Coherence (physics)

Summary

In physics, coherence expresses the potential for two waves to interfere. Two monochromatic beams from a single source always interfere. Physical sources are not strictly monochromatic: they may be partly coherent. Beams from different sources are mutually incoherent. When interfering, two waves add together to create a wave of greater amplitude than either one (constructive interference) or subtract from each other to create a wave of minima which may be zero (destructive interference), depending on their relative phase. Constructive or destructive interference are limit cases, and two waves always interfere, even if the result of the addition is complicated or not remarkable. Two waves with constant relative phase will be coherent. The amount of coherence can readily be measured by the interference visibility, which looks at the size of the interference fringes relative to the input waves (as the phase offset is varied); a precise mat

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3D Reconstruction of Optical Diffraction Tomography Based on a Neural Network Model

Morteza Hasani Shoreh

Optical tomography has been widely investigated for biomedical imaging applications. In recent years, it has been combined with digital holography and has been employed to produce high quality images of phase objects such as cells. In this Thesis, we look into some of the newest optical Diffraction Tomography (DT) based techniques to solve Three-Dimensional (3D) reconstruction problems and discuss and compare some of the leading ideas and papers. Then we propose a neural-network-based algorithm to solve this problem and apply it on both synthetic and biological samples. Conventional phase tomography with coherent light and off axis recording is performed. The Beam Propagation Method (BPM) is used to model scattering and each x-y plane is modeled by a layer of neurons in the BPM. The network's output (simulated data) is compared to the experimental measurements and the error is used for correcting the weights of the neurons (the refractive indices of the nodes) using standard error back-propagation techniques. The proposed algorithm is detailed and investigated. Then, we look into resolution-conserving regularization and discuss a method for selecting regularizing parameters. In addition, the local minima and phase unwrapping problems are discussed and ways of avoiding them are investigated. It is shown that the proposed learning tomography (LT) achieves better performance than other techniques such as, DT especially when insufficient number or incomplete set of measurements is available. We also explore the role of regularization in obtaining higher fidelity images without losing resolution. It is experimentally shown that due to overcoming multiple scattering, the LT reconstruction greatly outperforms the DT when the sample contains two or more layers of cells or beads. Then, reconstruction using intensity measurements is investigated. 3D reconstruction of a live cell during apoptosis is presented in a time-lapse format. At the end, we present a final comparison with leading papers and commercially available systems. It is shown that -compared to other existing algorithms- the results of the proposed method have better quality. In particular, parasitic granular structures and the missing cone artifact are improved. Overall, the perspectives of our approach are pretty rich for high-resolution tomographic imaging in a range of practical applications.

EPFL2018

Chemical exchange in proteins

Mariachiara Verde

Nuclear Magnetic Resonance (NMR) spectroscopy offers many ways to investigate dynamic properties of molecules. A wide variety of experimental techniques can probe molecular dynamics on time scales that range from 10-12 to 103 seconds. Many lines of evidence point to the existence of large scale dynamics on milli- to microsecond time scale that are essential to molecular function. Those conformational motions can give rise to chemical exchange effects. So far in the literature two methods have been mainly used to study such processes: CPMG echo trains and R1ρ spin-lock relaxation experiments. The former is suited to investigate processes on the millisecond time scale, whereas R1ρ can probe processes ranging from milliseconds down to ca. microseconds. CPMG and R1ρ studies of the relaxation rates of single quantum (SQ) coherences can be complemented by multiple quantum coherence (MQ) coherences experiments which can provide information whether two (or more) spins are affected simultaneously by chemical exchange. The goal of this thesis is to characterize chemical exchange in proteins by new (Heteronuclear Double Resonance, HDR) and existing (relaxation compensated CPMG) methods. The presence of chemical exchange has been identified in APO-rMUP using the classical CPMG experiment on single quantum 15N magnetization, whereas in HOLO-rMUP no presence of chemical exchange has been found. Most of the thesis is dedicated to the analysis and the application of a new method, HDR, which is designed to determine the cross-relaxation rates between MQ operators. In fact, in heteronuclear systems, correlated chemical exchange contributes to cross-relaxation between MQ coherences 2IxSx and 2IySy. This method, based on MLEV-32 and WALTZ-16 used in double resonance mode, is designed to effectively preserve all relevant MQ coherences simultaneously so that the interconversion between MQ operators can only arise through cross-relaxation. This is an essential requirement if we want to measure, for example, small cross-relaxation rates between MQ operators. We have treated the effects of coherent evolution during the HDR sequences by numerical simulations and Average Hamiltonian Theory (AHT) showing that, under most conditions, the dynamics of MQ coherences is not affected by coherent evolution. This result is proved experimentally on the 15N-1H pair of selectively deuterated tBoc-glycine. The effect of relaxation during HDR sequences leads to an effective relaxation superoperator which is explored by numerical simulations and predicted by Average Liouvillian Theory (ALT). Finally the HDR MLEV-32 sequence is applied to amide 1H-15N pairs in ubiquitin and KIX proteins. In the case of ubiquitin the HDR MLEV-32 experiments and the numerical simulations run with parameters obtained from the literature are in good agreement, suggesting that HDR sequences could be used as a tool to obtain information about the dynamics of the system.

EPFL2009

High Tc superconductivity in cuprates is still an unresolved topic, and one particular challenge is why in-plane compressive strain enhances Tc in ultra thin LSCO-214 films (< 40nm), whilst tensile strain diminishes it. Especially intriguing is whether altering this strain at a given doping has an effect on T* (pseudogap) or Tc (condensation/phase coherence). As the ratio between T* and Tc is so high, we systematically grew a series of BSCCO-2201 films by in house pulsed laser deposition (PLD), and then thoroughly analysed these films with X-Rays, four point resistivity measurements and XPS. We succeeded to induce strain into the films; however, the strain was lost in the annealing process necessary for superconductivity. Subsequently, we focused on LSCO-214 films, and grew a series of strained ultra thin films of this compound. While the films were superconducting, none of our samples showed enhanced superconduc- tivity, probably due to growth disorder.Therefore, we eventually studied high quality films grown by MBE from BNL. We used the low energy muon beamline at PSI to perform μSR studies on two different com- pressive strain states. The successful measurements of the penetration depth and Ginzburg- Landau parameter κ on ultra thin films of this type using low energy muons showed the benefits of this technique. As the 2 films were of different thicknesses, further studies need to be done to disentangle which observed effects are due to strain and/or variation in c-axis, and which are due solely to thickness. Our accumulated results and those of other groups, (notably Naito et. al. at NTT) on strain in LSCO-214 films, and the ensemble of data, including our study, indicate that most likely it is a phase coherence enhancement due to the in-plane compressive strain that raises the Tc. In summary, in addition to the succesful implementation of PLD heteroepitaxy, XRD analysis and ρ(T) studies of LSCO-214 films we were able to establish that: 1. Phase coherence is improved by in plane compressive strain, hence Tc enhancement 2. Tc also seems to scale with apical oxygen, as previously reported by H. Keller et. al., and local distortions around the copper-oxygen tetrahedra 3. Last but not least, we were even able to induce strain into BSCCO-2201 films, yet at present the full electronic properties of this system are neither measured nor under- stood. Finally, further systematic studies on μSR are proposed, and are indeed underway at PSI, to further elucidate the microscopic role of strain in the mechanism of high Tc superconductivity.

EPFL2013