An attempt on the calculation of relativistic potential energy curves: noble gas difluorides

Total energy SCF calculations were performed for noble gas difluorides in a relativistic procedure and compared with analogous non-relativistic calculations. The discrete variational method with numerical basis functions was used. Rather smooth potential energy curves could be obtained. The theoretical Kr - F and Xe - F bond distances were calculated to be 3.5 a.u. and 3.6 a.u. which should be compared with the experimental values of 3.54 a.u. and 3.7 a.u. Although the dissociation energies are off by a factor of about five it was found that ArF_2 may be a stable molecule. Theoretical ionization energies for the outer levels reproduce the experimental values for KrF_2 and XeF_2 to within 2 eV.

Relativistic Dirac-Fock-Slater program to calculate potential-energy curves for diatomic molecules

A LCAO-MO (linear combination of atomic orbitals - molecular orbitals) relativistic Dirac-Fock-Slater program is presented, which allows one to calculate accurate total energies for diatomic molecules. Numerical atomic Dirac-Fock-Slater wave functions are used as basis functions. All integrations as well as the solution of the Poisson equation are done fully numerical, with a relative accuracy of 10{^-5} - 10{^-6}. The details of the method as well as first results are presented here.

Adsorption of element 112 on a Au surface

Während der letzten 20 Jahre hat sich das Periodensystem bis zu den Elementen 114 und 116 erweitert. Diese sind kernphysikalisch nachgewiesen, so dass jetzt die chemische Untersuchung an erster Selle steht. Nachdem sich das Periodensystem bis zum Element 108 so verhält, wie man es dem Periodensystem nach annimmt, wird in dieser Arbeit die Chemie des Elements 112 untersucht. Dabei geht es um die Adsorptionsenergie auf einer Gold-Ober fläche, weil dies der physikalisch/chemische Prozess ist, der bei der Analyse angewandt wird. Die Methode, die in dieser Arbeit angwandt wird, ist die relativistische Dichtefunktionalmethode. Im ersten Teil wird das Vielkörperproblem in allgemeiner Form behandelt, und im zweiten die grundlegenden Eigenschaften und Formulierungen der Dichtefunktionaltheorie. Die Arbeit beschreibt zwei prinzipiell unterschiedliche Ansätze, wie die Adsorptionsenergie berechnet werden kann. Zum einen ist es die sogenannte Clustermethode, bei der ein Atom auf ein relativ kleines Cluster aufgebracht und dessen Adsorptionsenergie berechnet wird. Wenn es gelingt, die Konvergenz mit der Größe des Clusters zu erreichen, sollte dies zu einem Wert für die Adsorptionsenergie führen. Leider zeigt sich in den Rechnungen, dass aufgrund des zeitlichen Aufwandes die Konvergenz für die Clusterrechnungen nicht erreicht wird. Es werden sehr ausführlich die drei verschiedenen Adsorptionsplätze, die Top-, die Brücken- und die Muldenposition, berechnet. Sehr viel mehr Erfolg erzielt man mit der Einbettungsmethode, bei der ein kleiner Cluster von vielen weiteren Atomen an den Positionen, die sie im Festkörpers auf die Adsorptionsenergie soweit sichergestellt ist, dass physikalisch-chemisch gute Ergebnisse erzielt werden. Alle hier gennanten Rechnungen sowohl mit der Cluster- wie mit der Einbettungsmethode verlangen sehr, sehr lange Rechenzeiten, die, wie oben bereits erwähnt, nicht zu einer Konvergenz für die Clusterrechnungen ausreichten. In der Arbeit wird bei allen Rechnungen sehr detailliert auf die Abhängigkeit von den möglichen Basissätzen eingegangen, die ebenfalls in entscheidender Weise zur Länge und Qualität der Rechnungen beitragen. Die auskonvergierten Rechnungen werden in der Form von Potentialkurven, Density of States (DOS), Overlap Populations sowie Partial Crystal Overlap Populations analysiert. Im Ergebnis zeigt sich, dass die Adsoptionsenergie für das Element 112 auf einer Goldoberfläche ca. 0.2 eV niedriger ist als die Adsorption von Quecksilber auf der gleichen Ober fläche. Mit diesem Ergebnis haben die experimentellen Kernchemiker einen Wert an der Hand, mit dem sie eine Anhaltspunkt haben, wo sie bei den Messungen die wenigen zu erwartenden Ereignisse finden können.

An ab-initio calculation of the Coulomb explosion of N_2 after heavy-ion bombardement

Self-consistent-field calculations for the total potential energy of highly ionized N_2 molecules are presented. We compare these calculations to the experimentally observed energy released in the Coulomb explosion of ionized N_2 molecules created after collision with fast heavy ions. The most important electronic states of the fragment ions are determined.

Total differential scattering cross section of {Ar^+}-Ar at 15 to 400 keV

We report on the measurement of the total differential scattering cross section of {Ar^+}-Ar at laboratory energies between 15 and 400 keV. Using an ab initio relativistic molecular program which calculates the interatomic potential energy curve with high accuracy, we are able to reproduce the detailed structure found in the experiment.

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.

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.

Squeezed thermal phonons precurse nonthermal melting of silicon as a function of fluence

A femtosecond-laser pulse can induce ultrafast nonthermal melting of various materials along pathways that are inaccessible under thermodynamic conditions, but it is not known whether there is any structural modification at fluences just below the melting threshold. Here, we show for silicon that in this regime the room-temperature phonons become thermally squeezed, which is a process that has not been reported before in this material. We find that the origin of this effect is the sudden femtosecond-laser-induced softening of interatomic bonds, which can also be described in terms of a modification of the potential energy surface. We further find in ab initio molecular-dynamics simulations on laser-excited potential energy surfaces that the atoms move in the same directions during the first stages of nonthermal melting and thermal phonon squeezing. Our results demonstrate how femtosecond-laser-induced coherent fluctuations precurse complete atomic disordering as a function of fluence. The common underlying bond-softening mechanism indicates that this relation between thermal squeezing and nonthermal melting is not material specific.

Transport magnetischer Partikel durch maßgeschneiderte magnetische Feldlandschaften zur Anwendung in mikrofluidischen Mischprozessen

Die Miniaturisierung von konventioneller Labor- und Analysetechnik nimmt eine zentrale Rolle im Bereich der allgemeinen Lebenswissenschaften und medizinischen Diagnostik ein. Neuartige und preiswerte Technologieplattformen wie Lab-on-a-Chip (LOC) oder Mikrototalanalysesysteme (µTAS) versprechen insbesondere im Bereich der Individualmedizin einen hohen gesellschaftlichen Nutzen zur frühzeitigen und nichtinvasiven Diagnose krankheitsspezifischer Indikatoren. Durch den patientennahen Einsatz preiswerter und verlässlicher Mikrochips auf Basis hoher Qualitätsstandards entfallen kostspielige und zeitintensive Zentrallaboranalysen, was gleichzeitig Chancen für den globalen Einsatz - speziell in Schwellen- und Entwicklungsländern - bietet. Die technischen Herausforderungen bei der Realisierung moderner LOC-Systeme sind in der kontrollierten und verlässlichen Handhabung kleinster Flüssigkeitsmengen sowie deren diagnostischem Nachweis begründet. In diesem Kontext wird der erfolgreichen Integration eines fernsteuerbaren Transports von biokompatiblen, magnetischen Mikro- und Nanopartikeln eine Schlüsselrolle zugesprochen. Die Ursache hierfür liegt in der vielfältigen Einsetzbarkeit, die durch die einzigartigen Materialeigenschaften begründet sind. Diese reichen von der beschleunigten, aktiven Durchmischung mikrofluidischer Substanzvolumina über die Steigerung der molekularen Interaktionsrate in Biosensoren bis hin zur Isolation und Aufreinigung von krankheitsspezifischen Indikatoren. In der Literatur beschriebene Ansätze basieren auf der dynamischen Transformation eines makroskopischen, zeitabhängigen externen Magnetfelds in eine mikroskopisch veränderliche potentielle Energielandschaft oberhalb magnetisch strukturierter Substrate, woraus eine gerichtete und fernsteuerbare Partikelbewegung resultiert. Zentrale Kriterien, wie die theoretische Modellierung und experimentelle Charakterisierung der magnetischen Feldlandschaft in räumlicher Nähe zur Oberfläche der strukturierten Substrate sowie die theoretische Beschreibung der Durchmischungseffekte, wurden jedoch bislang nicht näher beleuchtet, obwohl diese essentiell für ein detailliertes Verständnis der zu Grunde liegenden Mechanismen und folglich für einen Markteintritt zukünftiger Geräte sind. Im Rahmen der vorgestellten Arbeit wurde daher ein neuartiger Ansatz zur erfolgreichen Integration eines Konzepts zum fernsteuerbaren Transport magnetischer Partikel zur Anwendung in modernen LOC-Systemen unter Verwendung von magnetisch strukturierten Exchange-Bias (EB) Dünnschichtsystemen verfolgt. Die Ergebnisse zeigen, dass sich das Verfahren der ionenbe-schussinduzierten magnetischen Strukturierung (IBMP) von EB-Systemen zur Herstellung von maßgeschneiderten magnetischen Feldlandschaften (MFL) oberhalb der Substratoberfläche, deren Stärke und räumlicher Verlauf auf Nano- und Mikrometerlängenskalen gezielt über die Veränderung der Materialparameter des EB-Systems via IBMP eingestellt werden kann, eignet. Im Zuge dessen wurden erstmals moderne, experimentelle Verfahrenstechniken (Raster-Hall-Sonden-Mikroskopie und rastermagnetoresistive Mikroskopie) in Kombination mit einem eigens entwickelten theoretischen Modell eingesetzt, um eine Abbildung der MFL in unterschiedlichen Abstandsbereichen zur Substratoberfläche zu realisieren. Basierend auf der quantitativen Kenntnis der MFL wurde ein neuartiges Konzept zum fernsteuerbaren Transport magnetischer Partikel entwickelt, bei dem Partikelgeschwindigkeiten im Bereich von 100 µm/s unter Verwendung von externen Magnetfeldstärken im Bereich weniger Millitesla erzielt werden können, ohne den magnetischen Zustand des Substrats zu modifizieren. Wie aus den Untersuchungen hervorgeht, können zudem die Stärke des externen Magnetfelds, die Stärke und der Gradient der MFL, das magnetfeldinduzierte magnetische Moment der Partikel sowie die Größe und der künstlich veränderliche Abstand der Partikel zur Substratoberfläche als zentrale Einflussgrößen zur quantitativen Modifikation der Partikelgeschwindigkeit genutzt werden. Abschließend wurde erfolgreich ein numerisches Simulationsmodell entwickelt, das die quantitative Studie der aktiven Durchmischung auf Basis des vorgestellten Partikeltransportkonzepts von theoretischer Seite ermöglicht, um so gezielt die geometrischen Gegebenheiten der mikrofluidischen Kanalstrukturen auf einem LOC-System für spezifische Anwendungen anzupassen.