Quantum-chemical insights into mixed-valence systems: within and beyond the Robin-Day scheme

In mixed-valence (MV) systems essentially identical, more or less electronically coupled, redox centres are brought into formally different oxidation states by removal or addition of an electron. Depending on the strength of electronic coupling, an electron or a hole is either concentrated on one of the redox centres, or it is symmetrically delocalised onto several sites, or the situation is somewhere in between, which leads to the classification system for MV systems introduced by Melvin Robin and Peter Day. These different characteristics are of fundamental importance for the understanding of electron transfer processes. Applications of quantum-chemical methods to aid the classification and to unravel the nature of the electronic structure and spectroscopic data of both organic and transition-metal MV systems, have gained tremendous importance over the last two decades. In this review, we emphasise the prerequisites the quantum-chemical methods need to fulfill to successfully describe MV systems close to the borderline between Robin–Day classes II and III. These are, in particular, a balanced treatment of exchange, dynamical and non-dynamical correlation effects, as well as consideration of the crucial influence of the (solvent or solid-state) environment on the partial localisation of charge. A large variety of applications of quantum-chemical methods to both organic and inorganic MV systems are critically appraised here in view of these prerequisites. Practical protocols based on a combination of suitable density functional methods with continuum or non-continuum solvent models provided good agreement with experimental data for the ground states and the electronic excitations of a large range of MV systems close to the borderline. Recent applications of such methods have highlighted the crucial importance of conformational effects on electronic coupling, all the way to systems where conformational motion may cause a thermal mixing of class II and class III situations in one system.DFG, EXC 314, Unifying Concepts in CatalysisDFG, GRK 1221, Steuerung elektronischer Eigenschaften von Aggregaten pi-konjugierter Molekül

Ab-initio molecular dynamics studies of laser- and collision-induced processes in multielectron diatomics, organic molecules and fullerenes

This work presents applications of an ab-initio molecular dynamics method, the so-called nonadiabatic quantum molecular dynamics (NA-QMD), for various molecular systems with many electronic and nuclear degrees of freedom. Thereby, the nuclei will be treated classically and the electrons with time-dependent density functional theory (TD-DFT) in basis expansion. Depending on the actual system and physical process, well suited basis sets for the Kohn-Sham orbitals has to be chosen. For the ionization process a novel absorber acting in the energy space as well as additional basis functions will be used depending on the laser frequency. In the first part of the applications, a large variety of different laser-induced molecular processes will be investigated. This concerns, the orientation dependence of the ionization of multielectronic diatomics (N2, O2), the isomerization of organic molecules (N2H2) and the giant excitation of the breathing mode in fullerenes (C60). In the second part, fullerene-fullerene collisions are investigated, for the first time in the whole range of relevant impact velocities concerning the vibrational and electronic energy transfer (\"stopping~power\"). For low energetic (adiabatic) collisions, it is surprisingly found, that a two-dimensional, phenomenological collision model can reproduce (even quantitatively) the basic features of fusion and scattering observed in the fully microscopic calculations as well as in the experiment. For high energetic (nonadiabatic) collisions, the electronic and vibrational excitation regimes are predicted, leading to multifragmentation up to complete atomization

A General Formalism for Continuous Feedback Control in Quantum Systems

This thesis devolops a general formalism for continuous feedback control in quantum systems. The main result is a quantum Fokker-Planck master equation describing the joint dynamics of a quantum system and a detector with finite bandwidth. For a fast detector, this equation can be reduced to a Markovian master equation for the system dynamics. In particular, the formalism is amenable to analytical treatments of feedback protocols that depend nonlinearly on the measured signal. Previously, only numerical methods were available for this. We apply the formalism on two toy models to highlight its usefuleness. We find that the formalism provides insight into the connection between thermodynamics and information theory

Quantum Chemistry in Nanoscale Environments: Insights on Surface-Enhanced Raman Scattering and Organic Photovoltaics

The understanding of molecular effects in nanoscale environments is becoming increasingly relevant for various emerging fields. These include spectroscopy for molecular identification as well as in finding molecules for energy harvesting. Theoretical quantum chemistry has been increasingly useful to address these phenomena to yield an understanding of these effects. In the first part of this dissertation, we study the chemical effect of surface-enhanced Raman scattering (SERS). We use quantum chemistry simulations to study the metal-molecule interactions present in these systems. We find that the excitations that provide a chemical enhancement contain a mixed contribution from the metal and the molecule. Moreover, using atomistic studies we propose an additional source of enhancement, where a transition metal dopant surface could provide an additional enhancement. We also develop methods to study the electrostatic effects of molecules in metallic environments. We study the importance of image-charge effects, as well as field-bias to molecules interacting with perfect conductors. The atomistic modeling and the electrostatic approximation enable us to study the effects of the metal interacting with the molecule in a complementary fashion, which provides a better understanding of the complex effects present in SERS. In the second part of this dissertation, we present the Harvard Clean Energy project, a high-throughput approach for a large-scale computational screening and design of organic photovoltaic materials. We create molecular libraries to search for candidates structures and use quantum chemistry, machine learning and cheminformatics methods to characterize these systems and find structure-property relations. The scale of this study requires an equally large computational resource. We rely on distributed volunteer computing to obtain these properties. In the third part of this dissertation we present our work related to the acceleration of electronic structure methods using graphics processing units. This hardware represents a change of paradigm with respect to the typical CPU device architectures. We accelerate the resolution-of-the-identity Moller-Plesset second-order perturbation theory algorithm using graphics cards. We also provide detailed tools to address memory and single-precision issues that these cards often present

40th Rocky Mountain Conference on Analytical Chemistry

Final program, abstracts, and information about the 40th annual meeting of the Rocky Mountain Conference on Analytical Chemistry, co-sponsored by the Colorado Section of the American Chemical Society and the Rocky Mountain Section of the Society for Applied Spectroscopy. Held in Denver, Colorado, July 25 - August 1, 1998

CMB anisotropies and spectral distortions: constraining inflation at small scales

Anisotropies in the angular power spectra of the Cosmic Microwave Background (CMB) temperature and polarization are sourced by inflationary perturbations on scales from 10^1 Mpc to 10^4 Mpc. Deviations of the CMB frequency spectrum from a black-body, instead, can probe inflationary perturbations on scales from 10^−4 Mpc to 10^−2 Mpc. These length scales are inaccessible to CMB and large-scale structure measurements. CMB spectral distortions, averaged over the whole sky, constrain the two-point function of primordial perturbations. Correlation of temperature and spectral distortion anisotropies, instead, can constrain their three-point function (making them a probe of primordial non-Gaussianity). In the first part of this thesis I study what is the level of sensitivity needed, by an experiment measuring the CMB frequency spectrum, to detect the running of the spectral index of inflationary perturbations. I then investigate what is the minimal contribution to the correlation function between temperature and spectral distortion anisotropies that is expected in standard inflationary scenarios. Finally, I discuss what are the secondary contributions (arising from late-time gravitational evolution) to such angular correlation, and how they could bias constraints on primordial non-Gaussianity

Synthesis of Highly Branched Polystyrene Model Systems with Superior Strain Hardening and their Influence on Foaming Properties

Die molekulare Struktur bestimmt maßgeblich die Verarbeitbarkeit eines Polymers in der Schmelze und die daraus resultierenden makroskopischen Eigenschaften des Endprodukts, die wiederum über seine Anwendung entscheiden. Viele dieser Anwendungen beruhen auf dünnen Film- und Faserstrukturen, von denen polymere Schäume mit ihrer porösen Zellmorphologie ein wichtiger Vertreter sind. Die Schmelzefestigkeit ist entscheidend für die Expandierbarkeit eines Schaums, da sie die Zellwände und Verstrebungen auf mikro- und nanoskaliger Ebene stabilisiert. Verzweigungen, insbesondere Langkettenverzweigungen sind eine Schlüsseleigenschaft eines Polymers um eine gute Schmelzefestigkeit in Dehnströmung zu erreichen. Es ist von großem Interesse, den Einfluss der Topologie eines Polymers auf das rheologische Verhalten zu verstehen und die Struktur-Eigenschafts-Beziehung vorherzusagen und letztendlich effizient zu nutzen. Die hier vorgestellte Arbeit untersucht den Einfluss von mehrfach verzweigten Polymerarchitekturen auf die Schäumbarkeit, speziell auf die Volumenexpansion und korreliert die erzielten Schaumeigenschaften mit der Molekularstruktur mittels dem Fließverhalten aus der Scher- und Dehnrheologie. Um einen systematischen Ansatz zu ermöglichen, werden definierte Modellpolystyrole (PS) mit Kamm- und Dendrigraft-Topologie und einer variierenden Anzahl von Verzweigungen mittels anionischer Synthese hergestellt. Die Schmelzeeigenschaften werden in oszillatorischer Scherung und uniaxialer Dehnung rheologisch charakterisiert. Das Batch-Schäumen wird bei $180$ und $500\,\text{bar}$ unter Verwendung von Kohlendioxid (CO$_2$) als physikalisches Treibmittel durchgeführt. Die resultierenden Schäume werden hinsichtlich ihrer Volumenausdehnung, Zellgröße und Zelldichte analysiert. Es wird eine Reihe von Kamm-PS mit gut verzweigten, aber unterschiedlicher Anzahl von Langkettenverzweigungen synthetisiert, die von spärlich verzweigt bis hin zu flaschenbürstenartiger Strukturen reichen. Die Korrelation der rheologischen und der Schaumeigenschaften zeigt einen Bereich optimaler Verzweigungszahl, die in einen maximalen Volumenexpansionskoeffizient von 40 bei gleichzeitig maximalem Dehnverfestigungsfaktor (\textit{strain hardening factor}) von $\text{SHF}=200$ resultiert, wobei die Nullscherviskosität auch am niedrigsten ist. Dendrigraft-PS werden aus einem langkettenverzweigten Kamm-PS synthetisiert, auf den eine Korona aus Kurzkettenverzweigungen aufgepfropft wird. Die sogenannte ``branch-on-Branch\u27\u27 (bob)-Architektur weist molekulare Parameter auf, die eindeutig drei verschiedene Relaxationsmodi zeigen, die jeder Verzweigungsgeneration zugeordnet werden können und auf die hierarchische Kettendynamik hinweisen. In uniaxialer Dehnung wird ein enormer Dehnungsverfestigungfaktor bis zu $\text{SHF}=700$ erreicht. Dabei zeigt sich die Dehnrate als ein wichtiges Kriterium dafür, ob eine hohe Dehnverfestigung zu einer verbesserten Schäumbarkeit führt. Dies wird durch das Schäumen eines kurzkettenverzweigten Kamm-PS validiert, der sich durch eine Dehnverfestigung von $\text{SHF}=200$ bei schnellen Dehnungsraten von $\dot\varepsilon_\text{H}=3\text{--}10\,\text{s}^{-1}$ auszeichnet und im Vergleich zu Dendrigraft- und langkettenverzweigten Kamm-PS konstant höhere Volumenexpansionen liefert, insbesondere bei hohen Schäumungstemperaturen und schnellen Druckentlastungsraten. Weiterhin werden bimodale Kamm-Lineare PS-Blends hergestellt, um das Zusammenspiel zwischen verzweigter und linearer Kettentopologie zu untersuchen. Die Schmelzrheologie gibt einen Einblick in Relaxationsdynamiken und deren Skalengesetze und zeigt das Potenzial von verzweigt-linearen Blends zur Einstellung und Optimierung der Schmelzeeigenschaften für Verarbeitungsprozesse in Dehnung oder Scherung

Waves, ChIPs, GEMMs, gears, markers and maps:Computational systems biology from cell cycle oscillations to metabolic fluxes

This thesis discusses six scientific works within the fields of systems biology and bioinformatics. These works are unified in their conception of the cell as a system of integrated fluxes of mass and information, in the application of computational approaches to answer the questions at hand and in their aim for computation to drive new biological discoveries. The overarching theme is that by bringing computational methodologies in contact with quantitative experimental data, new principles can be proposed and/or tested that would not otherwise have been discovered. The first three chapters of this thesis focus on (the cell cycle of) budding yeast. Specifically, Ch. 2 deals with kinetic models for waves-of-cyclins. Ch. 3 concerns analysis of ChIP-exo experiments to retrieve the specific binding sites at gene promoters where Forkhead transcription factors Fkh1 and Fkh2 bind. Ch. 4 presents a web-based database and visualization tool which integrates a variety of sources of information concerning all protein-coding genes and allows users to craft specific and visualizations of the topology of interaction networks. The last three chapters of this thesis focus on that other process by which life produces more of itself: metabolism. Specifically, our focus is on thermodynamics and metabolic networks in acetogenic bacteria (Ch. 5) and human liver (Ch. 6-7). Ch. 5 is concerned with the concept of gear-shifting: an organism's hypothetical ability to express metabolic enzymes that result in different stoichiometric yields in order to navigate a trade-off between rate and yield. In Ch. 6 and 7 we discuss two approaches to deal partially with concentrations in flux balance analysis, i.e. in terms of serum concentrations of biomarkers (Ch. 6) and in terms of uptake fluxes and concentrations of medium metabolites and metabolic enzymes (Ch. 7). The six chapters present new datasets, provide novel tools, develop new models, propose novel (extensions of) computational methodologies and rationalize and assess existing methodologies. As such, this thesis provides a glance into the cutting-edge of biomedical research in this data-driven, computation-assisted age

Bayesian Inference for Diffusion Processes with Applications in Life Sciences

Diffusion processes are a promising instrument to realistically model the time-continuous evolution of natural phenomena in life sciences. However, approximation of a given system is often carried out heuristically, leading to diffusions that do not correctly reflect the true dynamics of the original process. Moreover, statistical inference for diffusions proves to be challenging in practice as the likelihood function is typically intractable. This thesis contributes to stochastic modelling and statistical estimation of real problems in life sciences by means of diffusion processes. In particular, it creates a framework from existing and novel techniques for the correct approximation of pure Markov jump processes by diffusions. Concerning statistical inference, the thesis reviews existing practices and analyses and further develops a well-known Bayesian approach which introduces auxiliary observations by means of Markov chain Monte Carlo (MCMC) techniques. This procedure originally suffers from convergence problems which stem from a deterministic link between the model parameters and the quadratic variation of a continuously observed diffusion path. This thesis formulates a neat modification of the above approach for general multi-dimensional diffusions and provides the mathematical and empirical proof that the so-constructed MCMC scheme converges. The potential of the newly developed modelling and estimation methods is demonstrated in two real-data application studies: the spatial spread of human influenza in Germany and the in vivo binding behaviour of proteins in cell nuclei