Highly accurate quantum chemistry : spin-orbit splittings via multireference coupled-cluster methods and applications in heavy-atom main-group chemistry

Diese Dissertation demonstriert und verbessert die Vorhersagekraft der Coupled-Cluster-Theorie im Hinblick auf die hochgenaue Berechnung von Moleküleigenschaften. Die Demonstration erfolgt mittels Extrapolations- und Additivitätstechniken in der Single-Referenz-Coupled-Cluster-Theorie, mit deren Hilfe die Existenz und Struktur von bisher unbekannten Molekülen mit schweren Hauptgruppenelementen vorhergesagt wird. Vor allem am Beispiel von cyclischem SiS_2, einem dreiatomigen Molekül mit 16 Valenzelektronen, wird deutlich, dass die Vorhersagekraft der Theorie sich heutzutage auf Augenhöhe mit dem Experiment befindet: Theoretische Überlegungen initiierten eine experimentelle Suche nach diesem Molekül, was schließlich zu dessen Detektion und Charakterisierung mittels Rotationsspektroskopie führte. Die Vorhersagekraft der Coupled-Cluster-Theorie wird verbessert, indem eine Multireferenz-Coupled-Cluster-Methode für die Berechnung von Spin-Bahn-Aufspaltungen erster Ordnung in 2^Pi-Zuständen entwickelt wird. Der Fokus hierbei liegt auf Mukherjee's Variante der Multireferenz-Coupled-Cluster-Theorie, aber prinzipiell ist das vorgeschlagene Berechnungsschema auf alle Varianten anwendbar. Die erwünschte Genauigkeit beträgt 10 cm^-1. Sie wird mit der neuen Methode erreicht, wenn Ein- und Zweielektroneneffekte und bei schweren Elementen auch skalarrelativistische Effekte berücksichtigt werden. Die Methode eignet sich daher in Kombination mit Coupled-Cluster-basierten Extrapolations-und Additivitätsschemata dafür, hochgenaue thermochemische Daten zu berechnen.

Comparative study of the different models for the calculation of BLEVEs overpressure effects

The BLEVE, acronym for Boiling Liquid Expanding Vapour Explosion, is one of the most dangerous accidents that can occur in pressure vessels. It can be defined as an explosion resulting from the failure of a vessel containing a pressure liquefied gas stored at a temperature significantly above its boiling point at atmospheric pressure. This phenomenon frequently appears when a vessel is engulfed by a fire: the heat causes the internal pressure to raise and the mechanical proprieties of the wall to decrease, with the consequent rupture of the tank and the instantaneous release of its whole content. After the breakage, the vapour outflows and expands and the liquid phase starts boiling due to the pressure drop. The formation and propagation of a distructive schock wave may occur, together with the ejection of fragments, the generation of a fireball if the stored fluid is flammable and immediately ignited or the atmospheric dispersion of a toxic cloud if the fluid contained inside the vessel is toxic. Despite the presence of many studies on the BLEVE mechanism, the exact causes and conditions of its occurrence are still elusive. In order to better understand this phenomenon, in the present study first of all the concept and definition of BLEVE are investigated. A historical analysis of the major events that have occurred over the past 60 years is described. A research of the principal causes of this event, including the analysis of the substances most frequently involved, is presented too. Afterwards a description of the main effects of BLEVEs is reported, focusing especially on the overpressure. Though the major aim of the present thesis is to contribute, with a comparative analysis, to the validation of the main models present in the literature for the calculation and prediction of the overpressure caused by BLEVEs. In line with this purpose, after a short overview of the available approaches, their ability to reproduce the trend of the overpressure is investigated. The overpressure calculated with the different models is compared with values deriving from events happened in the past and ad-hoc experiments, focusing the attention especially on medium and large scale phenomena. The ability of the models to consider different filling levels of the reservoir and different substances is analyzed too. The results of these calculations are extensively discussed. Finally some conclusive remarks are reported.

Quantum dot / optical protein bio-nano hybrid system biosensing

The integration of novel nanomaterials with highly-functional biological molecules has advanced multiple fields including electronics, sensing, imaging, and energy harvesting. This work focuses on the creation of a new type of bio-nano hybrid substrate for military biosensing applications. Specifically it is shown that the nano-scale interactions of the optical protein bacteriorhodopsin and colloidal semiconductor quantum dots can be utilized as a generic sensing substrate. This work spans from the basic creation of the protein to its application in a novel biosensing system. The functionality of this sensor design originates from the unique interactions between the quantum dot and bacteriorhodopsin molecule when in nanoscale proximity. A direct energy transfer relationship has been established between coreshell quantum dots and the optical protein bacteriorhodopsin that substantially enhances the protein’s native photovoltaic capabilities. This energy transfer phenomena is largely distance dependent, in the sub-10nm realm, and is characterized experimentally at multiple separation distances. Experimental results on the energy transfer efficiency in this hybrid system correlate closely to theoretical predictions. Deposition of the hybrid system with nano-scale control has allowed for the utilization of this energy transfer phenomena as a modulation point for a functional biosensor prototype. This work reveals that quantum dots have the ability to activate the bacteriorhodopsin photocycle through both photonic and non-photonic energy transfer mechanisms. By altering the energy transferred to the bacteriorhodopsin molecule from the quantum dot, the electrical output of the protein can be modulated. A biosensing prototype was created in which the energy transfer relationship is altered upon target binding, demonstrating the applicability of a quantum dot/bacteriorhodopsin hybrid system for sensor applications. The electrical nature of this sensing substrate will allow for its efficient integration into a nanoelectronics array form, potentially leading to a small-low power sensing platform for remote toxin detection applications.

Calculation of crystal optical properties from molecular electron density

We have recently developed a method to obtain distributed atomic polarizabilities adopting a partitioning of the molecular electron density (for example, the Quantum Theory of Atoms in Molecules, [1]), calculated with or without an applied electric field. The procedure [2] allows to obtained atomic polarizability tensors, which are perfectly exportable, because quite representative of an atom in a given functional group. Among the many applications of this idea, the calculation of crystal susceptibility is easily available, either from a rough estimation (the polarizability of the isolated molecule is used) or from a more precise estimation (the polarizability of a molecule embedded in a cluster representing the first coordination sphere is used). Lorentz factor is applied to include the long range effect of packing, which is enhancing the molecular polarizability. Simple properties like linear refractive index or the gyration tensor can be calculated at relatively low costs and with good precision. This approach is particularly useful within the field of crystal engineering of organic/organometallic materials, because it would allow a relatively easy prediction of a property as a function of the packing, thus allowing "reverse crystal engineering". Examples of some amino acid crystals and salts of amino acids [3] will be illustrated, together with other crystallographic or non-crystallographic applications. For example, the induction and dispersion energies of intermolecular interactions could be calculated with superior precision (allowing anisotropic van der Waals interactions). This could allow revision of some commonly misunderstood intermolecular interactions, like the halogen bonding (see for example the recent remarks by Stone or Gilli [4]). Moreover, the chemical reactivity of coordination complexes could be reinvestigated, by coupling the conventional analysis of the electrostatic potential (useful only in the circumstances of hard nucleophilic/electrophilic interaction) with the distributed atomic polarizability. The enhanced reactivity of coordinated organic ligands would be better appreciated. [1] R. F. W. Bader, Atoms in Molecules: A Quantum Theory. Oxford Univ. Press, 1990. [2] A. Krawczuk-Pantula, D. Pérez, K. Stadnicka, P. Macchi, Trans. Amer. Cryst. Ass. 2011, 1-25 [3] A. S. Chimpri1, M. Gryl, L. H.R. Dos Santos1, A. Krawczuk, P. Macchi Crystal Growth & Design, in the press. [4] a) A. J. Stone, J. Am. Chem. Soc. 2013, 135, 7005−7009; b) V. Bertolasi, P. Gilli, G. Gilli Crystal Growth & Design, 2013, 12, 4758-4770.

COMPREHENSIVE CALCULATION-BASED IMRT QA USING R&V DATA, TREATMENT RECORDS, AND A SECOND TREATMENT PLANNING SYSTEM

Purpose: Traditional patient-specific IMRT QA measurements are labor intensive and consume machine time. Calculation-based IMRT QA methods typically are not comprehensive. We have developed a comprehensive calculation-based IMRT QA method to detect uncertainties introduced by the initial dose calculation, the data transfer through the Record-and-Verify (R&V) system, and various aspects of the physical delivery. Methods: We recomputed the treatment plans in the patient geometry for 48 cases using data from the R&V, and from the delivery unit to calculate the “as-transferred” and “as-delivered” doses respectively. These data were sent to the original TPS to verify transfer and delivery or to a second TPS to verify the original calculation. For each dataset we examined the dose computed from the R&V record (RV) and from the delivery records (Tx), and the dose computed with a second verification TPS (vTPS). Each verification dose was compared to the clinical dose distribution using 3D gamma analysis and by comparison of mean dose and ROI-specific dose levels to target volumes. Plans were also compared to IMRT QA absolute and relative dose measurements. Results: The average 3D gamma passing percentages using 3%-3mm, 2%-2mm, and 1%-1mm criteria for the RV plan were 100.0 (σ=0.0), 100.0 (σ=0.0), and 100.0 (σ=0.1); for the Tx plan they were 100.0 (σ=0.0), 100.0 (σ=0.0), and 99.0 (σ=1.4); and for the vTPS plan they were 99.3 (σ=0.6), 97.2 (σ=1.5), and 79.0 (σ=8.6). When comparing target volume doses in the RV, Tx, and vTPS plans to the clinical plans, the average ratios of ROI mean doses were 0.999 (σ=0.001), 1.001 (σ=0.002), and 0.990 (σ=0.009) and ROI-specific dose levels were 0.999 (σ=0.001), 1.001 (σ=0.002), and 0.980 (σ=0.043), respectively. Comparing the clinical, RV, TR, and vTPS calculated doses to the IMRT QA measurements for all 48 patients, the average ratios for absolute doses were 0.999 (σ=0.013), 0.998 (σ=0.013), 0.999 σ=0.015), and 0.990 (σ=0.012), respectively, and the average 2D gamma(5%-3mm) passing percentages for relative doses for 9 patients was were 99.36 (σ=0.68), 99.50 (σ=0.49), 99.13 (σ=0.84), and 98.76 (σ=1.66), respectively. Conclusions: Together with mechanical and dosimetric QA, our calculation-based IMRT QA method promises to minimize the need for patient-specific QA measurements by identifying outliers in need of further review.

Calculation Methodology and Fabrication Procedures for Particle Accelerator Strip-Line Kickers: Application to the CTF3 Combiner Ring Extraction Kicker and TL2 Tail Clippers

A particle accelerator is any device that, using electromagnetic fields, is able to communicate energy to charged particles (typically electrons or ionized atoms), accelerating and/or energizing them up to the required level for its purpose. The applications of particle accelerators are countless, beginning in a common TV CRT, passing through medical X-ray devices, and ending in large ion colliders utilized to find the smallest details of the matter. Among the other engineering applications, the ion implantation devices to obtain better semiconductors and materials of amazing properties are included. Materials supporting irradiation for future nuclear fusion plants are also benefited from particle accelerators. There are many devices in a particle accelerator required for its correct operation. The most important are the particle sources, the guiding, focalizing and correcting magnets, the radiofrequency accelerating cavities, the fast deflection devices, the beam diagnostic mechanisms and the particle detectors. Most of the fast particle deflection devices have been built historically by using copper coils and ferrite cores which could effectuate a relatively fast magnetic deflection, but needed large voltages and currents to counteract the high coil inductance in a response in the microseconds range. Various beam stability considerations and the new range of energies and sizes of present time accelerators and their rings require new devices featuring an improved wakefield behaviour and faster response (in the nanoseconds range). This can only be achieved by an electromagnetic deflection device based on a transmission line. The electromagnetic deflection device (strip-line kicker) produces a transverse displacement on the particle beam travelling close to the speed of light, in order to extract the particles to another experiment or to inject them into a different accelerator. The deflection is carried out by the means of two short, opposite phase pulses. The diversion of the particles is exerted by the integrated Lorentz force of the electromagnetic field travelling along the kicker. This Thesis deals with a detailed calculation, manufacturing and test methodology for strip-line kicker devices. The methodology is then applied to two real cases which are fully designed, built, tested and finally installed in the CTF3 accelerator facility at CERN (Geneva). Analytical and numerical calculations, both in 2D and 3D, are detailed starting from the basic specifications in order to obtain a conceptual design. Time domain and frequency domain calculations are developed in the process using different FDM and FEM codes. The following concepts among others are analyzed: scattering parameters, resonating high order modes, the wakefields, etc. Several contributions are presented in the calculation process dealing specifically with strip-line kicker devices fed by electromagnetic pulses. Materials and components typically used for the fabrication of these devices are analyzed in the manufacturing section. Mechanical supports and connexions of electrodes are also detailed, presenting some interesting contributions on these concepts. The electromagnetic and vacuum tests are then analyzed. These tests are required to ensure that the manufactured devices fulfil the specifications. Finally, and only from the analytical point of view, the strip-line kickers are studied together with a pulsed power supply based on solid state power switches (MOSFETs). The solid state technology applied to pulsed power supplies is introduced and several circuit topologies are modelled and simulated to obtain fast and good flat-top pulses.

Rotation-Induced Breakdown of Torsional Quantum Control

Control of the torsional angles of nonrigid molecules is key for the development of emerging areas like molecular electronics and nanotechnology. Based on a rigorous calculation of the rotation-torsion-Stark energy levels of nonrigid biphenyl-like molecules, we show that, unlike previously believed, instantaneous rotation-torsion-Stark eigenstates of such molecules, interacting with a strong laser field, present a large degree of delocalization in the torsional coordinate even for the lowest energy states. This is due to a strong coupling between overall rotation and torsion leading to a breakdown of the torsional alignment. Thus, adiabatic control of changes on the planarity of this kind of molecule is essentially impossible unless the temperature is on the order of a few Kelvin.

Teaching and evaluating mechanical vibrations with Matlab®

The study of the response of mechanical systems to external excitations, even in the simplest cases, involves solving second-order ordinary differential equations or systems thereof. Finding the natural frequencies of a system and understanding the effect of variations of the excitation frequencies on the response of the system are essential when designing mechanisms [1] and structures [2]. However, faced with the mathematical complexity of the problem, students tend to focus on the mathematical resolution rather than on the interpretation of the results. To overcome this difficulty, once the general theoretical problem and its solution through the state space [3] have been presented, Matlab®[4] and Simulink®[5] are used to simulate specific situations. Without them, the discussion of the effect of slight variations in input variables on the outcome of the model becomes burdensome due to the excessive calculation time required. Conversely, with the help of those simulation tools, students can easily reach practical conclusions and their evaluation can be based on their interpretation of results and not on their mathematical skills

Comparing the Luttinger–Kohn–Pikus–Bir and the Empiric K·P Hamiltonians in quantum dot intermediate band solar cells manufactured in zincblende semiconductors

The calculation of the energy spectrum and absorption coefficients of quantum dot nanostructured intermediate band solar cells using the Empiric K·P Hamiltonian method and its agreement with experimental data are summarized. The well established Luttinger Kohn Hamiltonian modified by Pikus and Bir for strained material, such as quantum dot arrays, is presented using a simplified strain field that allows for square band offsets. The energy spectrum and absorption coefficients are calculated with this new Hamiltonian. With the approximations made the energy spectrum results to be exactly the same but the absorption coefficient fits experiments less accurately. The computer time using the latter Hamiltonian is much longer than the former one.

Mapping strain exerted on blood vessel walls using deuterium double-quantum-filtered MRI

A technique is described for displaying distinct tissue layers of large blood vessel walls as well as measuring their mechanical strain. The technique is based on deuterium double-quantum-filtered (DQF) spectroscopic imaging. The effectiveness of the double-quantum filtration in suppressing the signal of bulk water is demonstrated on a phantom consisting of rat tail tendon fibers. Only intrafibrillar water is displayed, excluding all other signals of water molecules that reorient isotropically. One- and two-dimensional spectroscopic imaging of bovine aorta and coronary arteries show the characteristic DQF spectrum of each of the tissue layers. This property is used to obtain separate images of the outer layer, the tunica adventitia, or the intermediate layer, the tunica media, or both. To visualize the effect of elongation, the average residual quadrupole splitting <Δνq> is calculated for each pixel. Two-dimensional deuterium quadrupolar splitting images are obtained for a fully relaxed and a 55% elongated sample of bovine coronary artery. These images indicate that the strong effect of strain is associated with water molecules in the tunica adventitia whereas the DQF NMR signal of water in the tunica media is apparently strain-insensitive. After appropriate calibration, these average quadrupolar splitting images can be interpreted as strain maps.

Ab initio calculation of electronic coupling in the photosynthetic reaction center

We have carried out an ab initio electronic structure calculations of electron transfer couplings between chromophores in the bacterial photosynthetic reaction center. The couplings agree remarkably well with parameters obtained from recent quantum dynamical modeling of experimental data assuming an explicit intermediate mechanism. We also have computed couplings on the M-side of the reaction center and have found that the interaction of the primary donor to the M-side intermediate bacteriochlorophyll is quite small because of destructive interference of the two localized coupling matrix elements. This may explain the slow rate of electron transfer down the M-side of the reaction center.

Progress toward chemical accuracy in the computer simulation of condensed phase reactions.

We describe a procedure for the generation of chemically accurate computer-simulation models to study chemical reactions in the condensed phase. The process involves (i) the use of a coupled semiempirical quantum and classical molecular mechanics method to represent solutes and solvent, respectively; (ii) the optimization of semiempirical quantum mechanics (QM) parameters to produce a computationally efficient and chemically accurate QM model; (iii) the calibration of a quantum/classical microsolvation model using ab initio quantum theory; and (iv) the use of statistical mechanical principles and methods to simulate, on massively parallel computers, the thermodynamic properties of chemical reactions in aqueous solution. The utility of this process is demonstrated by the calculation of the enthalpy of reaction in vacuum and free energy change in aqueous solution for a proton transfer involving methanol, methoxide, imidazole, and imidazolium, which are functional groups involved with proton transfers in many biochemical systems. An optimized semiempirical QM model is produced, which results in the calculation of heats of formation of the above chemical species to within 1.0 kcal/mol (1 kcal = 4.18 kJ) of experimental values. The use of the calibrated QM and microsolvation QM/MM (molecular mechanics) models for the simulation of a proton transfer in aqueous solution gives a calculated free energy that is within 1.0 kcal/mol (12.2 calculated vs. 12.8 experimental) of a value estimated from experimental pKa values of the reacting species.

Topologically protected quantum transport in locally exfoliated bismuth at room temperature

We report electrical conductance measurements of Bi nanocontacts created by repeated tip-surface indentation using a scanning tunneling microscope at temperatures of 4 and 300 K. As a function of the elongation of the nanocontact, we measure robust, tens of nanometers long plateaus of conductance G0=2e2/h at room temperature. This observation can be accounted for by the mechanical exfoliation of a Bi(111) bilayer, a predicted quantum spin Hall (QSH) insulator, in the retracing process following a tip-surface contact. The formation of the bilayer is further supported by the additional observation of conductance steps below G0 before breakup at both temperatures. Our finding provides the first experimental evidence of the possibility of mechanical exfoliation of Bi bilayers, the existence of the QSH phase in a two-dimensional crystal, and, most importantly, the observation of the QSH phase at room temperature.

Experimental tests of quantum nonlinear dynamics in atom optics

Cold atoms in optical potentials provide an ideal test bed to explore quantum nonlinear dynamics. Atoms are prepared in a magneto-optic trap or as a dilute Bose-Einstein condensate and subjected to a far detuned optical standing wave that is modulated. They exhibit a wide range of dynamics, some of which can be explained by classical theory while other aspects show the underlying quantum nature of the system. The atoms have a mixed phase space containing regions of regular motion which appear as distinct peaks in the atomic momentum distribution embedded in a sea of chaos. The action of the atoms is of the order of Planck's constant, making quantum effects significant. This tutorial presents a detailed description of experiments measuring the evolution of atoms in time-dependent optical potentials. Experimental methods are developed providing means for the observation and selective loading of regions of regular motion. The dependence of the atomic dynamics on the system parameters is explored and distinct changes in the atomic momentum distribution are observed which are explained by the applicable quantum and classical theory. The observation of a bifurcation sequence is reported and explained using classical perturbation theory. Experimental methods for the accurate control of the momentum of an ensemble of atoms are developed. They use phase space resonances and chaotic transients providing novel ensemble atomic beamsplitters. The divergence between quantum and classical nonlinear dynamics is manifest in the experimental observation of dynamical tunnelling. It involves no potential barrier. However a constant of motion other than energy still forbids classically this quantum allowed motion. Atoms coherently tunnel back and forth between their initial state of oscillatory motion and the state 180 out of phase with the initial state.

Full S matrix calculation via a single real-symmetric Lanczos recursion: The Lanczos artificial boundary inhomogeneity method

We present an efficient and robust method for the calculation of all S matrix elements (elastic, inelastic, and reactive) over an arbitrary energy range from a single real-symmetric Lanczos recursion. Our new method transforms the fundamental equations associated with Light's artificial boundary inhomogeneity approach [J. Chem. Phys. 102, 3262 (1995)] from the primary representation (original grid or basis representation of the Hamiltonian or its function) into a single tridiagonal Lanczos representation, thereby affording an iterative version of the original algorithm with greatly superior scaling properties. The method has important advantages over existing iterative quantum dynamical scattering methods: (a) the numerically intensive matrix propagation proceeds with real symmetric algebra, which is inherently more stable than its complex symmetric counterpart; (b) no complex absorbing potential or real damping operator is required, saving much of the exterior grid space which is commonly needed to support these operators and also removing the associated parameter dependence. Test calculations are presented for the collinear H+H-2 reaction, revealing excellent performance characteristics. (C) 2004 American Institute of Physics.