Theoretical and Experimental Study of Cooperativity Effects in Noncovalent Interactions

L’any 2002 tres grups de recerca, entre ells el nostre grup, van demostrar teòricament que la interacció entre anions i anells aromàtics electrodeficients, anomenada interacció anió–, era favorable. Des de llavors s’ha dut a terme un intens estudi de la seva naturalesa física fins la total comprensió. Aquesta tesi es basa amb l’estudi de la interacció anió– des de tres punts de vista. Primerament, la investigació es basa en el disseny teòric de motius estructurals per donar lloc a un receptor on la interacció anió– siga molt favorable, per posteriorment avaluar la força de la interacció experimentalment en dissolució. A continuació, es va analitzar la interrelació entre un gran nombre de combinacions d’interaccions no covalents. A partir d’aquest estudi es defineixen nous conceptes i es proposen diferents formules per calcular efectes de cooperativitat. Finalment, hem anat un pas més enllà en l’estudi de la interacció analitzant: 1) l’impacte de la interacció anió– a sistemes biològics; 2) la influència de modificacions a l’anió sobre la naturalesa física de la interacció.In 2002 three research groups, among them our research group, theoretically demonstrated that the interaction between anions and electron-deficient aromatic rings, named anion– interaction, was favourable. Since then, an intense study of its physical nature has been performed to understand it completely. This thesis is based on the study of the anion– interaction from three points of view. Firstly, theoretical design of binding units to build a receptor and to obtain the most favourable binding based on anion– interactions. The binding properties of these receptors have been experimentally assessed in solution. Secondly, we have studied the interplay between a great combination of noncovalent interactions. From this study, new concepts and formula to calculate cooperativity effects have been described. Finally, we have study one step further the anion– interaction analysing: 1) the impact of anion– interaction in biological systems; 2) how the modifications in the anion influence the physical nature of the interaction

Quantum electrodynamics in modern optics and photonics: tutorial

One of the key frameworks for developing the theory of light–matter interactions in modern optics and photonics is quantum electrodynamics (QED). Contrasting with semiclassical theory, which depicts electromagnetic radiation as a classical wave, QED representations of quantized light fully embrace the concept of the photon. This tutorial review is a broad guide to cutting-edge applications of QED, providing an outline of its underlying foundation and an examination of its role in photon science. Alongside the full quantum methods, it is shown how significant distinctions can be drawn when compared to semiclassical approaches. Clear advantages in outcome arise in the predictive capacity and physical insights afforded by QED methods, which favors its adoption over other formulations of radiation–matter interaction

Resonance Energy Transfer: From Fundamental Theory to Recent Applications

Resonance energy transfer (RET), the transport of electronic energy from one atom or molecule to another, has significant importance to a number of diverse areas of science. Since the pioneering experiments on RET by Cario and Franck in 1922, the theoretical understanding of the process has been continually refined. This review presents a historical account of the post-Förster outlook on RET, based on quantum electrodynamics, up to the present-day viewpoint. It is through this quantum framework that the short-range, R–6 distance dependence of Förster theory was unified with the long range, radiative transfer governed by the inverse-square law. Crucial to the theoretical knowledge of RET is the electric dipole-electric dipole coupling tensor; we outline its mathematical derivation with a view to explaining some key physical concepts of RET. The higher order interactions that involve magnetic dipoles and electric quadrupoles are also discussed. To conclude, a survey is provided on the latest research, which includes transfer between nanomaterials, enhancement due to surface plasmons, possibilities outside the usual ultraviolet or visible range and RET within a cavity

Nonlinear Optics

This book examines nonlinear optical effects in nonlinear nanophotonics, plasmonics, and novel materials for nonlinear optics. It discusses different types of plasmonic excitations such as volume plasmons, localized surface plasmons, and surface plasmon polaritons. It also examines the specific features of nonlinear optical phenomena in plasmonic nanostructures and metamaterials. Chapters cover such topics as applications of nanophotonics, novel materials for nonlinear optics based on nanoparticles, polymers, and photonic glasses

Scalar and vector correlations in molecular collision dynamics

This thesis concerns the fundamental scalar and vector attributes of molecular collisions. A translationally relaxed sample of fully state-selected and rotationally anisotropic CN(A² ∏,v = 4, jFɛ) was prepared within a thermal bath (~298 K) of partner gas (either Ar, N2, O2 or CO2) by ns-pulsed laser excitation. The collisional evolution of the prepared polarised rotational angular momentum was monitored using highresolution frequency modulation spectroscopy (FMS). The total removal and depolarisation of oriented or aligned rotational angular momentum was measured in CN(A² ∏,v = 4, j = 2.5, 3.5, 6.5, 11.5, 13.5, and 18.5, F1e). The state-to-state rotational energy transfer (RET) and orientation transfer from CN(A² ∏,v = 4, j = 6.5 F1e or j = 10.5 F2f) to ∆j ≤ |5| was investigated. The results for the CN(A² ∏,+Ar system generally agree very well with complementary exact quantum scattering (QS) calculations on the best available ab initio potential energy surfaces (PESs). For all systems, a three-level multiple-collision kinetic model satisfactorily reproduces the observed removal of population and polarisation. Elastic depolarisation is found to be a relatively minor pathway relative to population removal and inelastic depolarisation, as confirmed by complete master equation (ME) simulations for CN(A² ∏, v=4, j = 6.5 F1e)+Ar. The total removal efficiencies lie in the order CO2 > N2 > O2 > Ar, loosely correlated with long-range attractive forces. O2 and CO2 exhibit rapid removal channels in addition to RET, likely to be electronic quenching to CN(X2∑+). There are substantial parity-dependent alternations with Dj in state-to-state RET and polarisation transfer, sufficient for a striking change in sign of orientation for specific transitions. This is attributed to the near-homonuclear nature of CN(A² ∏) and consequent even character of the PESs. QS calculations indicate that the dynamics of parity-conserving and changing transitions differ fundamentally. A preference for spinorbit conservation, strongest for Ar, comes from the near-Hund’s case-(a) character of CN(A² ∏) at low-j. Despite the additional dimensions available, the qualitatively similar behaviour of the molecular partners with Ar suggests that these systems have comparable interaction potentials with CN(A² ∏). Therefore, small centrosymmetric molecules, such as N2, O2 and CO2, may approximately be treated as spherical targets. This is supported by recent spherically-averaged CN(A² ∏)-N2 PESs and associated QS calculations from the literature.EPSR

Advanced gravitational lensing techniques for precision cosmology

Gravitational lensing - the deflection of light by gravity - has greatly developed since its famous first observation in 1919, which validated Einstein's General Theory of Relativity. The strength of this effect does not depend on the nature of the mass which produces the gravitational field and thus it is a great tool to weigh both the visible and the invisible parts of the universe. Consequently gravitational lensing has become a pillar of observational cosmology over the last decades, and it is used to study the nature of Dark Matter and Dark Energy, the two mysterious quantities which dominate our universe, but are not yet understood by physics theory. The success of this endeavor rests on a thorough understanding of lensing theory and observations, including their systematics, the availability of a sufficient amount of precise data, and the development of efficient software to precisely measure these lensing effects in digital astronomical images. This thesis presents advanced techniques which can improve several of these areas. In the first part, we develop a new theoretical method to break the mass-sheet degeneracy, which prevents accurate mass determinations from lensing observations. The second part focuses on spectroscopic data from MUSE, a second-generation Integral-Field Spectrograph installed on one of the largest ground-based telescopes on earth. We present a pipeline which permits the efficient determination of the redshift of a source observed by MUSE. The redshift indicates the distance of the source from us and depends on the expansion of the universe. In addition, we use MUSE observations of a galaxy cluster to improve the determination of its total weight, including the dominant Dark Matter component. In the third part of this thesis, we investigate how we can accelerate the computation of these mass maps. In the era of big data and large surveys, computing efficiency is key to obtaining new scientific insights. We use High Performance Computing techniques like graphics card acceleration to improve the code performance and we develop a method which harnesses extra performance from using single precision without loosing the required accuracy. In the last section, we present first results from measuring flexion, a higher order lensing effect which could substantially increase the resolution of lensing mass maps and thus lead to a sharper view of structure in the universe

Quantenklassische Hybridbeschreibung von Solvatisierungseffekten

Eine aussagekräftige theoretische Beschreibung des Infrarot (IR)-Schwingungsspektrums eines Biomoleküls in seiner nativen Umgebung durch Molekulardynamik (MD)-Simulationen benötigt hinreichend genaue Modelle sowohl für das Biomolekül, als auch für das umgebende Lösungsmittel. Die quantenmechanische Dichtefunktionaltheorie (DFT) stellt solche genauen Modelle zur Verfügung, zieht aber hohen Rechenaufwand nach sich. Daher ist dieser Ansatz nicht zur Simulation der MD ausgedehnter Biomolekül-Lösungsmittel-Komplexe einsetzbar. Solche Systeme können effizient mit polarisierbaren molekülmechanischen (PMM) Kraftfeldern behandelt werden, die jedoch nicht die zur Berechnung von IR-Spektren nötige Genauigkeit liefern. Einen Ausweg aus dem skizzierten Dilemma bieten Hybridverfahren, die einen relevanten Teil eines Simulationssystems mit DFT, und die ausgedehnte Lösungsmittelumgebung mit einem (P)MM-Kraftfeld beschreiben. Im Rahmen dieser Arbeit wird, ausgehend von einer DFT/MM-Hybridmethode [Eichinger et al., J. Chem. Phys. 110, 10452-10467 (1999)], ein genaues und hocheffizientes DFT/PMM-Rechenverfahren entwickelt, das der wissenschaftlichen Ọ̈ffentlichkeit nun in Form des auf Großrechnern einsetzbaren Programmpakets IPHIGENIE/CPMD zur Verfügung steht. Die neue DFT/PMM-Methode fußt auf der optimalen Integration des DFT-Fragments in die "schnelle strukturadaptierte Multipolmethode" (SAMM) zur effizienten approximativen Berechnung der Wechselwirkungen zwischen den mit gitterbasierter DFT bzw. mit PMM beschriebenen Subsystemen. Dies erlaubt stabile Hamilton'sche MD-Simulationen sowie die Steigerung der Performanz (d.h. dem Produkt aus Genauigkeit und Recheneffizienz) um mehr als eine Größenordnung. Die eingeführte explizite Modellierung der elektronischen Polarisierbarkeit im PMM-Subsystem durch induzierbare Gauß'sche Dipole ermöglicht die Verwendung wesentlich genauerer PMM-Lösungsmittelmodelle. Ein effizientes Abtastens von Peptidkonformationen mit DFT/ PMM-MD kann mit einer generalisierten Ensemblemethode erfolgen. Durch die Entwicklung eines Gauß'schen polarisierbaren Sechspunktmodells (GP6P) für Wasser und die Parametrisierung der Modellpotentiale für van der Waals-Wechselwirkungen zwischen GP6P-Molekülen und der Amidgruppe (AG) von N-Methyl-Acetamid (NMA) wird ein DFT/PMM-Modell für (Poly-)Peptide und Proteine in wässriger Lösung konstruiert. Das neue GP6P-Modell kann die Eigenschaften von flüssigem Wasser mit guter Qualität beschreiben. Ferner können die mit DFT/PMM-MD berechneten IR-Spektren eines in GP6P gelösten DFT-Modells von NMA die experimentelle Evidenz mit hervorragender Genauigkeit reproduzieren. Somit ist nun ein hocheffizientes und ausgereiftes DFT/PMM-MD-Verfahren zur genauen Berechnung der Konformationslandschaften und IR-Schwingungsspektren von in Wasser gelösten Proteinen verfügbar.A meaningful theoretical description of the infrared (IR) spectrum of a biomolecule in its native environment by molecular dynamics (MD) simulations requires adequately accurate models both for the biomolecule and for its solvent environment. The quantum mechanical density functional theory (DFT) provides such accurate models, but entails high computational effort. Therefore, this approach is not suited for the simulation of the MD of extended biomolecule-solvent-complexes. Such systems can be handled efficiently by polarizable molecular mechanics (PMM) force fields, which, however, do not provide the accuracy required for the computation of IR spectra. The sketched dilemma is resolved by hybrid approaches, which describe a relevant part of a simulation system by DFT, and the extended solvent environment by a (P)MM force field. Based on a DFT/MM hybrid method [Eichinger et al., J. Chem. Phys. 110, 10452-10467 (1999)], an accurate and highly efficient DFT/PMM approach is developed in this thesis. Its implementation in the program package IPHIGENIE/CPMD is suitable for high-performance computing applications and available to the scientific community. The new DFT/PMM method is based on the optimal integration of the DFT fragment into the "structure-adapted fast multipole method" (SAMM) for the efficient approximative computation of interactions between the subsystems described by grid-based DFT and PMM, respectively. It enables stable, Hamiltonian MD simulations, and increases the performance (i.e. accuracy times efficiency) by more than one order of magnitude. The explicit modeling of electronic polarizability in the PMM subsystem by induced Gaussian dipoles allows the use of much more accurate PMM solvent models. The efficiency of peptide conformational sampling with DFT/PMM-MD is increased by applying a generalized ensemble method. By constructing a Gaussian polarizable six-point (GP6P) model for water and by parametrizing the model potentials for van der Waals interactions between GP6P molecules and the amide group (AG) of N-Methyl-Acetamide (NMA), a DFT/PMM model for (poly-)peptides and proteins in aqueous solution is developed. The new GP6P model can describe the properties of liquid water with good quality. Furthermore, the IR spectra of a DFT model of NMA solvated in GP6P, which were calculated by DFT/PMM-MD, can reproduce the experimental evidence with excellent quality. Thus, a highly efficient and mature DFT/PMM-MD approach for the accurate computation of conformational landscapes and IR spectra of proteins in aqueous solution is now available

Spin densities in 4f and 3d magnetic systems

This thesis documents investigations into three novel magnetic materials: the predicted halfmetal, NiMnSb; the magnetoelectric perovskite, TbMnO3; and the layered superconductor, EuFe