Computersimulationen zum Einfluss topologischer Beschränkungen auf Polymere

Topologische Beschränkungen beeinflussen die Eigenschaften von Polymeren. Im Rahmen dieser Arbeit wird mit Hilfe von Computersimulationen im Detail untersucht, inwieweit sich die statischen Eigenschaften von kollabierten Polymerringen, Polymerringen in konzentrierten Lösungen und aus Polymerringen aufgebauten Bürsten mit topologischen Beschränkungen von solchen ohne topologische Beschränkungen unterscheiden. Des Weiteren wird analysiert, welchen Einfluss geometrische Beschränkungen auf die topologischen Eigenschaften von einzelnen Polymerketten besitzen. Im ersten Teil der Arbeit geht es um den Einfluss der Topologie auf die Eigenschaften einzelner Polymerketten in verschiedenen Situationen. Da allerdings gerade die effiziente Durchführung von Monte-Carlo-Simulationen von kollabierten Polymerketten eine große Herausforderung darstellt, werden zunächst drei Bridging-Monte-Carlo-Schritte für Gitter- auf Kontinuumsmodelle übertragen. Eine Messung der Effizienz dieser Schritte ergibt einen Beschleunigungsfaktor von bis zu 100 im Vergleich zum herkömmlichen Slithering-Snake-Algorithmus. Darauf folgt die Analyse einer einzelnen, vergröberten Polystyrolkette in sphärischer Geometrie hinsichtlich Verschlaufungen und Knoten. Es wird gezeigt, dass eine signifikante Verknotung der Polystrolkette erst eintritt, wenn der Radius des umgebenden Kapsids kleiner als der Gyrationsradius der Kette ist. Des Weiteren werden sowohl Monte-Carlo- als auch Molekulardynamiksimulationen sehr großer Ringe mit bis zu einer Million Monomeren im kollabierten Zustand durchgeführt. Während die Konfigurationen aus den Monte-Carlo-Simulationen aufgrund der Verwendung der Bridging-Schritte sehr stark verknotet sind, bleiben die Konfigurationen aus den Molekulardynamiksimulationen unverknotet. Hierbei zeigen sich signifikante Unterschiede sowohl in der lokalen als auch in der globalen Struktur der Ringpolymere. Im zweiten Teil der Arbeit wird das Skalierungsverhalten des Gyrationsradius der einzelnen Polymerringe in einer konzentrierten Lösung aus völlig flexiblen Polymerringen im Kontinuum untersucht. Dabei wird der Anfang des asymptotischen Skalierungsverhaltens, welches mit dem Modell des “fractal globules“ konsistent ist, erreicht. Im abschließenden, dritten Teil dieser Arbeit wird das Verhalten von Bürsten aus linearen Polymeren mit dem von Ringpolymerbürsten verglichen. Dabei zeigt sich, dass die Struktur und das Skalierungsverhalten beider Systeme mit identischem Dichteprofil parallel zum Substrat deutlich voneinander abweichen, obwohl die Eigenschaften beider Systeme in Richtung senkrecht zum Substrat übereinstimmen. Der Vergleich des Relaxationsverhaltens einzelner Ketten in herkömmlichen Polymerbürsten und Ringbürsten liefert keine gravierenden Unterschiede. Es stellt sich aber auch heraus, dass die bisher verwendeten Erklärungen zur Relaxationsverhalten von herkömmlichen Bürsten nicht ausreichen, da diese lediglich den anfänglichen Zerfall der Korrelationsfunktion berücksichtigen. Bei der Untersuchung der Dynamik einzelner Monomere in einer herkömmlichen Bürste aus offenen Ketten vom Substrat hin zum offenen Ende zeigt sich, dass die Monomere in der Mitte der Kette die langsamste Relaxation besitzen, obwohl ihre mittlere Verrückung deutlich kleiner als die der freien Endmonomere ist.

Computer simulations of two-dimensional colloidal crystals under confinement and shear

In this thesis we are presenting a broadly based computer simulation study of two-dimensional colloidal crystals under different external conditions. In order to fully understand the phenomena which occur when the system is being compressed or when the walls are being sheared, it proved necessary to study also the basic motion of the particles and the diffusion processes which occur in the case without these external forces. In the first part of this thesis we investigate the structural transition in the number of rows which occurs when the crystal is being compressed by placing the structured walls closer together. Previous attempts to locate this transition were impeded by huge hysteresis effects. We were able to determine the transition point with higher precision by applying both the Schmid-Schilling thermodynamic integration method and the phase switch Monte Carlo method in order to determine the free energies. These simulations showed not only that the phase switch method can successfully be applied to systems with a few thousand particles and a soft crystalline structure with a superimposed pattern of defects, but also that this method is way more efficient than a thermodynamic integration when free energy differences are to be calculated. Additionally, the phase switch method enabled us to distinguish between several energetically very similar structures and to determine which one of them was actually stable. Another aspect considered in the first result chapter of this thesis is the ensemble inequivalence which can be observed when the structural transition is studied in the NpT and in the NVT ensemble. The second part of this work deals with the basic motion occurring in colloidal crystals confined by structured walls. Several cases are compared where the walls are placed in different positions, thereby introducing an incommensurability into the crystalline structure. Also the movement of the solitons, which are created in the course of the structural transition, is investigated. Furthermore, we will present results showing that not only the well-known mechanism of vacancies and interstitial particles leads to diffusion in our model system, but that also cooperative ring rotation phenomena occur. In this part and the following we applied Langevin dynamics simulations. In the last chapter of this work we will present results on the effect of shear on the colloidal crystal. The shear was implemented by moving the walls with constant velocity. We have observed shear banding and, depending on the shear velocity, that the inner part of the crystal breaks into several domains with different orientations. At very high shear velocities holes are created in the structure, which originate close to the walls, but also diffuse into the inner part of the crystal.

Comparison of actual surgical outcomes and 3-dimensional surgical simulations

PURPOSE: The advent of imaging software programs has proved to be useful for diagnosis, treatment planning, and outcome measurement, but precision of 3-dimensional (3D) surgical simulation still needs to be tested. This study was conducted to determine whether the virtual surgery performed on 3D models constructed from cone-beam computed tomography (CBCT) can correctly simulate the actual surgical outcome and to validate the ability of this emerging technology to recreate the orthognathic surgery hard tissue movements in 3 translational and 3 rotational planes of space. MATERIALS AND METHODS: Construction of pre- and postsurgery 3D models from CBCTs of 14 patients who had combined maxillary advancement and mandibular setback surgery and 6 patients who had 1-piece maxillary advancement surgery was performed. The postsurgery and virtually simulated surgery 3D models were registered at the cranial base to quantify differences between simulated and actual surgery models. Hotelling t tests were used to assess the differences between simulated and actual surgical outcomes. RESULTS: For all anatomic regions of interest, there was no statistically significant difference between the simulated and the actual surgical models. The right lateral ramus was the only region that showed a statistically significant, but small difference when comparing 2- and 1-jaw surgeries. CONCLUSIONS: Virtual surgical methods were reliably reproduced. Oral surgery residents could benefit from virtual surgical training. Computer simulation has the potential to increase predictability in the operating room.

Simulation of titration experiments

Nowadays computer simulation is used in various fields, particularly in laboratories where it is used for the exploration data which are sometimes experimentally inaccessible. In less developed countries where there is a need for up to date laboratories for the realization of practical lessons in chemistry, especially in secondary schools and some higher institutions of learning, it may permit learners to carryout experiments such as titrations without the use of laboratory materials and equipments. Computer simulations may also permit teachers to better explain the realities of practical lessons, given that computers have now become very accessible and less expensive compared to the acquisition of laboratory materials and equipments. This work is aimed at coming out with a virtual laboratory that shall permit the simulation of an acid-base titration and an oxidation-reduction titration with the use of synthetic images. To this effect, an appropriate numerical method was used to obtain appropriate organigram, which were further transcribed into source codes with the help of a programming language so as to come out with the software.

Understanding Electrophoretic Stacking Of In-Capillary Generated Reaction Products

The separation of small molecules by capillary electrophoresis is governed by a complex interplay among several physical effects. Until recently, a systematic understanding of how the influence of all of these effects is observed experimentally has remained unclear. The work presented in this thesis involves the use of transient isotachophoretic stacking (tITP) and computer simulation to improve and better understand an in-capillary chemical assay for creatinine. This assay involves the use of electrophoretically mediated micro-analysis (EMMA) to carry out the Jaffé reaction inside a capillary tube. The primary contribution of this work is the elucidation of the role of the length and concentration of the hydroxide plug used to achieve tITP stacking of the product formed by the in-capillary EMMA/Jaffé method. Computer simulation using SIMUL 5.0 predicts that a 3-4 fold gain in sensitivity can be recognized by timing the tITP stacking event such that the Jaffé product peak is at its maximum height as that peak is electrophoresing past the detection window. Overall, the length of the hydroxide plug alters the timing of the stacking event and lower concentration plugs of hydroxide lead to more rapidly occurring tITP stacking events. Also, the inclusion of intentional tITP stacking in the EMMA/Jaffé method improves the sensitivity of the assay, including creatinine concentrations within the normal biological range. Ultimately, improvement in assay sensitivity can be rationally designed by using the length and concentration of the hydroxide plug to engineer the timing of the tITP stacking event such that stacking occurs as the Jaffé product is passing the detection window.

High-resolution computer simulations of stacking of weak bases using a transient pH boundary in capillary electrophoresis. 1. Concept and impact of sample ionic strength

The dynamics of focusing weak bases using a transient pH boundary was examined via high-resolution computer simulation software. Emphasis was placed on the mechanism and impact that the presence of salt, namely, NaCl, has on the ability to focus weak bases. A series of weak bases with mobilities ranging from 5 x 10(-9) to 30 x 10(-9) m2/V x s and pKa values between 3.0 and 7.5 were examined using a combination of 65.6 mM formic acid, pH 2.85, for the separation electrolyte, and 65.6 mM formic acid, pH 8.60, for the sample matrix. Simulation data show that it is possible to focus weak bases with a pKa value similar to that of the separation electrolyte, but it is restricted to weak bases having an electrophoretic mobility of 20 x 10(-9) m2/V x s or quicker. This mobility range can be extended by the addition of NaCl, with 50 mM NaCl allowing stacking of weak bases down to a mobility of 15 x 10(-9) m2/V x s and 100 mM extending the range to 10 x 10(-9) m2/V x s. The addition of NaCl does not adversely influence focusing of more mobile bases, but does prolong the existence of the transient pH boundary. This allows analytes to migrate extensively through the capillary as a single focused band around the transient pH boundary until the boundary is dissipated. This reduces the length of capillary that is available for separation and, in extreme cases, causes multiple analytes to be detected as a single highly efficient peak.

Charge induced enhancement of adsorption for hydrogen storage materials

The rising concerns about environmental pollution and global warming have facilitated research interest in hydrogen energy as an alternative energy source. To apply hydrogen for transportations, several issues have to be solved, within which hydrogen storage is the most critical problem. Lots of materials and devices have been developed; however, none is able to meet the DOE storage target. The primary issue for hydrogen physisorption is a weak interaction between hydrogen and the surface of solid materials, resulting negligible adsorption at room temperature. To solve this issue, there is a need to increase the interaction between the hydrogen molecules and adsorbent surface. In this study, intrinsic electric dipole is investigated to enhance the adsorption energy. The results from the computer simulation of single ionic compounds with hydrogen molecules to form hydrogen clusters showed that electrical charge of substances plays an important role in generation of attractive interaction with hydrogen molecules. In order to further examine the effects of static interaction on hydrogen adsorption, activated carbon with a large surface area was impregnated with various ionic salts including LiCl, NaCl, KCl, KBr, and NiCl and their performance for hydrogen storage was evaluated by using a volumetric method. Corresponding computer simulations have been carried out by using DFT (Density Functional Theory) method combined with point charge arrays. Both experimental and computational results prove that the adsorption capacity of hydrogen and its interaction with the solid materials increased with electrical dipole moment. Besides the intrinsic dipole, an externally applied electric field could be another means to enhance hydrogen adsorption. Hydrogen adsorption under an applied electric field was examined by using porous nickel foil as electrodes. Electrical signals showed that adsorption capacity increased with the increasing of gas pressure and external electric voltage. Direct measurement of the amount of hydrogen adsorption was also carried out with porous nickel oxides and magnesium oxides using the piezoelectric material PMN-PT as the charge supplier due to the pressure. The adsorption enhancement from the PMN-PT generated charges is obvious at hydrogen pressure between 0 and 60 bars, where the hydrogen uptake is increased at about 35% for nickel oxide and 25% for magnesium oxide. Computer simulation reveals that under the external electric field, the electron cloud of hydrogen molecules is pulled over to the adsorbent site and can overlap with the adsorbent electrons, which in turn enhances the adsorption energy Experiments were also carried out to examine the effects of hydrogen spillover with charge induced enhancement. The results show that the overall storage capacity in nickel oxide increased remarkably by a factor of 4.

Parameter estimation for transformer modeling

Large Power transformers, an aging and vulnerable part of our energy infrastructure, are at choke points in the grid and are key to reliability and security. Damage or destruction due to vandalism, misoperation, or other unexpected events is of great concern, given replacement costs upward of $2M and lead time of 12 months. Transient overvoltages can cause great damage and there is much interest in improving computer simulation models to correctly predict and avoid the consequences. EMTP (the Electromagnetic Transients Program) has been developed for computer simulation of power system transients. Component models for most equipment have been developed and benchmarked. Power transformers would appear to be simple. However, due to their nonlinear and frequency-dependent behaviors, they can be one of the most complex system components to model. It is imperative that the applied models be appropriate for the range of frequencies and excitation levels that the system experiences. Thus, transformer modeling is not a mature field and newer improved models must be made available. In this work, improved topologically-correct duality-based models are developed for three-phase autotransformers having five-legged, three-legged, and shell-form cores. The main problem in the implementation of detailed models is the lack of complete and reliable data, as no international standard suggests how to measure and calculate parameters. Therefore, parameter estimation methods are developed here to determine the parameters of a given model in cases where available information is incomplete. The transformer nameplate data is required and relative physical dimensions of the core are estimated. The models include a separate representation of each segment of the core, including hysteresis of the core, λ-i saturation characteristic, capacitive effects, and frequency dependency of winding resistance and core loss. Steady-state excitation, and de-energization and re-energization transients are simulated and compared with an earlier-developed BCTRAN-based model. Black start energization cases are also simulated as a means of model evaluation and compared with actual event records. The simulated results using the model developed here are reasonable and more correct than those of the BCTRAN-based model. Simulation accuracy is dependent on the accuracy of the equipment model and its parameters. This work is significant in that it advances existing parameter estimation methods in cases where the available data and measurements are incomplete. The accuracy of EMTP simulation for power systems including three-phase autotransformers is thus enhanced. Theoretical results obtained from this work provide a sound foundation for development of transformer parameter estimation methods using engineering optimization. In addition, it should be possible to refine which information and measurement data are necessary for complete duality-based transformer models. To further refine and develop the models and transformer parameter estimation methods developed here, iterative full-scale laboratory tests using high-voltage and high-power three-phase transformer would be helpful.

LATTICE BOLTZMANN METHOD AND CELLULAR AUTOMATA SIMULATION OF PARTICLE MOTION AND DEPOSITION IN 2-D CASE

This technical report discusses the application of the Lattice Boltzmann Method (LBM) and Cellular Automata (CA) simulation in fluid flow and particle deposition. The current work focuses on incompressible flow simulation passing cylinders, in which we incorporate the LBM D2Q9 and CA techniques to simulate the fluid flow and particle loading respectively. For the LBM part, the theories of boundary conditions are studied and verified using the Poiseuille flow test. For the CA part, several models regarding simulation of particles are explained. And a new Digital Differential Analyzer (DDA) algorithm is introduced to simulate particle motion in the Boolean model. The numerical results are compared with a previous probability velocity model by Masselot [Masselot 2000], which shows a satisfactory result.

Introduction to Realistic Neural Modeling

This document corresponds to the tutorial on realistic neural modeling given by David Beeman at WAM-BAMM*05, the first annual meeting of the World Association of Modelers (WAM) Biologically Accurate Modeling Meeting (BAMM) on March 31, 2005 in San Antonio, TX. Part I - Introduction to Realistic Neural Modeling for the Beginner: This is a general overview and introduction to compartmental cell modeling and realistic network simulation for the beginner. Although examples are drawn from GENESIS simulations, the tutorial emphasizes the general modeling approach, rather than the details of using any particular simulator. Part II - Getting Started with Modeling Using GENESIS: This builds upon the background of Part I to describe some details of how this approach is used to construct cell and network simulations in GENESIS. It serves as an introduction and roadmap to the extended hands-on GENESIS Modeling Tutorial.

Recent Developments in NEURON

We describe four recent additions to NEURON's suite of graphical tools that make it easier for users to create and manage models: an enhancement to the Channel Builder that facilitates the specification and efficient simulation of stochastic channel models

Neural Networks as Cybernetic Systems - Part I

Neural Networks as Cybernetic Systems is a textbox that combines classical systems theory with artificial neural network technology.

Neural Networks as Cybernetic Systems - Part II

Neural Networks as Cybernetic Systems is a textbox that combines classical systems theory with artificial neural network technology.