Parallel exact enumeration of self-avoiding walk on cubic lattices and its applications to protein folding studies

Exact enumeration of self-avoiding walk on many lattices have been studied extensively recently. Even a short chain polymer (about 30 monomers) represented as a chain of cubic lattice sites requires a considerable amount of computer time to exhaustively search for all unique conformations. However, self-avoiding walk process can be modified such that it exhibits a high degree of independence among subprocesses. Parallel implementation of such subprocesses can reduce a great amount of enumeration time. Parallel enumeration makes longer chain enumeration possible. Enumerating only unique conformations requires that all rotation and mirror conformations be removed. An algorithm to avoid generating such symmetrical conformations is presented. A set of parallel algorithms to solve exact enumeration of cubic lattice graphs subjected to various constraints (volume and/or contact constraints) is presented. The speed up and communication cost are analyzed. One of the most important application of lattice enumeration, enumerative kinetics of protein folding, is also discussed

Correct-by-Construction Development of Dynamic Topology Control Algorithms

Wireless devices are influencing our everyday lives today and will even more so in the future. A wireless sensor network (WSN) consists of dozens to hundreds of small, cheap, battery-powered, resource-constrained sensor devices (motes) that cooperate to serve a common purpose. These networks are applied in safety- and security-critical areas (e.g., e-health, intrusion detection). The topology of such a system is an attributed graph consisting of nodes representing the devices and edges representing the communication links between devices. Topology control (TC) improves the energy consumption behavior of a WSN by blocking costly links. This allows a mote to reduce its transmission power. A TC algorithm must fulfill important consistency properties (e.g., that the resulting topology is connected). The traditional development process for TC algorithms only considers consistency properties during the initial specification phase. The actual implementation is carried out manually, which is error prone and time consuming. Thus, it is difficult to verify that the implementation fulfills the required consistency properties. The problem becomes even more severe if the development process is iterative. Additionally, many TC algorithms are batch algorithms, which process the entire topology, irrespective of the extent of the topology modifications since the last execution. Therefore, dynamic TC is desirable, which reacts to change events of the topology. In this thesis, we propose a model-driven correct-by-construction methodology for developing dynamic TC algorithms. We model local consistency properties using graph constraints and global consistency properties using second-order logic. Graph transformation rules capture the different types of topology modifications. To specify the control flow of a TC algorithm, we employ the programmed graph transformation language story-driven modeling. We presume that local consistency properties jointly imply the global consistency properties. We ensure the fulfillment of the local consistency properties by synthesizing weakest preconditions for each rule. The synthesized preconditions prohibit the application of a rule if and only if the application would lead to a violation of a consistency property. Still, this restriction is infeasible for topology modifications that need to be executed in any case. Therefore, as a major contribution of this thesis, we propose the anticipation loop synthesis algorithm, which transforms the synthesized preconditions into routines that anticipate all violations of these preconditions. This algorithm also enables the correct-by-construction runtime reconfiguration of adaptive WSNs. We provide tooling for both common evaluation steps. Cobolt allows to evaluate the specified TC algorithms rapidly using the network simulator Simonstrator. cMoflon generates embedded C code for hardware testbeds that build on the sensor operating system Contiki

Hardware, Software, and Low-Level Control Scheme Development for a Real-Time Autonomous Rover

The objective of this research is to develop a low-cost autonomous rover platform for experiments in autonomous navigation. This thesis describes the design, development, and testing of an autonomous rover platform, based on the commercial, off-the-shelf Tamiya TXT-1 radio controlled vehicle. This vehicle is outfitted with an onboard computer based on the Mini-ITX architecture and an array of sensors for localization and obstacle avoidance, and programmed with Matlab/SimulinkRTM Real-Time Workshop (RTW) utilizing the Linux Real-Time Application Interface (RTAI) operating system.;First, a kinematic model is developed and verified for the rover. Then a proportional-integral-derivative (PID) feedback controller is developed for translational and rotational velocity regulation. Finally, a hybrid navigation controller is developed combining a potential field controller and an obstacle avoidance controller for waypoint tracking.;Experiments are performed to verify the functionality of the kinematic model and the PID velocity controller, and to demonstrate the capabilities of the hybrid navigation controller. These experiments prove that the rover is capable of successfully navigating in an unknown indoor environment. Suggestions for future research include the integration of additional sensors for localization and creation of multiple platforms for autonomous coordination experiments

Automated Quantification of Human Alpha Rhythm

This thesis seeks to quantify human alpha rhythm in order to obtain better measures to test theoretical models of neurodynamics, with potential clinical applications for the method of identification. An automated algorithm is developed in Chapter 2 to facilitate collection of objective data from an expanded alpha band (4–14 Hz) in a large number of subjects. This method avoids subjective bias inherent to traditional visual identification of the alpha activity, produced multiple peak information (if multiple peaks exist) that is absent in qEEG measures, and uses information from multiple electrode sites to eliminate spurious peaks. This method is tested and validated on 100 subjects. In addition to traditional measures of alpha activities such as the frequency and amplitude, further measures were devised to better quantify the alpha rhythm and its spatial characteristics. Background spectra in the alpha range are also characterized. In Chapter 3 the algorithm is applied to a large (1498 subjects) database of normal healthy subjects of approximately equal number in each sex, as well as a large span in age (6–86 years), in order to establish typical parameter ranges. Analysis is done comparing the age and the topological trends that are known variants in the alpha rhythm. Investigations are also performed to test for potential sex differences and/or lateralities. Key results are that double alpha peaks are resolved in a large proportion of the subjects ( 50%), while single alpha peak cases are likely to be double-peak cases in which the two peaks are not resolved. Age trends in measures of alpha activity show increase of alpha frequency from childhood to adolescence, a plateau in adulthood, and a slight decline in old age; a decrease in alpha amplitude in old age is also observed. These findings are consistent with previous literature and provide better statistics. Topological distribution of the alpha activity on the head is also explored, with little lateral asymmetry observed. No statistically significant differences between the sexes are found. The C++ code that was developed and utilized in this thesis is included in Appendix B. It is provided on disk and is available online. A study carried out on the same group of subjects to determine age-related trends of EEG parameters produced by model fitting is included in Appendixes C, to provide a comparison between the methods and highlights corresponding results

Materiales compuestos multifuncionales para aplicaciones médicas: Uso de sulfato de bario y nanotubos de carbono con poliésteres bioabsorbibles

186 p.La presente tesis doctoral es un estudio de diferentes materiales compuestos biodegradables cuyo objetivo es encontrar materiales con nuevas y mejores funcionalidades para la aplicación en medicina como: liberación controlada de fármacos, catéteres no permanentes, regeneración de tejido óseo o regeneración de tejido nervioso.Para esto se han estudiado dos tipo de refuerzo: Sulfato de Bario de tamaño micrométrico y nanotubos de carbono de pared múltiple, además de dos tipos de matriz biodegradable: El polímero de degradación lenta Poli(¿-caprolactona) y el terpolimero de rápida degradación Poly(L,D-L-lactida-co-¿-caprolactona).Durante los diferentes capítulos de la tesis se estudian principalemente las propiedades mechanicas, dinámico-mecánicas, estructurales de estos materiales, así como propiedades nuevas que aportan los refuerzo como es la radio-opacidad aportada por el sulfato de bario o la bioactividad aportada por los nanotubos de carbono de pared múltiple. También se realiza un estudio en profundidad de la interfase entre matriz/polímero y sus consecuencias en las propiedades. Y por último un estudio en profundidad de los efectos de la fatiga en el material Poli(¿-caprolactona) simulando condiciones del cuerpo humano y la mejora producida por los nanotubos de carbono de pared múltiple en estas circunstancias

Development of Rules of Attraction for Intercalated Guest Molecules Inside of a Hydrogen Bonded Framework

Supramolecular chemistry has synthesized large and small molecules which host guest molecules for several decades. What started as a way to mimic of enzymes in nature, has exploded into a sea of materials such as porous coordination polymers, low-density metal-organic frameworks, inclusion compounds, and hydrogen bonded frameworks. We previously designed a layered framework consisting of a metal complex with coordinate covalent ligands. These ligands have peripheral carboxylic acid groups which hydrogen bond to organic pillars containing terminal amines. The layered structure is separated by these pillars, which are closed-packed, creating 1-dimensional channels able to co-crystallize molecules. There is interest in selectively binding molecules for separation, catalysis, molecular recognition or transport. How do guests selectively co-crystallize into the framework? Do properties of guest molecules such as size, shape or electronics dictate preference? By establishing a set of selectivity rules, potential applications appear. In our pursuit, we devised a new way of coupling a thermogravimetric analyzer to a mass spectrometer using solid-phase microextraction fibers. These two instruments can be used together for a fraction existing coupling cost. By testing guests of different size and shape, we found large guest molecules will co-crystallize over smaller ones. If a guest is too large, the selectivity can become concentration dependent. Maintaining the size difference between two molecules, we changed to geometric isomers. The framework lost selectivity due to poor guest co-crystallization and low guest inclusion rates. Next, we tested guest molecules whose size and shape was similar but had different electronics. Aromatic guests with electron donating substituents were preferred over those with electron withdrawing groups. The framework could detect subtle changes in the electronic structure, e.g., substituting chloro- for a methyl. Guests containing anchor points, σ-hole, were showed preference. Selectivity correlated to physical properties such as boiling point and density of the guests containing electron withdrawing substituents. Finally, we focused on single co-crystallized guests tested by thermogravimetric analysis, gas chromatography, and powder x-ray diffraction. The preferred guests in the previous study contained electron donating groups and high occupancy. Outliers such as iodobenzene were preferred in competition but had low concentrations as a single guest