Ab initio Molecular Dynamics Simulations of the Structural Response of Solids to Ultrashort Laser and XUV Pulses

The theoretical model and underlying physics described in this thesis are about the interaction of femtosecond-laser and XUV pulses with solids. The key to understand the basics of such interaction is to study the structural response of the materials after laser interaction. Depending on the laser characteristics, laser-solid interaction can result in a wide range of structural responses such as solid-solid phase transitions, vacuum phonon squeezing, ultrafast melting, generation of coherent phonons, etc. During my research work, I have modeled the systems irradiated by low-, medium- and high-laser intensities, and studied different types of structural dynamics of solids at various laser fluences.

Beschreibung von Oberflächenphänomenen durch relativistische Clusterrechnungen unter Verwendung eines Einbettungsverfahrens

For the theoretical investigation of local phenomena (adsorption at surfaces, defects or impurities within a crystal, etc.) one can assume that the effects caused by the local disturbance are only limited to the neighbouring particles. With this model, that is well-known as cluster-approximation, an infinite system can be simulated by a much smaller segment of the surface (Cluster). The size of this segment varies strongly for different systems. Calculations to the convergence of bond distance and binding energy of an adsorbed aluminum atom on an Al(100)-surface showed that more than 100 atoms are necessary to get a sufficient description of surface properties. However with a full-quantummechanical approach these system sizes cannot be calculated because of the effort in computer memory and processor speed. Therefore we developed an embedding procedure for the simulation of surfaces and solids, where the whole system is partitioned in several parts which itsself are treated differently: the internal part (cluster), which is located near the place of the adsorbate, is calculated completely self-consistently and is embedded into an environment, whereas the influence of the environment on the cluster enters as an additional, external potential to the relativistic Kohn-Sham-equations. The basis of the procedure represents the density functional theory. However this means that the choice of the electronic density of the environment constitutes the quality of the embedding procedure. The environment density was modelled in three different ways: atomic densities; of a large prepended calculation without embedding transferred densities; bulk-densities (copied). The embedding procedure was tested on the atomic adsorptions of 'Al on Al(100) and Cu on Cu(100). The result was that if the environment is choices appropriately for the Al-system one needs only 9 embedded atoms to reproduce the results of exact slab-calculations. For the Cu-system first calculations without embedding procedures were accomplished, with the result that already 60 atoms are sufficient as a surface-cluster. Using the embedding procedure the same values with only 25 atoms were obtained. This means a substantial improvement if one takes into consideration that the calculation time increased cubically with the number of atoms. With the embedding method Infinite systems can be treated by molecular methods. Additionally the program code was extended by the possibility to make molecular-dynamic simulations. Now it is possible apart from the past calculations of fixed cores to investigate also structures of small clusters and surfaces. A first application we made with the adsorption of Cu on Cu(100). We calculated the relaxed positions of the atoms that were located close to the adsorption site and afterwards made the full-quantummechanical calculation of this system. We did that procedure for different distances to the surface. Thus a realistic adsorption process could be examined for the first time. It should be remarked that when doing the Cu reference-calculations (without embedding) we begun to parallelize the entire program code. Only because of this aspect the investigations for the 100 atomic Cu surface-clusters were possible. Due to the good efficiency of both the parallelization and the developed embedding procedure we will be able to apply the combination in future. This will help to work on more these areas it will be possible to bring in results of full-relativistic molecular calculations, what will be very interesting especially for the regime of heavy systems.

Profile simulations of gas chopping etching processes : model development and comparison with experiments

The progress in microsystem technology or nano technology places extended requirements to the fabrication processes. The trend is moving towards structuring within the nanometer scale on the one hand, and towards fabrication of structures with high aspect ratio (ratio of vertical vs. lateral dimensions) and large depths in the 100 µm scale on the other hand. Current procedures for the microstructuring of silicon are wet chemical etching and dry or plasma etching. A modern plasma etching technique for the structuring of silicon is the so-called "gas chopping" etching technique (also called "time-multiplexed etching"). In this etching technique, passivation cycles, which prevent lateral underetching of sidewalls, and etching cycles, which etch preferably in the vertical direction because of the sidewall passivation, are constantly alternated during the complete etching process. To do this, a CHF3/CH4 plasma, which generates CF monomeres is employed during the passivation cycle, and a SF6/Ar, which generates fluorine radicals and ions plasma is employed during the etching cycle. Depending on the requirements on the etched profile, the durations of the individual passivation and etching cycles are in the range of a few seconds up to several minutes. The profiles achieved with this etching process crucially depend on the flow of reactants, i.e. CF monomeres during the passivation cycle, and ions and fluorine radicals during the etching cycle, to the bottom of the profile, especially for profiles with high aspect ratio. With regard to the predictability of the etching processes, knowledge of the fundamental effects taking place during a gas chopping etching process, and their impact onto the resulting profile is required. For this purpose in the context of this work, a model for the description of the profile evolution of such etching processes is proposed, which considers the reactions (etching or deposition) at the sample surface on a phenomenological basis. Furthermore, the reactant transport inside the etching trench is modelled, based on angular distribution functions and on absorption probabilities at the sidewalls and bottom of the trench. A comparison of the simulated profiles with corresponding experimental profiles reveals that the proposed model reproduces the experimental profiles, if the angular distribution functions and absorption probabilities employed in the model is in agreement with data found in the literature. Therefor the model developed in the context of this work is an adequate description of the effects taking place during a gas chopping plasma etching process.

Experimentelle und numerische Untersuchungen zur Dispersion von Dichteströmungen in einem stochastischen Modellaquifer

Es ist bekannt, dass die Dichte eines gelösten Stoffes die Richtung und die Stärke seiner Bewegung im Untergrund entscheidend bestimmen kann. Eine Vielzahl von Untersuchungen hat gezeigt, dass die Verteilung der Durchlässigkeiten eines porösen Mediums diese Dichteffekte verstärken oder abmindern kann. Wie sich dieser gekoppelte Effekt auf die Vermischung zweier Fluide auswirkt, wurde in dieser Arbeit untersucht und dabei das experimentelle sowohl mit dem numerischen als auch mit dem analytischen Modell gekoppelt. Die auf der Störungstheorie basierende stochastische Theorie der macrodispersion wurde in dieser Arbeit für den Fall der transversalen Makodispersion. Für den Fall einer stabilen Schichtung wurde in einem Modelltank (10m x 1.2m x 0.1m) der Universität Kassel eine Serie sorgfältig kontrollierter zweidimensionaler Experimente an einem stochastisch heterogenen Modellaquifer durchgeführt. Es wurden Versuchsreihen mit variierenden Konzentrationsdifferenzen (250 ppm bis 100 000 ppm) und Strömungsgeschwindigkeiten (u = 1 m/ d bis 8 m/d) an drei verschieden anisotrop gepackten porösen Medien mit variierender Varianzen und Korrelationen der lognormal verteilten Permeabilitäten durchgeführt. Die stationäre räumliche Konzentrationsausbreitung der sich ausbreitenden Salzwasserfahne wurde anhand der Leitfähigkeit gemessen und aus der Höhendifferenz des 84- und 16-prozentigen relativen Konzentrationsdurchgang die Dispersion berechnet. Parallel dazu wurde ein numerisches Modell mit dem dichteabhängigen Finite-Elemente-Strömungs- und Transport-Programm SUTRA aufgestellt. Mit dem kalibrierten numerischen Modell wurden Prognosen für mögliche Transportszenarien, Sensitivitätsanalysen und stochastische Simulationen nach der Monte-Carlo-Methode durchgeführt. Die Einstellung der Strömungsgeschwindigkeit erfolgte - sowohl im experimentellen als auch im numerischen Modell - über konstante Druckränder an den Ein- und Auslauftanks. Dabei zeigte sich eine starke Sensitivität der räumlichen Konzentrationsausbreitung hinsichtlich lokaler Druckvariationen. Die Untersuchungen ergaben, dass sich die Konzentrationsfahne mit steigendem Abstand von der Einströmkante wellenförmig einem effektiven Wert annähert, aus dem die Makrodispersivität ermittelt werden kann. Dabei zeigten sich sichtbare nichtergodische Effekte, d.h. starke Abweichungen in den zweiten räumlichen Momenten der Konzentrationsverteilung der deterministischen Experimente von den Erwartungswerten aus der stochastischen Theorie. Die transversale Makrodispersivität stieg proportional zur Varianz und Korrelation der lognormalen Permeabilitätsverteilung und umgekehrt proportional zur Strömungsgeschwindigkeit und Dichtedifferenz zweier Fluide. Aus dem von Welty et al. [2003] mittels Störungstheorie entwickelten dichteabhängigen Makrodispersionstensor konnte in dieser Arbeit die stochastische Formel für die transversale Makrodispersion weiter entwickelt und - sowohl experimentell als auch numerisch - verifiziert werden.

Theoretical study of the structural dependence of nuclear quadrupole frequencies in high-T_c superconductors

The remarkable difference between the nuclear quadrupole frequencies v_Q of Cu(1) and Cu(2) in YBa_2Cu_3O_6 and YBa_2Cu_3O_7 is analyzed. We calculate the ionic contribution to the electric field gradients and estimate, by using experimental results for Cu_2O and La_2CuO_4, the contribution of the d valence electrons. Thus, we determine v_Q1, v_Q2, and the asymmetry parameter η for YBa_2Cu_3O_6 and YBa_2Cu_3O_7. The number of holes in dthe Cu-O planes and chains is found to be important for the different behavior of v_Q1 and v_Q2.

Theoretical evidence for quasi-molecular structure at small internuclear distances in elastic ion-atom scattering

The potential energy curve of the system Ne-Ne is calculated for small internuclear distances from 0.005 to 3.0 au using a newly developed relativistic molecular Dirac-Fock-Slater code. A significant structure in the potential energy curve is found which leads to a nearly complete agreement with experimental differential elastic scattering cross sections. This demonstrates the presence of quasi-molecular effects in elastic ion-atom collisions at keV energies.

First results of experimental and theoretical investigations on sextet states of doubly-excited five-electron ions

In continuation of our previous work on doubly-excited ions with three and four electrons we present the first results on optical transitions in the term system of doubly-excited ions with five electrons. Transitions between such sextet states were identified in beam-foil spectra of the ions nitrogen, oxygen and fluorine. Assignments were first established by comparison with Multi-Configuration Dirac-Fock calculations. Later assignments were aided by Multi-Configuration Hartree-Fock calculations (see the contribution by G. Miecznik et al. in this issue). Decay curves were recorded for all six candidate lines. The lifetime results are compared to theoretical values which confirm most of the assignments qualitatively.

Theoretical study of the physicochemical properties of the light transactinides

A theoretical study of the physicochemical properties of elements 104, 105, and 106 and their compounds in the gas phase and aqueous solutions has been undertaken using relativistic atomic and molecular codes. Trends in properties such as bonding, ionization potentials, electron affinities, energies of electronic transitions, stabilities of oxidation states etc. have been defined within the corresponding chemical groups and within the transactinides. These trends are shown to be determined by increasing relativistic effects within the groups. The behaviour of some gas phase compounds and complexes in solutions is predicted for the gas chromatography and solvent extraction experiments. Redox potentials in aqueous solutions of these elements are estimated.

Development of hybrid UV VCSEL with organic active material and dielectric DBR mirrors for medical, sensoric and data storage applications

Lasers play an important role for medical, sensoric and data storage devices. This thesis is focused on design, technology development, fabrication and characterization of hybrid ultraviolet Vertical-Cavity Surface-Emitting Lasers (UV VCSEL) with organic laser-active material and inorganic distributed Bragg reflectors (DBR). Multilayer structures with different layer thicknesses, refractive indices and absorption coefficients of the inorganic materials were studied using theoretical model calculations. During the simulations the structure parameters such as materials and thicknesses have been varied. This procedure was repeated several times during the design optimization process including also the feedback from technology and characterization. Two types of VCSEL devices were investigated. The first is an index coupled structure consisting of bottom and top DBR dielectric mirrors. In the space in between them is the cavity, which includes active region and defines the spectral gain profile. In this configuration the maximum electrical field is concentrated in the cavity and can destroy the chemical structure of the active material. The second type of laser is a so called complex coupled VCSEL. In this structure the active material is placed not only in the cavity but also in parts of the DBR structure. The simulations show that such a distribution of the active material reduces the required pumping power for reaching lasing threshold. High efficiency is achieved by substituting the dielectric material with high refractive index for the periods closer to the cavity. The inorganic materials for the DBR mirrors have been deposited by Plasma- Enhanced Chemical Vapor Deposition (PECVD) and Dual Ion Beam Sputtering (DIBS) machines. Extended optimizations of the technological processes have been performed. All the processes are carried out in a clean room Class 1 and Class 10000. The optical properties and the thicknesses of the layers are measured in-situ by spectroscopic ellipsometry and spectroscopic reflectometry. The surface roughness is analyzed by atomic force microscopy (AFM) and images of the devices are taken with scanning electron microscope (SEM). The silicon dioxide (SiO2) and silicon nitride (Si3N4) layers deposited by the PECVD machine show defects of the material structure and have higher absorption in the ultra violet range compared to ion beam deposition (IBD). This results in low reflectivity of the DBR mirrors and also reduces the optical properties of the VCSEL devices. However PECVD has the advantage that the stress in the layers can be tuned and compensated, in contrast to IBD at the moment. A sputtering machine Ionsys 1000 produced by Roth&Rau company, is used for the deposition of silicon dioxide (SiO2), silicon nitride (Si3N4), aluminum oxide (Al2O3) and zirconium dioxide (ZrO2). The chamber is equipped with main (sputter) and assisted ion sources. The dielectric materials were optimized by introducing additional oxygen and nitrogen into the chamber. DBR mirrors with different material combinations were deposited. The measured optical properties of the fabricated multilayer structures show an excellent agreement with the results of theoretical model calculations. The layers deposited by puttering show high compressive stress. As an active region a novel organic material with spiro-linked molecules is used. Two different materials have been evaporated by utilizing a dye evaporation machine in the clean room of the department Makromolekulare Chemie und Molekulare Materialien (mmCmm). The Spiro-Octopus-1 organic material has a maximum emission at the wavelength λemission = 395 nm and the Spiro-Pphenal has a maximum emission at the wavelength λemission = 418 nm. Both of them have high refractive index and can be combined with low refractive index materials like silicon dioxide (SiO2). The sputtering method shows excellent optical quality of the deposited materials and high reflection of the multilayer structures. The bottom DBR mirrors for all VCSEL devices were deposited by the DIBS machine, whereas the top DBR mirror deposited either by PECVD or by combination of PECVD and DIBS. The fabricated VCSEL structures were optically pumped by nitrogen laser at wavelength λpumping = 337 nm. The emission was measured by spectrometer. A radiation of the VCSEL structure at wavelength 392 nm and 420 nm is observed.

Protein Folding Simulations: Confinement, External Fields and Sequence Design

The present Thesis looks at the problem of protein folding using Monte Carlo and Langevin simulations, three topics in protein folding have been studied: 1) the effect of confining potential barriers, 2) the effect of a static external field and 3) the design of amino acid sequences which fold in a short time and which have a stable native state (global minimum). Regarding the first topic, we studied the confinement of a small protein of 16 amino acids known as 1NJ0 (PDB code) which has a beta-sheet structure as a native state. The confinement of proteins occurs frequently in the cell environment. Some molecules called Chaperones, present in the cytoplasm, capture the unfolded proteins in their interior and avoid the formation of aggregates and misfolded proteins. This mechanism of confinement mediated by Chaperones is not yet well understood. In the present work we considered two kinds of potential barriers which try to mimic the confinement induced by a Chaperon molecule. The first kind of potential was a purely repulsive barrier whose only effect is to create a cavity where the protein folds up correctly. The second kind of potential was a barrier which includes both attractive and repulsive effects. We performed Wang-Landau simulations to calculate the thermodynamical properties of 1NJ0. From the free energy landscape plot we found that 1NJ0 has two intermediate states in the bulk (without confinement) which are clearly separated from the native and the unfolded states. For the case of the purely repulsive barrier we found that the intermediate states get closer to each other in the free energy landscape plot and eventually they collapse into a single intermediate state. The unfolded state is more compact, compared to that in the bulk, as the size of the barrier decreases. For an attractive barrier modifications of the states (native, unfolded and intermediates) are observed depending on the degree of attraction between the protein and the walls of the barrier. The strength of the attraction is measured by the parameter $\epsilon$. A purely repulsive barrier is obtained for $\epsilon=0$ and a purely attractive barrier for $\epsilon=1$. The states are changed slightly for magnitudes of the attraction up to $\epsilon=0.4$. The disappearance of the intermediate states of 1NJ0 is already observed for $\epsilon =0.6$. A very high attractive barrier ($\epsilon \sim 1.0$) produces a completely denatured state. In the second topic of this Thesis we dealt with the interaction of a protein with an external electric field. We demonstrated by means of computer simulations, specifically by using the Wang-Landau algorithm, that the folded, unfolded, and intermediate states can be modified by means of a field. We have found that an external field can induce several modifications in the thermodynamics of these states: for relatively low magnitudes of the field ($<2.06 \times 10^8$ V/m) no major changes in the states are observed. However, for higher magnitudes than ($6.19 \times 10^8$ V/m) one observes the appearance of a new native state which exhibits a helix-like structure. In contrast, the original native state is a $\beta$-sheet structure. In the new native state all the dipoles in the backbone structure are aligned parallel to the field. The design of amino acid sequences constitutes the third topic of the present work. We have tested the Rate of Convergence criterion proposed by D. Gridnev and M. Garcia ({\it work unpublished}). We applied it to the study of off-lattice models. The Rate of Convergence criterion is used to decide if a certain sequence will fold up correctly within a relatively short time. Before the present work, the common way to decide if a certain sequence was a good/bad folder was by performing the whole dynamics until the sequence got its native state (if it existed), or by studying the curvature of the potential energy surface. There are some difficulties in the last two approaches. In the first approach, performing the complete dynamics for hundreds of sequences is a rather challenging task because of the CPU time needed. In the second approach, calculating the curvature of the potential energy surface is possible only for very smooth surfaces. The Rate of Convergence criterion seems to avoid the previous difficulties. With this criterion one does not need to perform the complete dynamics to find the good and bad sequences. Also, the criterion does not depend on the kind of force field used and therefore it can be used even for very rugged energy surfaces.

Theory of laser-induced ultrafast structural changes in solids

The present thesis is a contribution to the study of laser-solid interaction. Despite the numerous applications resulting from the recent use of laser technology, there is still a lack of satisfactory answers to theoretical questions regarding the mechanism leading to the structural changes induced by femtosecond lasers in materials. We provide here theoretical approaches for the description of the structural response of different solids (cerium, samarium sulfide, bismuth and germanium) to femtosecond laser excitation. Particular interest is given to the description of the effects of the laser pulse on the electronic systems and changes of the potential energy surface for the ions. Although the general approach of laser-excited solids remains the same, the potential energy surface which drives the structural changes is calculated with different theoretical models for each material. This is due to the difference of the electronic properties of the studied systems. We use the Falicov model combined with an hydrodynamic method to study photoinduced phase changes in cerium. The local density approximation (LDA) together with the Hubbard-type Hamiltonian (LDA+U) in the framework of density functional theory (DFT) is used to describe the structural properties of samarium sulfide. We parametrize the time-dependent potential energy surface (calculated using DFT+ LDA) of bismuth on which we perform quantum dynamical simulations to study the experimentally observed amplitude collapse and revival of coherent $A_{1g}$ phonons. On the basis of a time-dependent potential energy surface calculated from a non-orthogonal tight binding Hamiltonian, we perform molecular dynamics simulation to analyze the time evolution (coherent phonons, ultrafast nonthermal melting) of germanium under laser excitation. The thermodynamic equilibrium properties of germanium are also reported. With the obtained results we are able to give many clarifications and interpretations of experimental results and also make predictions.

Theoretical study of magnetism, structure and chemical order in transition-metal alloy clusters

Research on transition-metal nanoalloy clusters composed of a few atoms is fascinating by their unusual properties due to the interplay among the structure, chemical order and magnetism. Such nanoalloy clusters, can be used to construct nanometer devices for technological applications by manipulating their remarkable magnetic, chemical and optical properties. Determining the nanoscopic features exhibited by the magnetic alloy clusters signifies the need for a systematic global and local exploration of their potential-energy surface in order to identify all the relevant energetically low-lying magnetic isomers. In this thesis the sampling of the potential-energy surface has been performed by employing the state-of-the-art spin-polarized density-functional theory in combination with graph theory and the basin-hopping global optimization techniques. This combination is vital for a quantitative analysis of the quantum mechanical energetics. The first approach, i.e., spin-polarized density-functional theory together with the graph theory method, is applied to study the Fe$_m$Rh$_n$ and Co$_m$Pd$_n$ clusters having $N = m+n \leq 8$ atoms. We carried out a thorough and systematic sampling of the potential-energy surface by taking into account all possible initial cluster topologies, all different distributions of the two kinds of atoms within the cluster, the entire concentration range between the pure limits, and different initial magnetic configurations such as ferro- and anti-ferromagnetic coupling. The remarkable magnetic properties shown by FeRh and CoPd nanoclusters are attributed to the extremely reduced coordination number together with the charge transfer from 3$d$ to 4$d$ elements. The second approach, i.e., spin-polarized density-functional theory together with the basin-hopping method is applied to study the small Fe$_6$, Fe$_3$Rh$_3$ and Rh$_6$ and the larger Fe$_{13}$, Fe$_6$Rh$_7$ and Rh$_{13}$ clusters as illustrative benchmark systems. This method is able to identify the true ground-state structures of Fe$_6$ and Fe$_3$Rh$_3$ which were not obtained by using the first approach. However, both approaches predict a similar cluster for the ground-state of Rh$_6$. Moreover, the computational time taken by this approach is found to be significantly lower than the first approach. The ground-state structure of Fe$_{13}$ cluster is found to be an icosahedral structure, whereas Rh$_{13}$ and Fe$_6$Rh$_7$ isomers relax into cage-like and layered-like structures, respectively. All the clusters display a remarkable variety of structural and magnetic behaviors. It is observed that the isomers having similar shape with small distortion with respect to each other can exhibit quite different magnetic moments. This has been interpreted as a probable artifact of spin-rotational symmetry breaking introduced by the spin-polarized GGA. The possibility of combining the spin-polarized density-functional theory with some other global optimization techniques such as minima-hopping method could be the next step in this direction. This combination is expected to be an ideal sampling approach having the advantage of avoiding efficiently the search over irrelevant regions of the potential energy surface.