SCSA based MATLAB pre-processing toolbox for 1H MR spectroscopic water suppression and denoising

In vivo 1H Magnetic Resonance Spectroscopy (MRS) is a useful tool in assessing neurological and metabolic disease, and to improve tumor treatment. Different pre-processing pipelines have been developed to obtain optimal results from the acquired data with sophisticated data fitting, peak suppression, and denoising protocols. We introduce a Semi-Classical Signal Analysis (SCSA) based Spectroscopy pre-processing toolbox for water suppression and data denoising, which allows researchers to perform water suppression using SCSA with phase correction and apodization filters and denoising of MRS data, and data fitting has been included as an additional feature, but it is not the main aim of the work. The fitting module can be passed on to other software. The toolbox is easy to install and to use: 1) import water unsuppressed MRS data acquired in Siemens, Philips and .mat file format and allow visualization of spectroscopy data, 2) allow pre-processing of single voxel and multi-voxel spectra, 3) perform water suppression and denoising using SCSA, 4) incorporate iterative nonlinear least squares fitting as an extra feature. This article provides information about how the above features have been included, along with details of the graphical user interface using these features in MATLAB

References, Appendices & All Parts Merged

Includes: Appendix MA: Selected Mathematical Formulas; Appendix CA: Selected Physical Constants; References; EGP merged file (all parts, appendices, and references)https://commons.library.stonybrook.edu/egp/1007/thumbnail.jp

Graphene for Electronics

Graphene is an allotrope of carbon consisting of a single layer of atoms arranged in a two-dimensional (2D) honeycomb lattice. Graphene's unique properties of thinness and conductivity have led to global research into its applications as a semiconductor. With the ability to well conduct electricity at room temperature, graphene semiconductors could easily be implemented into the existing semiconductor technologies and, in some cases, successfully compete with the traditional ones, such as silicon. This reprint presents very recent results in the physics of graphene, which can be important for applying the material in electronics

Multiconfiguration methods for the numerical simulation of photoionization processes of many-electron atoms

Numerical simulations present an indispensable way to the understanding of physical processes. In quantum mechanics, where the theoretical description is given in terms of the time-dependent Schrödinger equation (TDSE), the road is, however, difficult for any but the simplest systems. This is particularly true if one considers photoionization processes of atoms and mole\-cules, which at the same time require an accurate description of bound and continuum states, and therefore an extensive region of space to be sampled during the calculation. As a consequence, direct simulations of photoionization processes are currently only feasible for systems composed of up to three particles. Despite this fundamental restriction, many physical effects can be essentially described by single- and two-electron models, among them high-order harmonic generation and non-sequential double-ionization of atoms and mole\-cules. A plethora of numerical investigations have been performed on atomic and molecular hydrogen and helium in the last two decades, and these have had a strong impact on the current understanding of photoionization. On the other hand, there are processes which are characterized by the interplay of a larger number of electrons, such as tunnel ionization, the Auger effect, and, to give a more recent example, the temporal delay between the photo-emission of electrons from different shells of neon and krypton. The many-electron character of these effects complicates the accurate, time-resolved simulation, and hence, no universally applicable method exists. The present work develops two theoretical methods which are promising candidates for closing this gap, the multiconfigurational time-dependent Hartree-Fock (MCTDHF) method and the time-dependent restricted active space configuration interaction (TD-RASCI) method. Both represent the wavefunction in a linear subspace of the many-body Hilbert space and follow particular strategies to avoid the exponential problem. This makes it possible to treat a much larger number of electrons than with the direct techniques mentioned previously. The MCTDHF method is already well established in the scientific community, but has been applied only rarely to photoionization processes so far. On the other hand, the TD-RASCI method is an original contribution, and is applied for the first time to solutions of the time-dependent Schrödinger equation. Further, through the invention of appropriate, grid-like single-particle basis sets, we adjust these general approaches to efficiently treat photoionization processes in many-electron atoms and molecules. After their thorough introduction, the MCTDHF and the TD-RASCI method are applied to several topics of photoionization physics. Among them is, first, the problem of calculating cross sections of atoms, for which we particularly consider helium, beryllium and neon. In most parts, this is accomplished for the first time in the framework of the developed methods. Next, we consider the two-photon double-ionization of helium, which has attracted considerable interest in recent years, and perform simulations with the MCTDHF method. We further apply the TD-RASCI method to study two-color pump-probe process in beryllium, the simulation of which requires an explicitly time-dependent treatment. We find that both methods are highly appropriate for accurately describing correlated single-ionization processes. Moreover, the TD-RASCI method is able to model relevant doubly-excited states, which are of central importance for a variety of physical processes.Trotz dieser fundamentalen Einschränkung lassen sich viele physikalische Effekte bereits durch Ein- und Zweiteilchenmodelle beschreiben, darunter zum Beispiel die Erzeugung höherer Harmonischer oder die nicht-sequentielle Doppelionisation. In diesem Sinne wurde in den letzten zwei Jahrzehnten eine Vielzahl numerischer Untersuchungen an atomarem und molekularem Wasserstoff sowie Helium unternommen, welche einen starken Einfluss auf das momentane Verständnis von Photoionisations-Prozessen nahmen. Andererseits gibt es jedoch physikalische Effekte, die durch das Zusammenwirken einer größeren Anzahl von Elektronen gekennzeichnet sind, etwa die Tunnel-Ionisation, der Auger-Effekt oder die kürzlich entdeckte zeitliche Verzögerung in der Emission von Elektronen aus verschiedenen atomaren Schalen von Neon und Krypton. Der immanente Vielteilchencharakter macht die zeitaufgelöste Simulation dieser Prozesse zu einer schwierigen Aufgabe, für die es bisher keine universell einsetzbare und gleichzeitig akkurate Methode gibt. In dieser Arbeit werden zwei theoretische Methoden zur Simulation von Photoionisations-Prozessen von Vielteilchenatomen und -molekülen vor\-gestellt, die vielversprechende Kandidaten zur Schließung dieser vorhandenen Lücke darstellen, nämlich die zeitabhängige Multikonfigurations-Hartree-Fock (MCTDHF) Methode sowie die zeitabhängige restricted-active-space Konfigurations-Wechselwirkungsmethode (TD-RASCI). Beide stellen die quantenmechanische Wellenfunktion in einem linearen Unterraum des Vielteilchen-Hilbertraumes dar und folgen dabei speziellen Ansätzen um das Problem des exponentiellen Wachstums zu vermeiden. Dadurch kann eine weitaus größere Teilchenzahl als mit der zuvor erwähnten direkten Technik simuliert werden. Weiterhin werden diese zunächst sehr allgemeinen Methoden durch den Gebrauch geeigneter Basissätze auf die effiziente Beschreibung von Photoionisations-Prozessen optimiert. Nach ihrer Einführung werden die MCTDHF und TD-RASCI Methode auf aktuelle Themen der Photoionisations-Physik angewandt. Zunächst wenden wir uns der Berechnung von Ionisations-Streuquerschnitten der Atome Helium, Beryllium und Neon zu, welche weitgehend zum ersten Male mithilfe der eingeführten Methoden untersucht wird. Des Weiteren studieren wir die Zwei-Photonen-Ionisation von Helium, der in jüngerer Zeit großes theoretisches Interesse zukam, mithilfe von Simulationen mit der MCTDHF Methode. Als grundlegendes Beispiel eines explizit zeitabhängigen Prozesses wird darüberhinaus die Pump-Probe Ionisation von Beryllium betrachtet. Unsere Untersuchungen zeigen, dass sowohl die MCTDHF Methode als auch die TD-RASCI Methode die Einelektronen-Photoionisation akkurat zu beschreiben vermag. Mithilfe der TD-RASCI Methode ist es zudem möglich, selektierte doppelt-angeregte Zustände in die Rechnung zu integrieren, welche eine zentrale Rolle bei einer Vielzahl physikalischer Prozesse spielen