Dynamical problems and phase transitions

Issued as Financial status report, Technical reports [nos. 1-12], and Final report, Project B-06-68

Inferring Gene Regulatory Networks from Time Series Microarray Data

The innovations and improvements in high-throughput genomic technologies, such as DNA microarray, make it possible for biologists to simultaneously measure dependencies and regulations among genes on a genome-wide scale and provide us genetic information. An important objective of the functional genomics is to understand the controlling mechanism of the expression of these genes and encode the knowledge into gene regulatory network (GRN). To achieve this, computational and statistical algorithms are especially needed. Inference of GRN is a very challenging task for computational biologists because the degree of freedom of the parameters is redundant. Various computational approaches have been proposed for modeling gene regulatory networks, such as Boolean network, differential equations and Bayesian network. There is no so called golden method which can generally give us the best performance for any data set. The research goal is to improve inference accuracy and reduce computational complexity. One of the problems in reconstructing GRN is how to deal with the high dimensionality and short time course gene expression data. In this work, some existing inference algorithms are compared and the limitations lie in that they either suffer from low inference accuracy or computational complexity. To overcome such difficulties, a new approach based on state space model and Expectation-Maximization (EM) algorithms is proposed to model the dynamic system of gene regulation and infer gene regulatory networks. In our model, GRN is represented by a state space model that incorporates noises and has the ability to capture more various biological aspects, such as hidden or missing variables. An EM algorithm is used to estimate the parameters based on the given state space functions and the gene interaction matrix is derived by decomposing the observation matrix using singular value decomposition, and then it is used to infer GRN. The new model is validated using synthetic data sets before applying it to real biological data sets. The results reveal that the developed model can infer the gene regulatory networks from large scale gene expression data and significantly reduce the computational time complexity without losing much inference accuracy compared to dynamic Bayesian network

Facilitation of I Kr current by some hERG channel blockers suppresses early afterdepolarizations.

Drug-induced block of the cardiac rapid delayed rectifying potassium current (I Kr), carried by the human ether-a-go-go-related gene (hERG) channel, is the most common cause of acquired long QT syndrome. Indeed, some, but not all, drugs that block hERG channels cause fatal cardiac arrhythmias. However, there is no clear method to distinguish between drugs that cause deadly arrhythmias and those that are clinically safe. Here we propose a mechanism that could explain why certain clinically used hERG blockers are less proarrhythmic than others. We demonstrate that several drugs that block hERG channels, but have favorable cardiac safety profiles, also evoke another effect; they facilitate the hERG current amplitude in response to low-voltage depolarization. To investigate how hERG facilitation impacts cardiac safety, we develop computational models of I Kr block with and without this facilitation. We constrain the models using data from voltage clamp recordings of hERG block and facilitation by nifekalant, a safe class III antiarrhythmic agent. Human ventricular action potential simulations demonstrate the ability of nifekalant to suppress ectopic excitations, with or without facilitation. Without facilitation, excessive I Kr block evokes early afterdepolarizations, which cause lethal arrhythmias. When facilitation is introduced, early afterdepolarizations are prevented at the same degree of block. Facilitation appears to prevent early afterdepolarizations by increasing I Kr during the repolarization phase of action potentials. We empirically test this prediction in isolated rabbit ventricular myocytes and find that action potential prolongation with nifekalant is less likely to induce early afterdepolarization than action potential prolongation with dofetilide, a hERG channel blocker that does not induce facilitation. Our data suggest that hERG channel blockers that induce facilitation increase the repolarization reserve of cardiac myocytes, rendering them less likely to trigger lethal ventricular arrhythmias

Research on digital image watermark encryption based on hyperchaos

The digital watermarking technique embeds meaningful information into one or more watermark images hidden in one image, in which it is known as a secret carrier. It is difficult for a hacker to extract or remove any hidden watermark from an image, and especially to crack so called digital watermark. The combination of digital watermarking technique and traditional image encryption technique is able to greatly improve anti-hacking capability, which suggests it is a good method for keeping the integrity of the original image. The research works contained in this thesis include: (1)A literature review the hyperchaotic watermarking technique is relatively more advantageous, and becomes the main subject in this programme. (2)The theoretical foundation of watermarking technologies, including the human visual system (HVS), the colour space transform, discrete wavelet transform (DWT), the main watermark embedding algorithms, and the mainstream methods for improving watermark robustness and for evaluating watermark embedding performance. (3) The devised hyperchaotic scrambling technique it has been applied to colour image watermark that helps to improve the image encryption and anti-cracking capabilities. The experiments in this research prove the robustness and some other advantages of the invented technique. This thesis focuses on combining the chaotic scrambling and wavelet watermark embedding to achieve a hyperchaotic digital watermark to encrypt digital products, with the human visual system (HVS) and other factors taken into account. This research is of significant importance and has industrial application value

MECA Workshop on Atmospheric H2O Observations of Earth and Mars. Physical Processes, Measurements and Interpretations

The workshop was held to discuss a variety of questions related to the detection and cycling of atmospheric water. Among the questions addressed were: what factors govern the storage and exchange of water between planetary surfaces and atmospheres; what instruments are best suited for the measurement and mapping of atmospheric water; do regolith sources and sinks of water have uniquely identifiable column abundance signatures; what degree of time and spatial resolution in column abundance data is necessary to determine dynamic behavior. Of special importance is the question, does the understanding of how atmospheric water is cycled on Earth provide any insights for the interpretation of Mars atmospheric data

Practical input optimization for aircraft parameter estimation experiments

The object of this research was to develop an algorithm for the design of practical, optimal flight test inputs for aircraft parameter estimation experiments. A general, single pass technique was developed which allows global optimization of the flight test input design for parameter estimation using the principles of dynamic programming with the input forms limited to square waves only. Provision was made for practical constraints on the input, including amplitude constraints, control system dynamics, and selected input frequency range exclusions. In addition, the input design was accomplished while imposing output amplitude constraints required by model validity and considerations of safety during the flight test. The algorithm has multiple input design capability, with optional inclusion of a constraint that only one control move at a time, so that a human pilot can implement the inputs. It is shown that the technique can be used to design experiments for estimation of open loop model parameters from closed loop flight test data. The report includes a new formulation of the optimal input design problem, a description of a new approach to the solution, and a summary of the characteristics of the algorithm, followed by three example applications of the new technique which demonstrate the quality and expanded capabilities of the input designs produced by the new technique. In all cases, the new input design approach showed significant improvement over previous input design methods in terms of achievable parameter accuracies

An investigation of MEVVA implanted germanium by scanning probe microscopy, ion beam analysis and x-ray diffraction.

by Lee, Chun-Sing.Thesis (M.Phil.)--Chinese University of Hong Kong, 1999.Includes bibliographical references (leaves 98-105).Abstracts in English and Chinese.Acknowledgements --- p.2Abstract --- p.3Table of Contents --- p.7List of Figures --- p.10List of Tables --- p.13Chapter Chapter 1 --- Introduction --- p.14Chapter 1.1. --- Ion implantation --- p.14Chapter 1.2. --- Scope of the thesis --- p.15Chapter Chapter 2 --- Background Theory --- p.17Chapter 2.1. --- Ion stopping --- p.17Chapter 2.2. --- The energy-loss process --- p.17Chapter 2.3. --- Kinematics of binary elastic collision --- p.20Chapter 2.4. --- Nuclear and electronic stopping --- p.21Chapter 2.5. --- Radiation Damage --- p.22Chapter 2.6. --- Spikes --- p.24Chapter 2.7. --- Topography of ion bombarded surface --- p.26Chapter Chapter 3 --- Equipment Reviews --- p.31Chapter 3.1. --- Metal Vapour Vacuum Arc Ion Source Implanter --- p.31Chapter 3.2. --- Atomic Force Microscopy --- p.34Chapter 3.3. --- Rutherford Backscattering Spectrometry --- p.37Chapter 3.4. --- X-ray Diffraction --- p.40Chapter Chapter 4 --- Study of Ion Beam Implanted Germanium by Atomic Force Microscopy and Rutherford Backscattering Spectrometry --- p.43Chapter 4.1. --- Introduction --- p.43Chapter 4.2. --- Experiments --- p.45Chapter 4.3. --- Results and discussion --- p.47Chapter 4.3.1. --- AFM --- p.47Chapter 4.3.2. --- RBS and ion channeling --- p.64Chapter 4.4. --- Conclusions --- p.71Chapter Chapter 5 --- Ion Beam Synthesised Cobalt Germanide Alloy by Metal Vapour Vacuum Arc Implantation --- p.73Chapter 5.1. --- Introduction --- p.73Chapter 5.2. --- Experiments --- p.74Chapter 5.3. --- Results and discussion --- p.74Chapter 5.3.1. --- XRD --- p.74Chapter 5.3.2. --- AFM --- p.78Chapter 5.3.3. --- RBS and ion channeling --- p.82Chapter 5.4. --- Conclusions --- p.87Chapter Chapter 6 --- Tip Artifacts in Atomic Force Microscope Imaging of Ion Bombarded Nanostructures on Germanium Surfaces --- p.89Chapter 6.1. --- Introduction --- p.89Chapter 6.2. --- Experiments --- p.90Chapter 6.3. --- Results and discussion --- p.90Chapter 6.4. --- Conclusions --- p.95Chapter Chapter 7 --- Conclusions --- p.96Bibliography --- p.98Publications --- p.10

An In-Situ TEM Study of High Temperature Helium Irradiation of 4H-SiC

SiC is an excellent candidate material for use in fusion and fission nuclear reactors. The work done in this thesis aims to understand the behaviour of SiC under He irradiation at high temperatures. Experiments of helium irradiation in 4H-SiC in temperature range of 700–900°C have been conducted with in-situ ion irradiation facility of MIAMI. A couple of results are derived from the experiments: The major experimental observations were the formation bubble discs. There is a critical temperature threshold around 700°C above which much higher number density of bubble discs were formed. At 800°C, bubble discs were observed to grow with increasing helium fluence. Growth of bubble discs was also observed when the temperature was held at 800°C after a fluence of 3.8×1016 ions.cm–2 as the bubble discs grew due to diffusion of helium and gain of vacancies. Bubble discs trended to stop growing with a mean size of 30 nm at a fluence of 6.1×1016 ions.cm–2. The evolution of bubble discs was similar at 900°C as at 800°C. Analysis done at room temperature of experiments conducted at 900°C revealed that bubble discs formed preferentially on the {001} and {100} planes

NASA Upper Atmosphere Research Program: Research summaries 1988-1989

Given here is a report on the state of our knowledge of the Earth's upper atmosphere, particularly the stratosphere, and the NASA Upper Atmosphere Research Program