Ligand diffusion on protein surface observed in molecular dynamics simulation

The process of binding of small ligands to dihydrofolate reductase protein has been investigated using all-atom molecular dynamics simulations. The existence of a mechanism that facilitates the search of the binding site by the ligand is demonstrated. The mechanism consists of ligand diffusing on the protein’s surface. It has been discussed in the literature before, but has not been explicitly confirmed for realistic molecular systems. The strength of this nonspecific binding is roughly estimated and found to be essential for the binding kinetics.

Large Numerical Models in Continuous Hybrid Simulation

Hybrid simulation is a technique that combines experimental and numerical testing and has been used for the last decades in the fields of aerospace, civil and mechanical engineering. During this time, most of the research has focused on developing algorithms and the necessary technology, including but not limited to, error minimisation techniques, phase lag compensation and faster hydraulic cylinders. However, one of the main shortcomings in hybrid simulation that has pre- vented its widespread use is the size of the numerical models and the effect that higher frequencies may have on the stability and accuracy of the simulation. The first chapter in this document provides an overview of the hybrid simulation method and the different hybrid simulation schemes, and the corresponding time integration algorithms, that are more commonly used in this field. The scope of this thesis is presented in more detail in chapter 2: a substructure algorithm, the Substep Force Feedback (Subfeed), is adapted in order to fulfil the necessary requirements in terms of speed. The effects of more complex models on the Subfeed are also studied in detail, and the improvements made are validated experimentally. Chapters 3 and 4 detail the methodologies that have been used in order to accomplish the objectives mentioned in the previous lines, listing the different cases of study and detailing the hardware and software used to experimentally validate them. The third chapter contains a brief introduction to a project, the DFG Subshake, whose data have been used as a starting point for the developments that are shown later in this thesis. The results obtained are presented in chapters 5 and 6, with the first of them focusing on purely numerical simulations while the second of them is more oriented towards a more practical application including experimental real-time hybrid simulation tests with large numerical models. Following the discussion of the developments in this thesis is a list of hardware and software requirements that have to be met in order to apply the methods described in this document, and they can be found in chapter 7. The last chapter, chapter 8, of this thesis focuses on conclusions and achievements extracted from the results, namely: the adaptation of the hybrid simulation algorithm Subfeed to be used in conjunction with large numerical models, the study of the effect of high frequencies on the substructure algorithm and experimental real-time hybrid simulation tests with vibrating subsystems using large numerical models and shake tables. A brief discussion of possible future research activities can be found in the concluding chapter.

REAL TIME FUZZY CONTROLLER FOR QUADROTOR STABILITY CONTROL

In this report, we develop an intelligent adaptive neuro-fuzzy controller by using adaptive neuro fuzzy inference system (ANFIS) techniques. We begin by starting with a standard proportional-derivative (PD) controller and use the PD controller data to train the ANFIS system to develop a fuzzy controller. We then propose and validate a method to implement this control strategy on commercial off-the-shelf (COTS) hardware. An analysis is made into the choice of filters for attitude estimation. These choices are limited by the complexity of the filter and the computing ability and memory constraints of the micro-controller. Simplified Kalman filters are found to be good at estimation of attitude given the above constraints. Using model based design techniques, the models are implemented on an embedded system. This enables the deployment of fuzzy controllers on enthusiast-grade controllers. We evaluate the feasibility of the proposed control strategy in a model-in-the-loop simulation. We then propose a rapid prototyping strategy, allowing us to deploy these control algorithms on a system consisting of a combination of an ARM-based microcontroller and two Arduino-based controllers. We then use a combination of the code generation capabilities within MATLAB/Simulink in combination with multiple open-source projects in order to deploy code to an ARM CortexM4 based controller board. We also evaluate this strategy on an ARM-A8 based board, and a much less powerful Arduino based flight controller. We conclude by proving the feasibility of fuzzy controllers on Commercial-off the shelf (COTS) hardware, we also point out the limitations in the current hardware and make suggestions for hardware that we think would be better suited for memory heavy controllers.

Product-line specification and verification with feature-oriented contracts

Magdeburg, Univ., Fak. für Informatik, Diss., 2015

Einführung in die stochastische Simulation mit Fathom

Die "Einführung in die stochastische Simulation mit Fathom" führt in die Simulation mit der Computersoftware Fathom ein und entstand im Rahmen meines Dissertationsprojekts. Voraussetzung sind elementare Grundkenntnisse in dieser Software, z.B. für die Analyse von eindimensionalen Daten. Die Arbeit basiert auf einer ausführlichen Analyse stochastischer Situationen, die als Zufallsexperimente modelliert werden können. Sie wurde ursprünglich für Studenten der Veranstaltung "Elementare Stochastik" an der Universität Kassel didaktisch aufbereitet. Sie ist aber auch für alle Lehrenden und Lernenden an Schule und Hochschule gedacht, die die stochastische Simulation mit Fathom erlernen wollen. Das Dokument dient dazu, eine systematische Anleitung zum Erstellen eigener Simulationen zu geben. Eine didaktische Hilfestellung bietet dazu das dreigegliederte Simulationskonzept: 1. Festlegen des stochastischen Modell, 2. Erstellen eines Simulationsplans und 3. Realisierung in FATHOM. Verschiedene Simulationsarten werden ausführlich an einem Beispiel vorgestellt und können in Arbeitsumgebungen selbst erzeugt werden. Die Erstellung der Arbeit wurde mit Mitteln des BLK-Projektes Netzwerk Wissenschaftliche Weiterbildung für Lehramtsberufe (NWWL) an der Universität Kassel gefördert.

Validation and verification of embedded neural systems

DUE TO COPYRIGHT RESTRICTIONS ONLY AVAILABLE FOR CONSULTATION AT ASTON UNIVERSITY LIBRARY AND INFORMATION SERVICES WITH PRIOR ARRANGEMENT

Validation and verification of embedded neural systems

DUE TO COPYRIGHT RESTRICTIONS ONLY AVAILABLE FOR CONSULTATION AT ASTON UNIVERSITY LIBRARY AND INFORMATION SERVICES WITH PRIOR ARRANGEMENT