Piezoresistive cantilevers with an integrated bimorph actuator

Scanning Probe Microscopy (SPM) has become of fundamental importance for research in area of micro and nano-technology. The continuous progress in these fields requires ultra sensitive measurements at high speed. The imaging speed limitation of the conventional Tapping Mode SPM is due to the actuation time constant of piezotube feedback loop that keeps the tapping amplitude constant. In order to avoid this limit a deflection sensor and an actuator have to be integrated into the cantilever. In this work has been demonstrated the possibility of realisation of piezoresistive cantilever with an embedded actuator. Piezoresistive detection provides a good alternative to the usual optical laser beam deflection technique. In frames of this thesis has been investigated and modelled the piezoresistive effect in bulk silicon (3D case) for both n- and p-type silicon. Moving towards ultra-sensitive measurements it is necessary to realize ultra-thin piezoresistors, which are well localized to the surface, where the stress magnitude is maximal. New physical effects such as quantum confinement which arise due to the scaling of the piezoresistor thickness was taken into account in order to model the piezoresistive effect and its modification in case of ultra-thin piezoresistor (2D case). The two-dimension character of the electron gas in n-type piezoresistors lead up to decreasing of the piezoresistive coefficients with increasing the degree of electron localisation. Moreover for p-type piezoresistors the predicted values of the piezoresistive coefficients are higher in case of localised holes. Additionally, to the integration of the piezoresistive sensor, actuator integrated into the cantilever is considered as fundamental for realisation of fast SPM imaging. Actuation of the beam is achieved thermally by relying on differences in the coefficients of thermal expansion between aluminum and silicon. In addition the aluminum layer forms the heating micro-resistor, which is able to accept heating impulses with frequency up to one megahertz. Such direct oscillating thermally driven bimorph actuator was studied also with respect to the bimorph actuator efficiency. Higher eigenmodes of the cantilever are used in order to increase the operating frequencies. As a result the scanning speed has been increased due to the decreasing of the actuation time constant. The fundamental limits to force sensitivity that are imposed by piezoresistive deflection sensing technique have been discussed. For imaging in ambient conditions the force sensitivity is limited by the thermo-mechanical cantilever noise. Additional noise sources, connected with the piezoresistive detection are negligible.

Effect of Auger recombination and leakage on the droop in InGaN/GaN quantum well LEDs

We investigate the effect of the epitaxial structure and the acceptor doping profile on the efficiency droop in InGaN/GaN LEDs by the physics based simulation of experimental internal quantum efficiency (IQE) characteristics. The device geometry is an integral part of our simulation approach. We demonstrate that even for single quantum well LEDs the droop depends critically on the acceptor doping profile. The Auger recombination was found to increase stronger than with the third power of the carrier density and has been found to dominate the droop in the roll over zone of the IQE. The fitted Auger coefficients are in the range of the values predicted by atomistic simulations.

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.

Controlling the transport of an ion: classical and quantum mechanical solutions

The accurate transport of an ion over macroscopic distances represents a challenging control problem due to the different length and time scales that enter and the experimental limitations on the controls that need to be accounted for. Here, we investigate the performance of different control techniques for ion transport in state-of-the-art segmented miniaturized ion traps. We employ numerical optimization of classical trajectories and quantum wavepacket propagation as well as analytical solutions derived from invariant based inverse engineering and geometric optimal control. The applicability of each of the control methods depends on the length and time scales of the transport. Our comprehensive set of tools allows us make a number of observations. We find that accurate shuttling can be performed with operation times below the trap oscillation period. The maximum speed is limited by the maximum acceleration that can be exerted on the ion. When using controls obtained from classical dynamics for wavepacket propagation, wavepacket squeezing is the only quantum effect that comes into play for a large range of trapping parameters. We show that this can be corrected by a compensating force derived from invariant based inverse engineering, without a significant increase in the operation time.