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We present classical and hybrid modeling approaches for genetic regulatory networks focusing on promoter analysis for negatively and positively autoregulated networks. The main aim of this thesis is to introduce an alternative mathematical approach to model gene regulatory networks based on piecewise deterministic Markov processes (PDMP). During somitogenesis, a process describing the early segmentation in vertebrates, molecular oscillators play a crucial role as part of a segmentation clock. In mice, these oscillators are called Hes1 and Hes7 and are commonly modeled by a system of two delay differential equations including a Hill function, which describes gene repression by their own gene products. The Hill coefficient, which is a measure of nonlinearity of the binding processes in the promoter, is assumed to be equal to two, based on the fact that Hes1 and Hes7 form dimers.However, by standard arguments applied to binding analysis, we show that a higher Hill coefficient is reasonable. This leads to results different from those in literature which requires a more sophisticated model. For the Hes7 oscillator we present a system of ordinary differential equations including a Michaelis-Menten term describing a nonlinear degradation of the proteins by the ubiquitinpathway. As demonstrated by the Hes1 and Hes7 oscillator, promoter behavior can have strong influence on the dynamical behavior of genetic networks. Since purely deterministic systems cannot reveal phenomenons caused by the inherent random fluctuations, we propose a novel approach based on PDMPs. Such models allow to model binding processes of transcription factors to binding sites in a promoter as random processes, where all other processes like synthesis, degradation or dimerization of the gene products are modeled in deterministic manner. We present and discuss a simulation algorithm for PDMPs and apply it to three types of genetic networks: an unregulated gene, a toggle switch, and a positively autoregulated network. The different regulation characteristics are analyzed and compared by numerical means. Furthermore, we determine analytical solutions of the stationary distributions of one negatively, and three positively autoregulated networks. Based on these results, we analyze attenuation of noise in a negative feedback loop, and the question of graded or binary response in autocatalytic networks.
Hintergrund: Trotz der geringen Versorgungsrate mit Cochlea-Implantaten (CIs) bei gleichzeitig steigender Indikation liegen die CI-Implantationszahlen bei Erwachsenen in Deutschland noch immer auf einem relativ niedrigen Niveau.
Methoden: Da in der Literatur kaum fundierte Prognosen vorliegen, wird ein System Dynamics-Modell entwickelt, das die Anzahl und Kosten von CI-Implantationen der erwachsenen Bevölkerung über 40 Jahre aus Sicht der Gesetzlichen Krankenversicherung (GKV) prognostiziert.
Ergebnisse: Die demografische Alterung wird zu einer geringfügigen Steigerung der CI-Nachfrage führen, die durchschnittliche jährliche Kosten von ca. 538 Mio. € verursacht. Der medizinisch-technische Fortschritt mit nachfolgender Ausweitung der CI-Indikationskriterien und die zunehmende Bereitschaft von CI-Kandidaten zur Implantation werden die Implantationszahlen deutlich erhöhen, sodass mit durchschnittlichen jährlichen Kosten von 2,3 Mrd. € zu rechnen ist.
Schlussfolgerung: Die CI-Nachfrage durch Erwachsene wird künftig steigen und damit auch die Kosten für die CI-Versorgung. Kontinuierliche Forschung und Entwicklung in CI-Technologie und -Versorgung sind von entscheidender Bedeutung, um die Finanzierung der wachsenden CI-Nachfrage durch kostensenkende Innovationen langfristig sicherzustellen.
The investigation of complex molecular systems by molecular dynamics simulations has been successfully established and proven as a standard method during the last decades. The use of highly optimized algorithms and steadily increasing, generally available computing resources enables even larger and longer simulations. However, the dynamics of the system itself is not accelerated, and it can be trapped in low energy minima that can only be overcome slowly. A number of methods have therefore been developed to address this problem.
Within the context of this dissertation, a novel algorithm based on replica exchange was developed to solve problems with existing methods, which can now be used for large molecular systems with a low resource consumption. Parameter dependence was systematically evaluated and optimized to define guidelines for correct application. This algorithm was successfully applied to various pharmaceutical and biochemical problems, such as protein folding or protein-protein interactions.
Telemedicine at the Emergency Site – Evaluated by emergency team members in simulated scenarios
(2015)
The hypothesis of this study states that emergency medicine can benefit from telemedicine, whenever paramedics at a remote emergency site request consultation or mentoring by a distant emergency doctor. The hypothesis was semi-qualitatively evaluated in accordance with the protocol of the EU project in the setting of a medical simulation centre. Paramedics encountered simulated standardized emergency case scenarios, connected for teleconsultation and telementoring with emergency doctors by video and audio link through a newly developed real-time HD-video system called LiveCity camera. Paramedics and emergency doctors regarded the simulated scenarios as realistic and relevant and took the simulation seriously. Thus,the following conclusions can be drawn: 1.) Emergency team members encounter situations at the emergency site, in which they would like to get help by a more experienced colleague, especially help with diagnostics and treatment. 2.) The telemedical contact to an emergency doctor makes paramedics feel confirmed in their work, more secure, even in legal aspects. Paramedics do not feel controlled by telemedicine or like a puppet on a string. Their relationship to the patient is not mainly deranged or interfered by the doctor and their course of action is not mainly disrupted. The tele-emergency doctors do not feel like puppet masters and continue feeling as doctors and do not perceive themselves as interferer within the emergency team. 3.) Emergency team members call for a telemedical system providing transmission of vital signs as well as audio- and video-connection. 4.) The LiveCity camera is an effective telemedical tool. The audio quality is good and the orientation on the screen is easy. Paramedics state, that filming the emergency site is easy, does not restrict the field of vision and paramedics can communicate the emergency doctors everything they want to show and tell. Thus the emergency doctors get additional information. While the LiveCity camera is mostly perceived as not too heavy, the LiveCity camera is not easy to operate, very failure-prone and can derange the communication among team members at the emergency site. Nevertheless, the LiveCity camera is not perceived as an additional burden. 5.) Telemedicine is predominantly and largely appreciated by the members of the emergency team. Connecting the tele-emergency doctor to the remote paramedics leads to a perceived faster start of the therapy and is considered as helpful, improving the situation and the quality of patient care. The adherence to medical guidelines and therefore the quality increased, when the paramedics were connected to an emergency doctor through the telemedicine connection. In general, the quality of diagnostics, the correctness of diagnosis and the quality of therapy were rated higher. The majority of paramedics would call a tele-emergency doctor in cases, they wouldn´t normally activate medical support. The emergency team members largely agree in perceiving the tele-emergency doctor system as useful, and they can imagine, working in a tele-emergency system. As a conclusion, the general hypothesis of this study is mainly and in many items supported: Emergency medicine benefits from telemedical support via video- and audio link as studied here with a newly developed real-time HD-video system called LiveCity camera, whenever paramedics at a remote emergency site request consultation or mentoring by a distant emergency doctor.
Modern space missions depend more and more on electric propulsion devices for in-space
flights. The superior efficiency by ionizing the feedgas and propelling them using electric
fields with regard to conventional chemical thrusters makes them a great alternative. To
find optimized thruster designs is of high importance for industrial applications. Building
new prototypes is very expensive and takes a lot of time. A cheaper alternative is to rely
on computer simulations to get a deeper understanding of the underlying physics. In order
to gain a realistic simulation the whole system has to be taken into account including the
channel and the plume region. Because numerical models have to resolve the smallest time
and spatial scales, simulations take up an unfeasible amount of time. Usually a self-similarity
scaling scheme is used to greatly speed up these simulations. Until now the limits of this
method have not been thoroughly discussed. Therefore, this thesis investigates the limits
and the influence of the self-similarity scheme on simulations of ion thrusters. The aim
is to validate the self-similarity scaling and to look for application oriented tools to use
for thruster design optimization. As a test system the High-Efficiency-Multistage-Plasma
thruster (HEMP-T) is considered.
To simulate the HEMP-T a fully kinetic method is necessary. For low-temperature plasmas,
as found in the HEMP-T, the Particle-in-Cell (PIC) method has proven to be the best
choice. Unfortunately, PIC requires high spatial and temporal resolution and is hence
computationally costly. This limits the size of the devices PIC is able to simulate as well
as limiting the exploration of a wider design space of different thrusters. The whole system
is physically described using the Boltzmann and Maxwell equations. Using these system
of equations invariants can be derived. In the past, these invariants were used to derive a
self-similarity scaling law, maintaining the exact solution for the plasma volume, which is
applicable to ion thrusters and other plasmas. With the aid of the self-similarity scaling
scheme the computation cost can be reduced drastically. The drawback of the geometrical
scaling of the system is, that the plasma density and therefore the Debye length does not
scale. This expands the length at which charge separation occurs in respect to the system
size. In this thesis the limits of this scaling are investigated and the influence of the scaling
at higher scaling factors is studied. The specific HEMP-T design chosen for these studies is
the DP1.
Because the application of scaling laws is limited by the increasing influence of charge separation with increased scaling, PIC simulations still are computationally costly. Another approach to explore a wider design space is given using Multi-Objective-Design-Optimization
(MDO). MDO uses different tools to generate optimized thruster designs in a comparatively
short amount of time. This new approach is validated using the PIC method. During this
validation the drawback of the MDO surfaces. The MDO calculations are not self-consistent
and are based on empirical values of old thruster designs as input parameters, which not
necessarily match the new optimized thruster design. By simulating the optimized thruster
design with PIC and recalculate the former input parameters, a more realistic thruster design is achieved. This process can be repeated iteratively. The combination of self-consistent
PIC simulations with the performance of MDO is a great way to generate optimized thruster
designs in a comparatively short amount of time. The proof of concept of such a combination
is the pinnacle of this thesis.
Manipulating and utilizing plasmas becomes a more and more important task in various research fields of physics and in industrial developments. Especially in nowadays spacerelevant applications there are different ideas to modify plasmas concerning particular tasks.
One major point of interest is the ability to influence plasmas using magnetic fields. To study the underlying physical effects that were achieved by these magnetic fields for both scenarios Particle-in-Cell simulations were done. Two examples are discussed in this thesis.
The first example originates from an experiment performed by the European Space Agency ESA in collaboration with the German Space Agency DLR. To verify the possibility of heat-flux reduction by magnetic fields onto the thermal protection system of a space vehicle a simplified experiment on earth was developed. Most of the heat that is created during re-entry comes from compression of the air ahead of the hypersonic vehicle, as a result of the basic thermodynamic relation between temperature and pressure. The shock front, which builds up in front of the vehicle deflects most of the heat and prohibits the surface of the space vehicle from direct contact with the maximum flux. State of the art spacecrafts use highly developed materials like ceramics to handle the enormous heat. An attractive approach to reduce costs is to use magnetic fields for heat-flux reduction. This would allow the use of cheaper materials and thus reduce costs for the whole space mission. A partially-ionized Argon beam was used to create a certain heat-flux onto a target. The main finding of the experimental campaign was a large mitigation of heat-flux by applying a dipole-like magnetic field. The Particle-in-Cell method was able to reproduce experimental observations like the heat-flux reduction. An additionally implemented optical diagnostics module allowed to confirm the results of the spectroscopy done during the experiment. The underlying effect that is responsible for the heat-flux reduction was identified as a coupling between the modified plasma and the dominating neutral flux component. The plasma, that is guided towards the target, act as a shield in front of the target surface for arriving neutrals. These neutrals are slowed down by charge-exchange collisions. Furthermore the magnetic field induces an increased turbulent transport that is also needed to reach a reduction in heat-ux. The turbulent transport was also obtained by three-dimensional Direct Simulation Monte Carlo simulations. Unfortunately, such source driven turbulence can not be expected in space, so that a heat flux reduction in real space applications is questionable. Nevertheless, other effects like the induced turbulence by the rotating vehicle can compensate the missing source driven effect.
The second scenario in which a magnetic field is used to modify the heat flux of a plasma is the operation of the pulsed cathodic arc thruster. The same Particle-in-Cell code was used to simulate a typical pulse of this newly developed thruster of Neumann Space Pty Ltd. The typical behavior of the thruster could be reproduced numerically. The thrust is mainly produced by fast electrons. These electrons are accelerated by electric fields as a result of a plasma-beam instability. This plasma-beam instability was verified by a phase space diagnostics for the electrons. To demonstrate the influence of the magnetic field a simulation of the cathodic arc thruster without magnetic field and one with magnetic field were compared. It was shown that the use of a magnetic field leads to a ten times larger thrust by directing the heat ux. The resulting narrow plume is an additional Advantage of the particle guiding magnetic field. This narrowness of the plume reduces the danger of interaction with other components of the space vehicle.
Both scenarios demonstrate the different capabilities for electromagnetic fields to manipulate plasmas and especially the corresponding heat-flux with respect to certain tasks. The possibilities range from reducing the heat-flux onto a target to maximizing the thrust by directing the heat-ux. This thesis demonstrates that simulations are a great tool to support experiments and to deliver an improved physics understanding. They help to identify the basic physics principles in the different systems, because they can deliver information not accessible to experiments.
In particular, a better understanding of the influence of electromagnetic fields on the heat-flux distribution in space-relevant applications was obtained. This can be the basis for further simulation-guided optimization, e.g. for the design of more effective cathodic arc thrusters. Here, the goal is to minimize costs for prototypes by replacing the hardware by virtual prototypes in the simulations. This allows to test basic design ideas in advance and get more highly-optimized designs at a fraction of time and costs.
Understanding the fundamental mechanisms in the extracellular matrix of cells (ECM) is crucial for the development of drugs and biomaterials. Therefore, an atomistic model of the extracellular matrix is a cost-efficient way to observe influences of drugs, test the effect of mutations or misfolds in proteins or study the properties of fibril or network-forming peptides.
With this thesis, a refined molecular model of an adhesion complex is proposed that contains collagen, fibronectin and the cell receptor integrin. During the building of the model, major new insights are given for each of these proteins and a powerful protein-folding algorithm is
developed.
Ziel dieser Untersuchung sollte eine Validierung der Sehschärfeprüfung mit einem modifizierten Optotypen sein, um Simulation und Aggravation im gutachterlichen Sehtest aufzudecken. Dieses Testverfahren wurde hier nicht an simulierenden, sondern an wahrheitsgemäß antwortenden Probanden erprobt, um deren Verhalten auf besondere Optotypen bei einem Sehtest standardisiert zu evaluieren.
Simulationsbasierte Analyse von Operationsprozessen am Beispiel eines Grund- und Regelversorgers
(2013)
Die ökonomische Analyse von Prozessen sowie der Auslastung einzelner Ressourcen spielen im Krankenhaus zunehmend eine wichtige Rolle. Werkzeuge aus dem Bereich des Operations Research können die Darstellung, die Bewertung und die Gestaltung von Prozessen im Allgemeinen und von Operationsprozessen im Speziellen maßgeblich unterstützen. Insbesondere die diskrete Ereignissimulation gilt als vielversprechendes Verfahren zur Unterstützung wichtiger Analysen im Krankenhaus. Die vorliegende Arbeit untersucht Operationsprozesse eines Grund- und Regelversorgers. Mit Hilfe einer stochastischen diskreten Ereignissimulation werden sowohl bestehende Prozessabläufe modelliert als auch Auswirkungen veränderter Parameter mittels Szenarienrechnungen simuliert und analysiert. Ein besonderer Fokus liegt auf der Untersuchung der personellen und räumlichen Ressourcen sowie wichtiger Prozesskennzahlen, die durch Betrachtungen der entstehenden Kosten ergänzt wird. Die Arbeit zeigt, dass mit Hilfe einer diskreten Ereignissimulation operative Prozesse eines Grund- und Regelversorgers abgebildet und mittels verschiedener Szenarien Auswirkungen von Prozessänderungen betrachtet werden können. In diesen Szenarien lassen sich sowohl die Auslastung der verschiedenen Ressourcen als auch andere wichtige Prozesskennzahlen beeinflussen. Beispielsweise könnte das derzeit im Krankenhaus durchgeführte Leistungsspektrum in einer geringeren Anzahl an OP-Sälen durchgeführt werden, so dass frei werdende Ressourcen für eine alternative Nutzung zur Verfügung stünden. So ließe sich die mittlere Gesamtauslastung der OP-Säle je nach Szenario maßgeblich steigern. Die diskrete Ereignissimulation zeigt sich als hervorragendes Werkzeug für die Analyse wichtiger Fragestellungen im Krankenhaus und dient somit als hilfreiche Unterstützung von Entscheidungsprozessen.
Ziel dieser Arbeit ist es, die Problematik des steigenden Qualitätsanspruchs und des Kostendrucks im Gesundheitssystem aufzugreifen und vor diesem Hintergrund zwei entscheidende Prozesse im Krankenhaus, die Poliklinik als ambulante medizinische Einheit und die Station als stationäre Pflegeeinheit, näher zu untersuchen. Derzeit sind diese beiden Einheiten noch weitgehend unabhängig voneinander bzw. sie sind im Behandlungsprozess hintereinandergeschaltet. Die Effizienz und die Wirksamkeit von Gesundheitsleistungen hängen maßgeblich von der Entwicklung der Arbeitsteilung und vom Zusammenspiel des ambulanten und des stationären Sektors ab. Im Rahmen dieser Arbeit sollen diese organisch gewachsenen Organisationsstrukturen nun aufgebrochen werden. Es findet ein Perspektivenwechsel von traditionellen Strukturen zu einer prozessualen Sichtweise statt. Anhand verschiedener Prozessoptimierungsansätze soll der Prozess der stationären Versorgung auf der Station in den Prozess der Versorgung in der Poliklinik teilweise integriert werden. Ein zentraler Punkt ist dabei die Identifizierung und Bewertung von Synergiepotenzialen durch die Bündelung bzw. durch die Verlagerung der Ressourcen Pflegepersonal und ärztliches Personal. Neben den quantifizierbaren Folgen für den Ressourceneinsatz sollen durch die Neugestaltung der Prozesse auch Verbesserungen in den medizinischen Behandlungsabläufen und in der Qualitätssicherung erreicht werden. Ein Kerngedanke für die Prozessoptimierung ist eine Klassifikation des Prozessobjektes Patient in mobile und immobile stationäre Patienten. Anhand einer Simulation mit dem Programm MedModel werden die Prozessveränderungen im Ist- und Sollzustand ausgewertet und verglichen. Der Erfolg der angestrebten Prozessoptimierung wird an den Dimensionen der Prozessleistungsfähigkeit Kosten, Qualität und Zeit gemessen.