Within a polymer thin film, free-volume elements have a wide range of size and topology. This broad range of free-volume element sizes determines the ability for a polymer to perform molecular separations. Herein, the free volume and transport properties (diffusion, permeability, and selectivity) in both rubbery and glassy polymers were simulated using fully atomistic models. Extension of the computational tool to study the void structure in proteins is also included in this thesis. Six permeable thermally rearranged (TR) polymers and their precursors were studied. Using atomistic models, cavity size (free volume) distributions determined by a combination of molecular dynamics and Monte Carlo methods were consistent with experimental observation that TR polymers are more permeable than their precursors. The cavity size distributions determined by simulation were also consistent with free volume distributions determined by positron annihilation lifetime spectroscopy. The diffusion, solubility and permeation of gases in TR polymers and their precursors were also simulated at 308 K, with results that agree qualitatively with experimental data. A new hybrid Monte Carlo/Molecular Dynamics method is developed for estimating the slow diffusion processes of light gases transporting in glassy polymers. Diffusion coefficients, as small as 10⁻⁵ to 10⁻⁹ cm²/s are estimated for penetrants in four different polymers at 298 K. In all cases, agreement between literature experimental data and values obtained from the fast hybrid molecular dynamics method ranges from good to excellent. A new technique is developed using Monte Carlo methods to characterize the cavity size distribution and surface atoms in globular proteins. New statistical metrics have been defined for the structural characterization of globular proteins. Some of these metrics include volume, surface area, asymmetry ratio, interior cavity size distribution, and the identification of percolation channels. Wild-type (WT) myoglobin (Mb) and 5 Mb mutants have been studied in this research as examples. An analysis of cavity statistics provides an efficient method to quantify local properties such as packing density and transport pathways. The average cavity sizes of WT Mb and its mutants are around 4.0-5.0 Å. / text

The modification of spontaneous emission, i.e. the Purcell effect, with optical cavities has been highly studied over the past 20 years as one of the most important goals for cavity quantum electrodynamics (cQED). The recent development of using surface plasmon resonances to concentrate optical field into sub-wavelength scale further extended cQED research of into a new regime. However, although metallic reflectors are used in some of the earliest demonstrations of cQED, the use of metals is not preferable in high Q optical cavities due to the lossy nature of metals. The presence of metals near an optical emitter also strongly alters its radiation dynamics. As a result, the development of plasmonic cavities brings not only new opportunities but also new problems and challenges. In this thesis we describe four different plasmonic cavity designs along with optical simulations and measurements on them to demonstrate: large spontaneous emission enhancement, controlled mode tuning, and control of the plasmonic band-gap and resonances of high-Q plasmonic cavities for coupling to specific emitters. We hope that our work can guide and inspire researchers who are moving from traditional cavity designs to novel plasmonic devices, helping them to establish design concepts, fabrication criteria, and baselines for characterizing these devices. / Engineering and Applied Sciences

The power/ground plane structure within an electronic system not only delivers power, but also provides return path for the currents associated with the propagating signals. The cavity resonances within the power/ground plane structure affect the signal integrity of the system at high frequencies. The chip complexity and clock speed continue to increase and new structures, such as meshed planes and electromagnetic bandgap structures, are used in plane pair structure design. The signal integrity analysis of the power/ground plane structure becomes exceedingly important and challenging.The primary goal of this research is an in-depth investigation of the impact of the cavity resonances associated with the plane pair structure on the signal integrity. This includes development of modeling, simulation, and measurement methodologies for accurate and efficient characterization or prediction of the time/frequency domain electrical characteristics of power/ground plane pair structures. This research is divided into three parts. First, new SPICE compatible models are proposed for the new structures, such as the meshed plane and EBG embedded plane pair designs, so that the power/ground plane designs with these new structures can be simulated efficiently. Second, the accuracy of the simulation results is vital. The behavior of the benchmark structures is simulated and simulation results are verified either experimentally or by comparing with those from tools that are proven to be accurate. Third, high frequency measurement data is vulnerable to all parasitic parameters. The factors that affect the accuracy of measured data are investigated and methods to improve the accuracy of the measured data are proposed and verified.

The development of new and effective drugs is strongly affected by the need to identify drug targets and to reduce side effects. Unfortunately, resolving these issues depends partially on a broad and thorough understanding of the biological function of many proteins, and the experimental determination of protein function is expensive and time consuming. In response to this problem, algorithms for computational function prediction have been designed to expand experimental impact by finding proteins with predictably similar function, mapping experimental knowledge onto very similar, unstudied proteins. This thesis seeks to develop one method that can identify useful geometric and chemical similarities between well studied and unstudied proteins. Our approach is to identify matches of geometric and chemical similarity between motifs , representing known functional sites, and substructures of functionally uncharacterized proteins ( targets ). It is commonly hypothesized that the existence of a match could imply that the target contains an active site similar to the motif. We have designed the MASH ( M atch A ugmentation with S tatistical H ypothesis Testing) pipeline, a software tool for computing matches. MASH is the first method to match point-based motifs, developed in earlier work, that represent functional sites as points in space with ranked priorities and alternative chemical labels. MASH is also first to match cavity-aware motifs, a novel contribution of this work, that extend point-based motifs with volumetric information describing active clefts critical to protein function. Controlled experiments demonstrate that matches for both types of motifs can identify cognate active sites. However, motifs can also identify matches to functionally unrelated proteins. For this reason, we developed M otif Profiling (MP), the first method for motif refinement that reduces geometric similarity to functionally unre lated proteins. MP is implemented in two forms: Geometric Sieving (GS) refines point-based motifs and Cavity Scaling (CS) refines cavity-aware motifs. Controlled experimentation demonstrates that GS and CS identify motif refinements that have more matches to functionally related proteins and less matches to functionally unrelated proteins. This thesis demonstrates the importance of computational tools for matching and refining motifs, emphasizing the applicability of large-scale geometric and statistical analysis for functional annotation. / National Science Foundation, National Library of Medicine, AMD, Cray

Making researches, specific “based on patients self rating” are created. Oscular cavity health researches subjective health rating measures may be used creating public healing strategy, more considering patients requirements. Using these measures, resources may be more effectively used, to get maximum effect. Will to improve general health condition and oscular cavity condition, are strongly motivating factors, reaching for odontological healing. Topicality characterizes on identifying health knowledge and skills, after using research creating prophylactic study programs, mouth illnesses prophylactic projects. Object: health of oscular cavity and hygiene in health keeping and strengthening process. Aim: identify oral cavity health and hygienic skills of oral cavity in health keeping and strengthening process of students, sustaining on research made. Tasks: 1. valuate health and oral cavity condition of respondents; 2. explore student‘s hygienic skills of oral cavity; 3. posit factors, determing respondent‘s knowledge about oral cavity health; 4. sort out respondents knowledge about importance of care of prosthesis. By data of research made, health and oral cavity condition of most respondents is well. Most respondents have enough knowledge about factors, determing oral cavity health. Third year students have more knowledge about oral cavity health than first year students.

No description available.

Hyperthermophilic proteins are of great interest in both the academic and industrial world in understanding how these proteins are capable of retaining their biological activity under such harsh environmental conditions. This thesis studies a tetrabrachion stalk domain from Staphylothermus marinus, know as Right Handed Coiled Coil (RHCC). This protein is of interest due to its extreme thermostability and its affinity for heavy metals. We aim to better understand the reason for the extreme thermal stability of the protein and to take advantage of the proteins affinity for heavy metals with a view to developing a novel approach to bioremediate Hg2+, a major environmental pollutant. Our results clearly indicated that the protein is more thermostable in alkaline conditions in comparison to acidic conditions. This observation can be explained by careful inspection of the high resolution structure. Our data also clearly show that RHCC is able to bind ionic mercury compounds such as mercury nitrate and dipotassium mercury iodide.

Conservative endodontic cavity (CEC) may improve fracture resistance of teeth but compromise instrumentation of canals. Extracted human intact maxillary incisors, mandibular premolars and molars were imaged with micro-CT and assigned to CEC or traditional endodontic cavity (TEC) groups (n=10/group/type). Canals were prepared and post-treatment micro-CT images obtained. These teeth along with the negative controls were then loaded to fracture. Mean proportion of untouched canal-wall was significantly higher only in distal canals of molars with CEC compared to TEC. Mean dentin volume removed was significantly smaller for CEC in all tooth types. Mean load-at-fracture for CEC was significantly higher in premolars and molars without differing significantly from the negative controls. While CEC was associated with compromised canal instrumentation only in the distal canals of molars, it conserved coronal dentin in all three tooth types and increased resistance to fracture in the mandibular molars and premolars.

Conservative endodontic cavity (CEC) may improve fracture resistance of teeth but compromise instrumentation of canals. Extracted human intact maxillary incisors, mandibular premolars and molars were imaged with micro-CT and assigned to CEC or traditional endodontic cavity (TEC) groups (n=10/group/type). Canals were prepared and post-treatment micro-CT images obtained. These teeth along with the negative controls were then loaded to fracture. Mean proportion of untouched canal-wall was significantly higher only in distal canals of molars with CEC compared to TEC. Mean dentin volume removed was significantly smaller for CEC in all tooth types. Mean load-at-fracture for CEC was significantly higher in premolars and molars without differing significantly from the negative controls. While CEC was associated with compromised canal instrumentation only in the distal canals of molars, it conserved coronal dentin in all three tooth types and increased resistance to fracture in the mandibular molars and premolars.

No description available.