Microarray based real-time analysis of nucleic acid hybridization kinetics and thermodynamics

Ziel dieser Dissertation ist die experimentelle Charakterisierung und quantitative Beschreibung der Hybridisierung von komplementären Nukleinsäuresträngen mit oberflächengebundenen Fängermolekülen für die Entwicklung von integrierten Biosensoren. Im Gegensatz zu lösungsbasierten Verfahren ist mit Microarray Substraten die Untersuchung vieler Nukleinsäurekombinationen parallel möglich. Als biologisch relevantes Evaluierungssystem wurde das in Eukaryoten universell exprimierte Actin Gen aus unterschiedlichen Pflanzenspezies verwendet. Dieses Testsystem ermöglicht es, nahe verwandte Pflanzenarten auf Grund von geringen Unterschieden in der Gen-Sequenz (SNPs) zu charakterisieren. Aufbauend auf dieses gut studierte Modell eines House-Keeping Genes wurde ein umfassendes Microarray System, bestehend aus kurzen und langen Oligonukleotiden (mit eingebauten LNA-Molekülen), cDNAs sowie DNA und RNA Targets realisiert. Damit konnte ein für online Messung optimiertes Testsystem mit hohen Signalstärken entwickelt werden. Basierend auf den Ergebnissen wurde der gesamte Signalpfad von Nukleinsärekonzentration bis zum digitalen Wert modelliert. Die aus der Entwicklung und den Experimenten gewonnen Erkenntnisse über die Kinetik und Thermodynamik von Hybridisierung sind in drei Publikationen zusammengefasst die das Rückgrat dieser Dissertation bilden. Die erste Publikation beschreibt die Verbesserung der Reproduzierbarkeit und Spezifizität von Microarray Ergebnissen durch online Messung von Kinetik und Thermodynamik gegenüber endpunktbasierten Messungen mit Standard Microarrays. Für die Auswertung der riesigen Datenmengen wurden zwei Algorithmen entwickelt, eine reaktionskinetische Modellierung der Isothermen und ein auf der Fermi-Dirac Statistik beruhende Beschreibung des Schmelzüberganges. Diese Algorithmen werden in der zweiten Publikation beschrieben. Durch die Realisierung von gleichen Sequenzen in den chemisch unterschiedlichen Nukleinsäuren (DNA, RNA und LNA) ist es möglich, definierte Unterschiede in der Konformation des Riboserings und der C5-Methylgruppe der Pyrimidine zu untersuchen. Die kompetitive Wechselwirkung dieser unterschiedlichen Nukleinsäuren gleicher Sequenz und die Auswirkungen auf Kinetik und Thermodynamik ist das Thema der dritten Publikation. Neben der molekularbiologischen und technologischen Entwicklung im Bereich der Sensorik von Hybridisierungsreaktionen oberflächengebundener Nukleinsäuremolekülen, der automatisierten Auswertung und Modellierung der anfallenden Datenmengen und der damit verbundenen besseren quantitativen Beschreibung von Kinetik und Thermodynamik dieser Reaktionen tragen die Ergebnisse zum besseren Verständnis der physikalisch-chemischen Struktur des elementarsten biologischen Moleküls und seiner nach wie vor nicht vollständig verstandenen Spezifizität bei.

Quantum kinematics of Fermi-Dirac vacuum-plus-one-electron problem

Following Weisskopf, the kinematics of quantum mechanics is shown to lead to a modified charge distribution for a test electron embedded in the Fermi-Dirac vacuum with interesting consequences.

The Complete Proof of the Virial Theorem in the Refined TFD Theory for all Electrons of an Atom in a Solid

The complete proof of the virial theorem in refined Thomas-Fermi-Dirac theory for all electrons of an atom in a solid is given.

Analysis of residual stress gradient in MEMS multi-layer structure

Residual stress and its gradient through the thickness are among the most important properties of as-deposited films. Recently, a new mechanism based on a revised Thomas-Fermi-Dirac (TFD) model was proposed for the origin of intrinsic stress in solid film

Non-linear photoluminescence from graphene

Graphene is in the focus of research due to its unique electronic and optical properties. Intrinsic graphene is a zero gap semiconductor with a linear dispersion relation for E-k leading to zero-effective-mass electrons and holes described by Fermi-Dirac theory. Since pristine graphene has no bandgap no photoluminescence would be expected. However, recently several groups showed non-linear photoluminescence from pristine graphene putting forward different physical models explaining this remarkable effect [1-3]. © 2011 IEEE.

Positive Correlations in Tunneling through coupled Quantum Dots

Due to the Fermi-Dirac statistics of electrons the temporal correlations of tunneling events in a double barrier setup are typically negative. Here, we investigate the shot noise behavior of a system of two capacitively coupled quantum dot states by means of a Master equation model. In an asymmetric setup positive correlations in the tunneling current can arise due to the bunching of tunneling events. The underlying mechanism will be discussed in detail in terms of the current-current correlation function and the frequency-dependent Fano factor.

Ultrafast collinear scattering and carrier multiplication in graphene.

Graphene is emerging as a viable alternative to conventional optoelectronic, plasmonic and nanophotonic materials. The interaction of light with charge carriers creates an out-of-equilibrium distribution, which relaxes on an ultrafast timescale to a hot Fermi-Dirac distribution, that subsequently cools emitting phonons. Although the slower relaxation mechanisms have been extensively investigated, the initial stages still pose a challenge. Experimentally, they defy the resolution of most pump-probe setups, due to the extremely fast sub-100 fs carrier dynamics. Theoretically, massless Dirac fermions represent a novel many-body problem, fundamentally different from Schrödinger fermions. Here we combine pump-probe spectroscopy with a microscopic theory to investigate electron-electron interactions during the early stages of relaxation. We identify the mechanisms controlling the ultrafast dynamics, in particular the role of collinear scattering. This gives rise to Auger processes, including charge multiplication, which is key in photovoltage generation and photodetectors.

Ultrafast non-thermal electron dynamics in single layer graphene

The impulsive optical excitation of carriers in graphene creates an out-of-equilibrium distribution, which thermalizes on an ultrafast timescale [1-4]. This hot Fermi-Dirac (FD) distribution subsequently cools via phonon emission within few hundreds of femtoseconds. While the relaxation mechanisms mediated by phonons have been extensively investigated, the initial stages, ruled by fundamental electron-electron (e-e) interactions still pose a challenge. © 2013 IEEE.

Electronic structure and optical gain saturation of InAs1-xNx/GaAs quantum dots

The electronic band structures and optical gains of InAs1-xNx/GaAs pyramid quantum dots (QDs) are calculated using the ten-band k . p model and the valence force field method. The optical gains are calculated using the zero-dimensional optical gain formula with taking into consideration of both homogeneous and inhomogeneous broadenings due to the size fluctuation of quantum dots which follows a normal distribution. With the variation of QD sizes and nitrogen composition, it can be shown that the nitrogen composition and the strains can significantly affect the energy levels especially the conduction band which has repulsion interaction with nitrogen resonant state due to the band anticrossing interaction. It facilitates to achieve emission of longer wavelength (1.33 or 1.55 mu m) lasers for optical fiber communication system. For QD with higher nitrogen composition, it has longer emission wavelength and less detrimental effect of higher excited state transition, but nitrogen composition can affect the maximum gain depending on the factors of transition matrix element and the Fermi-Dirac distributions for electrons in the conduction bands and holes in the valence bands respectively. For larger QD, its maximum optical gain is greater at lower carrier density, but it is slowly surpassed by smaller QD as carrier concentration increases. Larger QD can reach its saturation gain faster, but this saturation gain is smaller than that of smaller QD. So the trade-off between longer wavelength, maximum optical, saturation gain, and differential gain must be considered to select the appropriate QD size according to the specific application requirement. (C) 2009 American Institute of Physics. [DOI 10.1063/1.3143025]

Electronic structure and optical gain saturation of InAs1-xNx/GaAs quantum dots

The electronic band structures and optical gains of InAs1-xNx/GaAs pyramid quantum dots (QDs) are calculated using the ten-band k . p model and the valence force field method. The optical gains are calculated using the zero-dimensional optical gain formula with taking into consideration of both homogeneous and inhomogeneous broadenings due to the size fluctuation of quantum dots which follows a normal distribution. With the variation of QD sizes and nitrogen composition, it can be shown that the nitrogen composition and the strains can significantly affect the energy levels especially the conduction band which has repulsion interaction with nitrogen resonant state due to the band anticrossing interaction. It facilitates to achieve emission of longer wavelength (1.33 or 1.55 mu m) lasers for optical fiber communication system. For QD with higher nitrogen composition, it has longer emission wavelength and less detrimental effect of higher excited state transition, but nitrogen composition can affect the maximum gain depending on the factors of transition matrix element and the Fermi-Dirac distributions for electrons in the conduction bands and holes in the valence bands respectively. For larger QD, its maximum optical gain is greater at lower carrier density, but it is slowly surpassed by smaller QD as carrier concentration increases. Larger QD can reach its saturation gain faster, but this saturation gain is smaller than that of smaller QD. So the trade-off between longer wavelength, maximum optical, saturation gain, and differential gain must be considered to select the appropriate QD size according to the specific application requirement. (C) 2009 American Institute of Physics. [DOI: 10.1063/1.3143025]

Freak waves and electrostatic wavepacket modulation in a quantum electron-positron-ion plasma

The occurrence of rogue waves (freak waves) associated with electrostatic wavepacket propagation in a quantum electron-positron-ion plasma is investigated from first principles. Electrons and positrons follow a Fermi-Dirac distribution, while the ions are subject to a quantum (Fermi) pressure. A fluid model is proposed and analyzed via a multiscale technique. The evolution of the wave envelope is shown to be described by a nonlinear Schrödinger equation (NLSE). Criteria for modulational instability are obtained in terms of the intrinsic plasma parameters. Analytical solutions of the NLSE in the form of envelope solitons (of the bright or dark type) and localized breathers are reviewed. The characteristics of exact solutions in the form of the Peregrine soliton, the Akhmediev breather and the Kuznetsov-Ma breather are proposed as candidate functions for rogue waves (freak waves) within the model. The characteristics of the latter and their dependence on relevant parameters (positron concentration and temperature) are investigated. © 2014 IOP Publishing Ltd.

Electrostatic Solitary Waves in Relativistic Degenerate Electron-Positron-Ion Plasma

The linear and nonlinear properties of ion acoustic excitations propagating in warm dense electron-positron-ion plasma are investigated. Electrons and positrons are assumed relativistic and degenerate, following the Fermi-Dirac statistics, whereas the warm ions are described by a set of classical fluid equations. A linear dispersion relation is derived in the linear approximation. Adopting a reductive perturbation method, the Korteweg-de Vries equation is derived, which admits a localized wave solution in the form of a small-amplitude weakly super-acoustic pulse-shaped soliton. The analysis is extended to account for arbitrary amplitude solitary waves, by deriving a pseudoenergy-balance like equation, involving a Sagdeev-type pseudopotential. It is shown that the two approaches agree exactly in the small-amplitude weakly super-acoustic limit. The range of allowed values of the pulse soliton speed (Mach number), wherein solitary waves may exist, is determined. The effects of the key plasma configuration parameters, namely, the electron relativistic degeneracy parameter, the ion (thermal)-to-the electron (Fermi) temperature ratio, and the positron-to-electron density ratio, on the soliton characteristics and existence domain, are studied in detail. Our results aim at elucidating the characteristics of ion acoustic excitations in relativistic degenerate plasmas, e.g., in dense astrophysical objects, where degenerate electrons and positrons may occur.

Electron-phonon thermalization in a scalable method for real-time quantum dynamics

We present a quantum simulation method that follows the dynamics of out-of-equilibrium many-body systems of electrons and oscillators in real time. Its cost is linear in the number of oscillators and it can probe time scales from attoseconds to hundreds of picoseconds. Contrary to Ehrenfest dynamics, it can thermalize starting from a variety of initial conditions, including electronic population inversion. While an electronic temperature can be defined in terms of a nonequilibrium entropy, a Fermi-Dirac distribution in general emerges only after thermalization. These results can be used to construct a kinetic model of electron-phonon equilibration based on the explicit quantum dynamics.

Self-consistent theory of current and voltage noise in multimode ballistic conductors

Electron transport in a self-consistent potential along a ballistic two-terminal conductor has been investigated. We have derived general formulas which describe the nonlinear current-voltage characteristics, differential conductance, and low-frequency current and voltage noise assuming an arbitrary distribution function and correlation properties of injected electrons. The analytical results have been obtained for a wide range of biases: from equilibrium to high values beyond the linear-response regime. The particular case of a three-dimensional Fermi-Dirac injection has been analyzed. We show that the Coulomb correlations are manifested in the negative excess voltage noise, i.e., the voltage fluctuations under high-field transport conditions can be less than in equilibrium.