagrangian based approach is developed. The 5-fold differential cross section is determined and related to linear combinations of hadronic tensors. Under the assumption of one nucleon exchange, the hadronic tensors are expressed in terms of the 2 complex proton electromagnetic form factors. An extraction method which provides an access to the proton electromagnetic form factor ratio R = |GE|/|GM| and for the first time in an unpolarized experiment to the cosine of the phase difference is developed. Such measurements have never been performed in the unphysical region up to now. Extended simulations were performed to show how the ratio R and the cosine can be extracted from the positron angular distribution. Furthermore, a model is developed for the antiproton proton --> pi0 pi+ pi- background reaction considered as the most dangerous one. The background to signal cross section ratio was estimated under different cut combinations of the particle identification information from the different detectors and of the kinematic fits. The background contribution can be reduced to the percent level or even less. The corresponding signal efficiency ranges from a few % to 30%. The precision on the determination of the ratio R and of the cosine is determined using the expected counting rates via Monte Carlo method. A part of this thesis is also dedicated to more technical work with the study of the prototype of the electromagnetic calorimeter and the determination of its resolution.

Feasibility studies for accessing nucleon structure observables with the PANDA experiment at the future FAIR facility

The availability of a high-intensity antiproton beam with momentum up to 15,GeV/c at the future FAIR will open a unique opportunity to investigate wide areas of nuclear physics with the $overline{P}$ANDA (anti{$overline{P}$}roton ANnihilations at DArmstadt) detector. Part of these investigations concern the Electromagnetic Form Factors of the proton in the time-like region and the study of the Transition Distribution Amplitudes, for which feasibility studies have been performed in this Thesis. rnMoreover, simulations to study the efficiency and the energy resolution of the backward endcap of the electromagnetic calorimeter of $overline{P}$ANDA are presented. This detector is crucial especially for the reconstruction of processes like $bar pprightarrow e^+ e^- pi^0$, investigated in this work. Different arrangements of dead material were studied. The results show that both, the efficiency and the energy resolution of the backward endcap of the electromagnetic calorimeter fullfill the requirements for the detection of backward particles, and that this detector is necessary for the reconstruction of the channels of interest. rnrnThe study of the annihilation channel $bar pprightarrow e^+ e^-$ will improve the knowledge of the Electromagnetic Form Factors in the time-like region, and will help to understand their connection with the Electromagnetic Form Factors in the space-like region. In this Thesis the feasibility of a measurement of the $bar pprightarrow e^+ e^-$ cross section with $overline{P}$ANDA is studied using Monte-Carlo simulations. The major background channel $bar pprightarrow pi^+ pi^-$ is taken into account. The results show a $10^9$ background suppression factor, which assure a sufficiently clean signal with less than 0.1% background contamination. The signal can be measured with an efficiency greater than 30% up to $s=14$,(GeV/c)$^2$. The Electromagnetic Form Factors are extracted from the reconstructed signal and corrected angular distribution. Above this $s$ limit, the low cross section will not allow the direct extraction of the Electromagnetic Form Factors. However, the total cross section can still be measured and an extraction of the Electromagnetic Form Factors is possible considering certain assumptions on the ratio between the electric and magnetic contributions.rnrnThe Transition Distribution Amplitudes are new non-perturbative objects describing the transition between a baryon and a meson. They are accessible in hard exclusive processes like $bar pprightarrow e^+ e^- pi^0$. The study of this process with $overline{P}$ANDA will test the Transition Distribution Amplitudes approach. This work includes a feasibility study for measuring this channel with $overline{P}$ANDA. The main background reaction is here $bar pprightarrow pi^+ pi^- pi^0$. A background suppression factor of $10^8$ has been achieved while keeping a signal efficiency above 20%.rnrnrnPart of this work has been published in the European Physics Journal A 44, 373-384 (2010).rn