A semi-phenomenological approach to the structure and transport properties of macromolecules in solution

Motiviert durch die Lebenswissenschaften (Life sciences) haben sich Untersuchungen zur Dynamik von Makromolekülen in Lösungen in den vergangenen Jahren zu einem zukunftsweisenden Forschungsgebiet etabliert, dessen Anwendungen von der Biophysik über die physikalische Chemie bis hin zu den Materialwissenschaften reichen. Neben zahlreichen experimentellen Forschungsprogrammen zur räumlichen Struktur und den Transporteigenschaften grosser MolekÄule, wie sie heute praktisch an allen (Synchrotron-) Strahlungsquellen und den Laboren der Biophysik anzutreffen sind, werden gegenwärtig daher auch umfangreiche theoretische Anstrengungen unternommen, um das Diffusionsverhalten von Makromolekülen besser zu erklären. Um neue Wege für eine quantitative Vorhersagen des Translations- und Rotationsverhaltens grosser Moleküle zu erkunden, wurde in dieser Arbeit ein semiphänomenologischer Ansatz verfolgt. Dieser Ansatz erlaubte es, ausgehend von der Hamiltonschen Mechanik des Gesamtsystems 'Molekül + Lösung', eine Mastergleichung für die Phasenraumdichte der Makromoleküle herzuleiten, die den Einfluss der Lösung mittels effektiver Reibungstensoren erfasst. Im Rahmen dieses Ansatzes gelingt es z.B. (i) sowohl den Einfluss der Wechselwirkung zwischen den makromolekularen Gruppen (den sogenannten molekularen beads) und den Lösungsteilchen zu analysieren als auch (ii) die Diffusionseigen schaften für veschiedene thermodynamische Umgebungen zu untersuchen. Ferner gelang es auf der Basis dieser Näherung, die Rotationsbewegung von grossen Molekülen zu beschreiben, die einseitig auf einer Oberfläche festgeheftet sind. Im Vergleich zu den aufwendigen molekulardynamischen (MD) Simulationen grosser Moleküle zeichnet sich die hier dargestellte Methode vor allem durch ihren hohen `Effizienzgewinn' aus, der für komplexe Systeme leicht mehr als fünf Grössenordnungen betragen kann. Dieser Gewinn an Rechenzeit erlaubt bspw. Anwendungen, wie sie mit MD Simulationen wohl auch zukünftig nicht oder nur sehr zögerlich aufgegriffen werden können. Denkbare Anwendungsgebiete dieser Näherung betreffen dabei nicht nur dichte Lösungen, in denen auch die Wechselwirkungen der molekularen beads zu benachbarten Makromolekülen eine Rolle spielt, sondern auch Untersuchungen zu ionischen Flüssigkeiten oder zur Topologie grosser Moleküle.

Solution of the Hartree-Fock equations for atoms and diatomic molecules with the finite element method

The finite element method (FEM) is now developed to solve two-dimensional Hartree-Fock (HF) equations for atoms and diatomic molecules. The method and its implementation is described and results are presented for the atoms Be, Ne and Ar as well as the diatomic molecules LiH, BH, N_2 and CO as examples. Total energies and eigenvalues calculated with the FEM on the HF-level are compared with results obtained with the numerical standard methods used for the solution of the one dimensional HF equations for atoms and for diatomic molecules with the traditional LCAO quantum chemical methods and the newly developed finite difference method on the HF-level. In general the accuracy increases from the LCAO - to the finite difference - to the finite element method.

Finite element method for the accurate solution of diatomic molecules

We present the Finite-Element-Method (FEM) in its application to quantum mechanical problems solving for diatomic molecules. Results for Hartree-Fock calculations of H_2 and Hartree-Fock-Slater calculations of molecules like N_2 and C0 have been obtained. The accuracy achieved with less then 5000 grid points for the total energies of these systems is 10_-8 a.u., which is demonstrated for N_2.

Solution of the Hartree-Fock-Slater equations for diatomic molecules by the finite-element method

We present the finite-element method in its application to solving quantum-mechanical problems for diatomic molecules. Results for Hartree-Fock calculations of H_2 and Hartree-Fock-Slater calculations for molecules like N_2 and CO are presented. The accuracy achieved with fewer than 5000 grid points for the total energies of these systems is 10^-8 a.u., which is about two orders of magnitude better than the accuracy of any other available method.

Ions of the superheavy elements in vacuum and in solution

The extension of the Periodic Table into the range of unknown atomic numbers of above one hundred requires relativistic calculations. The results of the latter are used to indicate probable values for X-ray transition lines which will be useful for identification of the atomic species formed during collision between accelerated ions and the target. If the half-lives of the isotopes are long, then the chemistry of these new species becomes an important question which is reviewed for E110, E 111 and E112. The possible structural chemistry of the elements E108 to E112 is suggested. Finally the effects of solvation on ions of the actinide and superheavy elements have been studied.

Solution of the time dependent Dirac-Fock-Slater equation for many-electron collisions systems using a time window method

We present a new scheme to solve the time dependent Dirac-Fock-Slater equation (TDDFS) for heavy many electron ion-atom collision systems. Up to now time independent self consistent molecular orbitals have been used to expand the time dependent wavefunction and rather complicated potential coupling matrix elements have been neglected. Our idea is to minimize the potential coupling by using the time dependent electronic density to generate molecular basis functions. We present the first results for 16 MeV S{^16+} on Ar.

Femtosecond real-time probing of reactions. 12. Vectorial dynamics of transition states

Femtosecond time-resolved techniques with KETOF (kinetic energy time-of-flight) detection in a molecular beam are developed for studies of the vectorial dynamics of transition states. Application to the dissociation reaction of IHgI is presented. For this system, the complex [I---Hg---I](++)* is unstable and, through the symmetric and asymmetric stretch motions, yields different product fragments: [I---Hg---I](++)* -> HgI(X^2/sigma^+) + I(^2P_3/2) [or I*(^2P_l/2)] (1a); [I---Hg---I](++)* -> Hg(^1S_0) + I(^2P_3/2) + I(^2P_3/2) [or I* (^2P_1/2)] (1 b). These two channels, (1a) and (1b), lead to different kinetic energy distributions in the products. It is shown that the motion of the wave packet in the transition-state region can be observed by MPI mass detection; the transient time ranges from 120 to 300 fs depending on the available energy. With polarized pulses, the vectorial properties (transition moments alignment relative to recoil direction) are studied for fragment separations on the femtosecond time scale. The results indicate the nature of the structure (symmetry properties) and the correlation to final products. For 311-nm excitation, no evidence of crossing between the I and I* potentials is found at the internuclear separations studied. (Results for 287-nm excitation are also presented.) Molecular dynamics simulations and studies by laser-induced fluorescence support these findings.

Nichtüberlappende Gebietszerlegungsmethoden für lineare und quasilineare (monotone und nichtmonotone) Probleme

In dieser Arbeit werden nichtüberlappende Gebietszerlegungsmethoden einerseits hinsichtlich der zu lösenden Problemklassen verallgemeinert und andererseits in bisher nicht untersuchten Kontexten betrachtet. Dabei stehen funktionalanalytische Untersuchungen zur Wohldefiniertheit, eindeutigen Lösbarkeit und Konvergenz im Vordergrund. Im ersten Teil werden lineare elliptische Dirichlet-Randwertprobleme behandelt, wobei neben Problemen mit dominantem Hauptteil auch solche mit singulärer Störung desselben, wie konvektions- oder reaktionsdominante Probleme zugelassen sind. Der zweite Teil befasst sich mit (gleichmäßig) monotonen koerziven quasilinearen elliptischen Dirichlet-Randwertproblemen. In beiden Fällen wird das Lipschitz-Gebiet in endlich viele Lipschitz-Teilgebiete zerlegt, wobei insbesondere Kreuzungspunkte und Teilgebiete ohne Außenrand zugelassen sind. Anschließend werden Transmissionsprobleme mit frei wählbaren $L^{\infty}$-Parameterfunktionen hergeleitet, wobei die Konormalenableitungen als Funktionale auf geeigneten Funktionenräumen über den Teilrändern ($H_{00}^{1/2}(\Gamma)$) interpretiert werden. Die iterative Lösung dieser Transmissionsprobleme mit einem Ansatz von Deng führt auf eine Substrukturierungsmethode mit Robin-artigen Transmissionsbedingungen, bei der eine Auswertung der Konormalenableitungen aufgrund einer geschickten Aufdatierung der Robin-Daten nicht notwendig ist (insbesondere ist die bekannte Robin-Robin-Methode von Lions als Spezialfall enthalten). Die Konvergenz bezüglich einer partitionierten $H^1$-Norm wird für beide Problemklassen gezeigt. Dabei werden keine über $H^1$ hinausgehende Regularitätsforderungen an die Lösungen gestellt und die Gebiete müssen keine zusätzlichen Glattheitsvoraussetzungen erfüllen. Im letzten Kapitel werden nichtmonotone koerzive quasilineare Probleme untersucht, wobei das Zugrunde liegende Gebiet nur in zwei Lipschitz-Teilgebiete zerlegt sein soll. Das zugehörige nichtlineare Transmissionsproblem wird durch Kirchhoff-Transformation in lineare Teilprobleme mit nichtlinearen Kopplungsbedingungen überführt. Ein optimierungsbasierter Lösungsansatz, welcher einen geeigneten Abstand der rücktransformierten Dirichlet-Daten der linearen Teilprobleme auf den Teilrändern minimiert, führt auf ein optimales Kontrollproblem. Die dabei entstehenden regularisierten freien Minimierungsprobleme werden mit Hilfe eines Gradientenverfahrens unter minimalen Glattheitsforderungen an die Nichtlinearitäten gelöst. Unter zusätzlichen Glattheitsvoraussetzungen an die Nichtlinearitäten und weiteren technischen Voraussetzungen an die Lösung des quasilinearen Ausgangsproblems, kann zudem die quadratische Konvergenz des Newton-Verfahrens gesichert werden.

Constructing a ‘moment of crisis’ and its adequate solution

The rejection of the European Constitution marks an important crystallization point for debate about the European Union (EU) and the integration process. The European Constitution was envisaged as the founding document of a renewed and enlarged European Union and thus it was rather assumed to find wide public support. Its rejection was not anticipated. The negative referenda in France and the Netherlands therefore led to a controversial debate about the more fundamental meaning and the consequences of the rejection both for the immediate state of affairs as well as for the further integration process. The rejection of the Constitution and the controversy about its correct interpretation therefore present an intriguing puzzle for political analysis. Although the treaty rejection was taken up widely in the field of European Studies, the focus of existing analyses has predominantly been on explaining why the current situation occurred. Underlying these approaches is the premise that by establishing the reasons for the rejection it is possible to derive the ‘true’ meaning of the event for the EU integration process. In my paper I rely on an alternative, discourse theoretical approach which aims to overcome the positivist perspective dominating the existing analyses. I argue that the meaning of the event ‘treaty rejection’ is not fixed or inherent to it but discursively constructed. The critical assessment of this concrete meaning-production is of high relevance as the specific meaning attributed to the treaty rejection effectively constrains the scope for supposedly ‘reasonable’ options for action, both in the concrete situation and in the further European integration process more generally. I will argue that the overall framing suggests a fundamental technocratic approach to governance from part of the Commission. Political struggle and public deliberation is no longer foreseen as the concrete solutions to the citizens’ general concerns are designed by supposedly apolitical experts. Through the communicative diffusion and the active implementation of this particular model of governance the Commission shapes the future integration process in a more substantial way than is obvious from its seemingly limited immediate problem-solving orientation of overcoming the ‘constitutional crisis’. As the European Commission is a central actor in the discourse production my analysis focuses on the specific interpretation of the situation put forward by the Commission. In order to work out the Commission’s particular take on the event I conducted a frame analysis (according to Benford/Snow) on a body of key sources produced in the context of coping with the treaty rejection.

On Solution Sets of Information Inequalities

We investigate solution sets of a special kind of linear inequality systems. In particular, we derive characterizations of these sets in terms of minimal solution sets. The studied inequalities emerge as information inequalities in the context of Bayesian networks. This allows to deduce important properties of Bayesian networks, which is important within causal inference.

Biofuel as the solution of alternative energy production?

There have being increasing debate on the prospects of biofuel becoming the next best alternative to solving the problem of CO2 emission and the escalating fuel prices, but the question is whether this assertion is true and also if it comes without any cost to pay. This paper seeks to find out whether this much praised alternative to solving these problems is a better option or another way for the developed countries to find more areas where they could get cheap land, labour and raw materials for the production of biofuel. This will focus mainly on some effects the growing biofuel production has on food security, livelihood of people, the environment and some land conflicts developing as a result of land grabbing for biofuel production in the developing countries.

Exact Solution of the Nonlinear Dynamics of Recurrent Neural Mechanisms for Direction Selectivity

Different theoretical models have tried to investigate the feasibility of recurrent neural mechanisms for achieving direction selectivity in the visual cortex. The mathematical analysis of such models has been restricted so far to the case of purely linear networks. We present an exact analytical solution of the nonlinear dynamics of a class of direction selective recurrent neural models with threshold nonlinearity. Our mathematical analysis shows that such networks have form-stable stimulus-locked traveling pulse solutions that are appropriate for modeling the responses of direction selective cortical neurons. Our analysis shows also that the stability of such solutions can break down giving raise to a different class of solutions ("lurching activity waves") that are characterized by a specific spatio-temporal periodicity. These solutions cannot arise in models for direction selectivity with purely linear spatio-temporal filtering.

Characterization of ZnO Nanorods Grown on GaN Using Aqueous Solution Method

Uniformly distributed ZnO nanorods with diameter 70-100 nm and 1-2μm long have been successfully grown at low temperatures on GaN by using the inexpensive aqueous solution method. The formation of the ZnO nanorods and the growth parameters are controlled by reactant concentration, temperature and pH. No catalyst is required. The XRD studies show that the ZnO nanorods are single crystals and that they grow along the c axis of the crystal plane. The room temperature photoluminescence measurements have shown ultraviolet peaks at 388nm with high intensity, which are comparable to those found in high quality ZnO films. The mechanism of the nanorod growth in the aqueous solution is proposed. The dependence of the ZnO nanorods on the growth parameters was also investigated. While changing the growth temperature from 60°C to 150°C, the morphology of the ZnO nanorods changed from sharp tip (needle shape) to flat tip (rod shape). These kinds of structure are useful in laser and field emission application.

Growth of ZnO Nanorods on GaN Using Aqueous Solution Method

Uniformly distributed ZnO nanorods with diameter 80-120 nm and 1-2µm long have been successfully grown at low temperatures on GaN by using the inexpensive aqueous solution method. The formation of the ZnO nanorods and the growth parameters are controlled by reactant concentration, temperature and pH. No catalyst is required. The XRD studies show that the ZnO nanorods are single crystals and that they grow along the c axis of the crystal plane. The room temperature photoluminescence measurements have shown ultraviolet peaks at 388nm with high intensity, which are comparable to those found in high quality ZnO films. The mechanism of the nanorod growth in the aqueous solution is proposed. The dependence of the ZnO nanorods on the growth parameters was also investigated. While changing the growth temperature from 60°C to 150°C, the morphology of the ZnO nanorods changed from sharp tip with high aspect ratio to flat tip with smaller aspect ratio. These kinds of structure are useful in laser and field emission application.

Context Interchange as a Scalable Solution to Interoperating Amongst Heterogeneous Dynamic Services

Many online services access a large number of autonomous data sources and at the same time need to meet different user requirements. It is essential for these services to achieve semantic interoperability among these information exchange entities. In the presence of an increasing number of proprietary business processes, heterogeneous data standards, and diverse user requirements, it is critical that the services are implemented using adaptable, extensible, and scalable technology. The COntext INterchange (COIN) approach, inspired by similar goals of the Semantic Web, provides a robust solution. In this paper, we describe how COIN can be used to implement dynamic online services where semantic differences are reconciled on the fly. We show that COIN is flexible and scalable by comparing it with several conventional approaches. With a given ontology, the number of conversions in COIN is quadratic to the semantic aspect that has the largest number of distinctions. These semantic aspects are modeled as modifiers in a conceptual ontology; in most cases the number of conversions is linear with the number of modifiers, which is significantly smaller than traditional hard-wiring middleware approach where the number of conversion programs is quadratic to the number of sources and data receivers. In the example scenario in the paper, the COIN approach needs only 5 conversions to be defined while traditional approaches require 20,000 to 100 million. COIN achieves this scalability by automatically composing all the comprehensive conversions from a small number of declaratively defined sub-conversions.