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A theoretical analysis of microchannel flow boiling enhancement via cross-sectional expansion

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Microchannel heat sinks can possess heat transfer characteristics unavailable in conventional heat exchangers; such sinks offer compact solutions to otherwise intractable thermal management problems, notably in small-scale electronics cooling. Flow boiling in microchannels allows a very high heat transfer rate,

Microchannel heat sinks can possess heat transfer characteristics unavailable in conventional heat exchangers; such sinks offer compact solutions to otherwise intractable thermal management problems, notably in small-scale electronics cooling. Flow boiling in microchannels allows a very high heat transfer rate, but is bounded by the critical heat flux (CHF). This thesis presents a theoretical-numerical study of a method to improve the heat rejection capability of a microchannel heat sink via expansion of the channel cross-section along the flow direction. The thermodynamic quality of the refrigerant increases during flow boiling, decreasing the density of the bulk coolant as it flows. This may effect pressure fluctuations in the channels, leading to nonuniform heat transfer and local dryout in regions exceeding CHF. This undesirable phenomenon is counteracted by permitting the cross-section of the microchannel to increase along the direction of flow, allowing more volume for the vapor. Governing equations are derived from a control-volume analysis of a single heated rectangular microchannel; the cross-section is allowed to expand in width and height. The resulting differential equations are solved numerically for a variety of channel expansion profiles and numbers of channels. The refrigerant is R-134a and channel parameters are based on a physical test bed in a related experiment. Significant improvement in CHF is possible with moderate area expansion. Minimal additional manufacturing costs could yield major gains in the utility of microchannel heat sinks. An optimum expansion rate occurred in certain cases, and alterations in the channel width are, in general, more effective at improving CHF than alterations in the channel height. Modest expansion in height enables small width expansions to be very effective.

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2011

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Synthesis and evaluation of a new class of cancer chemotherapeutics based on purine-like extended amidines

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A potential new class of cancer chemotherapeutic agents has been synthesized by varying the 2 position of a benzimidazole based extended amidine. Compounds 6-amino-2-chloromethyl-4-imino-1-(2-methansulfonoxyethyl)-5-methyl-1H-benzimidazole-7-one (1A) and 6-amino-2-hydroxypropyl-4-imino-1-(2-methansulfonoxyethyl)-5-methyl-1H-benzimidazole-7-one (1B) were assayed at the National Cancer Institute's (NCI) Developmental Therapeutic Program (DTP)

A potential new class of cancer chemotherapeutic agents has been synthesized by varying the 2 position of a benzimidazole based extended amidine. Compounds 6-amino-2-chloromethyl-4-imino-1-(2-methansulfonoxyethyl)-5-methyl-1H-benzimidazole-7-one (1A) and 6-amino-2-hydroxypropyl-4-imino-1-(2-methansulfonoxyethyl)-5-methyl-1H-benzimidazole-7-one (1B) were assayed at the National Cancer Institute's (NCI) Developmental Therapeutic Program (DTP) and found to be cytotoxic at sub-micromolar concentrations, and have shown between a 100 and a 1000-fold increase in specificity towards lung, colon, CNS, and melanoma cell lines. These ATP mimics have been found to correlate with sequestosome 1 (SQSTM1), a protein implicated in drug resistance and cell survival in various cancer cell lines. Using the DTP COMPARE algorithm, compounds 1A and 1B were shown to correlate to each other at 77%, but failed to correlate with other benzimidazole based extended amidines previously synthesized in this laboratory suggesting they operate through a different biological mechanism.

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2011

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Mapping the RNA-protein interface in telomerase RNP

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In the 1970s James Watson recognized the inability of conventional DNA replication machinery to replicate the extreme termini of chromosomes known as telomeres. This inability is due to the requirement of a building block primer and was termed the

In the 1970s James Watson recognized the inability of conventional DNA replication machinery to replicate the extreme termini of chromosomes known as telomeres. This inability is due to the requirement of a building block primer and was termed the end replication problem. Telomerase is nature's answer to the end replication problem. Telomerase is a ribonucleoprotein which extends telomeres through reverse transcriptase activity by reiteratively copying a short intrinsic RNA sequence to generate 3' telomeric extensions. Telomeres protect chromosomes from erosion of coding genes during replication, as well as differentiate native chromosome ends from double stranded breaks. However, controlled erosion of telomeres functions as a naturally occurring molecular clock limiting the replicative capacity of cells. Telomerase is over activated in many cancers, while inactivation leads to multiple lifespan limiting human diseases. In order to further study the interaction between telomerase RNA (TR) and telomerase reverse transcriptase protein (TERT), vertebrate TERT fragments were screened for solubility and purity following bacterial expression. Soluble fragments of medaka TERT including the RNA binding domain (TRBD) were identified. Recombinant medaka TRBD binds specifically to telomerase RNA CR4/CR5 region. Ribonucleotide and amino acid pairs in close proximity within the medaka telomerase RNA-protein complex were identified using photo-activated cross-linking in conjunction with mass spectrometry. The identified cross-linking amino acids were mapped on known crystal structures of TERTs to reveal the RNA interaction interface of TRBD. The identification of this RNA TERT interaction interface furthers the understanding of the telomerase complex at a molecular level and could be used for the targeted interruption of the telomerase complex as a potential cancer treatment.

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2011

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Generalized statistical tolerance analysis and three dimensional model for manufacturing tolerance transfer in manufacturing process planning

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Mostly, manufacturing tolerance charts are used these days for manufacturing tolerance transfer but these have the limitation of being one dimensional only. Some research has been undertaken for the three dimensional geometric tolerances but it is too theoretical and yet

Mostly, manufacturing tolerance charts are used these days for manufacturing tolerance transfer but these have the limitation of being one dimensional only. Some research has been undertaken for the three dimensional geometric tolerances but it is too theoretical and yet to be ready for operator level usage. In this research, a new three dimensional model for tolerance transfer in manufacturing process planning is presented that is user friendly in the sense that it is built upon the Coordinate Measuring Machine (CMM) readings that are readily available in any decent manufacturing facility. This model can take care of datum reference change between non orthogonal datums (squeezed datums), non-linearly oriented datums (twisted datums) etc. Graph theoretic approach based upon ACIS, C++ and MFC is laid out to facilitate its implementation for automation of the model. A totally new approach to determining dimensions and tolerances for the manufacturing process plan is also presented. Secondly, a new statistical model for the statistical tolerance analysis based upon joint probability distribution of the trivariate normal distributed variables is presented. 4-D probability Maps have been developed in which the probability value of a point in space is represented by the size of the marker and the associated color. Points inside the part map represent the pass percentage for parts manufactured. The effect of refinement with form and orientation tolerance is highlighted by calculating the change in pass percentage with the pass percentage for size tolerance only. Delaunay triangulation and ray tracing algorithms have been used to automate the process of identifying the points inside and outside the part map. Proof of concept software has been implemented to demonstrate this model and to determine pass percentages for various cases. The model is further extended to assemblies by employing convolution algorithms on two trivariate statistical distributions to arrive at the statistical distribution of the assembly. Map generated by using Minkowski Sum techniques on the individual part maps is superimposed on the probability point cloud resulting from convolution. Delaunay triangulation and ray tracing algorithms are employed to determine the assembleability percentages for the assembly.

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2011

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Assessment of global model simulations of present and future climate

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Climate change has been one of the major issues of global economic and social concerns in the past decade. To quantitatively predict global climate change, the Intergovernmental Panel on Climate Change (IPCC) of the United Nations have organized a multi-national

Climate change has been one of the major issues of global economic and social concerns in the past decade. To quantitatively predict global climate change, the Intergovernmental Panel on Climate Change (IPCC) of the United Nations have organized a multi-national effort to use global atmosphere-ocean models to project anthropogenically induced climate changes in the 21st century. The computer simulations performed with those models and archived by the Coupled Model Intercomparison Project - Phase 5 (CMIP5) form the most comprehensive quantitative basis for the prediction of global environmental changes on decadal-to-centennial time scales. While the CMIP5 archives have been widely used for policy making, the inherent biases in the models have not been systematically examined. The main objective of this study is to validate the CMIP5 simulations of the 20th century climate with observations to quantify the biases and uncertainties in state-of-the-art climate models. Specifically, this work focuses on three major features in the atmosphere: the jet streams over the North Pacific and Atlantic Oceans and the low level jet (LLJ) stream over central North America which affects the weather in the United States, and the near-surface wind field over North America which is relevant to energy applications. The errors in the model simulations of those features are systematically quantified and the uncertainties in future predictions are assessed for stakeholders to use in climate applications. Additional atmospheric model simulations are performed to determine the sources of the errors in climate models. The results reject a popular idea that the errors in the sea surface temperature due to an inaccurate ocean circulation contributes to the errors in major atmospheric jet streams.

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2014

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Understanding plasticity and fracture in aluminum alloys and their composites by 3D X-ray synchrotron tomography and microdiffraction

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Aluminum alloys and their composites are attractive materials for applications requiring high strength-to-weight ratios and reasonable cost. Many of these applications, such as those in the aerospace industry, undergo fatigue loading. An understanding of the microstructural damage that occurs in

Aluminum alloys and their composites are attractive materials for applications requiring high strength-to-weight ratios and reasonable cost. Many of these applications, such as those in the aerospace industry, undergo fatigue loading. An understanding of the microstructural damage that occurs in these materials is critical in assessing their fatigue resistance. Two distinct experimental studies were performed to further the understanding of fatigue damage mechanisms in aluminum alloys and their composites, specifically fracture and plasticity. Fatigue resistance of metal matrix composites (MMCs) depends on many aspects of composite microstructure. Fatigue crack growth behavior is particularly dependent on the reinforcement characteristics and matrix microstructure. The goal of this work was to obtain a fundamental understanding of fatigue crack growth behavior in SiC particle-reinforced 2080 Al alloy composites. In situ X-ray synchrotron tomography was performed on two samples at low (R=0.1) and at high (R=0.6) R-ratios. The resulting reconstructed images were used to obtain three-dimensional (3D) rendering of the particles and fatigue crack. Behaviors of the particles and crack, as well as their interaction, were analyzed and quantified. Four-dimensional (4D) visual representations were constructed to aid in the overall understanding of damage evolution. During fatigue crack growth in ductile materials, a plastic zone is created in the region surrounding the crack tip. Knowledge of the plastic zone is important for the understanding of fatigue crack formation as well as subsequent growth behavior. The goal of this work was to quantify the 3D size and shape of the plastic zone in 7075 Al alloys. X-ray synchrotron tomography and Laue microdiffraction were used to non-destructively characterize the volume surrounding a fatigue crack tip. The precise 3D crack profile was segmented from the reconstructed tomography data. Depth-resolved Laue patterns were obtained using differential-aperture X-ray structural microscopy (DAXM), from which peak-broadening characteristics were quantified. Plasticity, as determined by the broadening of diffracted peaks, was mapped in 3D. Two-dimensional (2D) maps of plasticity were directly compared to the corresponding tomography slices. A 3D representation of the plastic zone surrounding the fatigue crack was generated by superimposing the mapped plasticity on the 3D crack profile.

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2014

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Novel strategies for producing proteins with non-proteinogenic amino acids

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The biological and chemical diversity of protein structure and function can be greatly expanded by position-specific incorporation of non-natural amino acids bearing a variety of functional groups. Non-cognate amino acids can be incorporated into proteins at specific sites by using

The biological and chemical diversity of protein structure and function can be greatly expanded by position-specific incorporation of non-natural amino acids bearing a variety of functional groups. Non-cognate amino acids can be incorporated into proteins at specific sites by using orthogonal aminoacyl-tRNA synthetase/tRNA pairs in conjunction with nonsense, rare, or 4-bp codons. There has been considerable progress in developing new types of amino acids, in identifying novel methods of tRNA aminoacylation, and in expanding the genetic code to direct their position. Chemical aminoacylation of tRNAs is accomplished by acylation and ligation of a dinucleotide (pdCpA) to the 3'-terminus of truncated tRNA. This strategy allows the incorporation of a wide range of natural and unnatural amino acids into pre-determined sites, thereby facilitating the study of structure-function relationships in proteins and allowing the investigation of their biological, biochemical and biophysical properties. Described in Chapter 1 is the current methodology for synthesizing aminoacylated suppressor tRNAs. Aminoacylated suppressor tRNACUAs are typically prepared by linking pre-aminoacylated dinucleotides (aminoacyl-pdCpAs) to 74 nucleotide (nt) truncated tRNAs (tRNA-COH) via a T4 RNA ligase mediated reaction. Alternatively, there is another route outlined in Chapter 1 that utilizes a different pre-aminoacylated dinucleotide, AppA. This dinucleotide has been shown to be a suitable substrate for T4 RNA ligase mediated coupling with abbreviated tRNA-COHs for production of 76 nt aminoacyl-tRNACUAs. The synthesized suppressor tRNAs have been shown to participate in protein synthesis in vitro, in an S30 (E. coli) coupled transcription-translation system in which there is a UAG codon in the mRNA at the position corresponding to Val10. Chapter 2 describes the synthesis of two non-proteinogenic amino acids, L-thiothreonine and L-allo-thiothreonine, and their incorporation into predetermined positions of a catalytically competent dihydrofolate reductase (DHFR) analogue lacking cysteine. Here, the elaborated proteins were site-specifically derivitized with a fluorophore at the thiothreonine residue. The synthesis and incorporation of phosphorotyrosine derivatives into DHFR is illustrated in Chapter 3. Three different phosphorylated tyrosine derivatives were prepared: bis-nitrobenzylphosphoro-L-tyrosine, nitrobenzylphosphoro-L-tyrosine, and phosphoro-L-tyrosine. Their ability to participate in a protein synthesis system was also evaluated.

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2013

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Feasibility of a negative pressure system to remove smoke from an aircraft flight deck

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Smoke entering a flight deck cabin has been an issue for commercial aircraft for many years. The issue for a flight crew is how to mitigate the smoke so that they can safely fly the aircraft. For this thesis, the

Smoke entering a flight deck cabin has been an issue for commercial aircraft for many years. The issue for a flight crew is how to mitigate the smoke so that they can safely fly the aircraft. For this thesis, the feasibility of having a Negative Pressure System that utilizes the cabin altitude pressure and outside altitude pressure to remove smoke from a flight deck was studied. Existing procedures for flight crews call for a descent down to a safe level for depressurizing the aircraft before taking further action. This process takes crucial time that is critical to the flight crew's ability to keep aware of the situation. This process involves a flight crews coordination and fast thinking to manually take control of the aircraft; which has become increasing more difficult due to the advancements in aircraft automation. Unfortunately this is the only accepted procedure that is used by a flight crew. Other products merely displace the smoke. This displacement is after the time it takes for the flight crew to set up the smoke displacement unit with no guarantee that a flight crew will be able to see or use all of the aircraft's controls. The Negative Pressure System will work automatically and not only use similar components already found on the aircraft, but work in conjunction with the smoke detection system and pressurization system so smoke removal can begin without having to descend down to a lower altitude. In order for this system to work correctly many factors must be taken into consideration. The size of a flight deck varies from aircraft to aircraft, therefore the ability for the system to efficiently remove smoke from an aircraft is taken into consideration. For the system to be feasible on an aircraft the cost and weight must be taken into consideration as the added fuel consumption due to weight of the system may be the limiting factor for installing such a system on commercial aircraft.

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2013

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FE simulation based friction coefficient factors for metal forming

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The friction condition is an important factor in controlling the compressing process in metalforming. The friction calibration maps (FCM) are widely used in estimating friction factors between the workpiece and die. However, in standard FEA, the friction condition is defined

The friction condition is an important factor in controlling the compressing process in metalforming. The friction calibration maps (FCM) are widely used in estimating friction factors between the workpiece and die. However, in standard FEA, the friction condition is defined by friction coefficient factor (µ), while the FCM is used to a constant shear friction factors (m) to describe the friction condition. The purpose of this research is to find a method to convert the m factor to u factor, so that FEA can be used to simulate ring tests with µ. The research is carried out with FEA and Design of Experiment (DOE). FEA is used to simulate the ring compression test. A 2D quarter model is adopted as geometry model. A bilinear material model is used in nonlinear FEA. After the model is established, validation tests are conducted via the influence of Poisson's ratio on the ring compression test. It is shown that the established FEA model is valid especially if the Poisson's ratio is close to 0.5 in the setting of FEA. Material folding phenomena is present in this model, and µ factors are applied at all surfaces of the ring respectively. It is also found that the reduction ratio of the ring and the slopes of the FCM can be used to describe the deformation of the ring specimen. With the baseline FEA model, some formulas between the deformation parameters, material mechanical properties and µ factors are generated through the statistical analysis to the simulating results of the ring compression test. A method to substitute the m factor with µ factors for particular material by selecting and applying the µ factor in time sequence is found based on these formulas. By converting the m factor into µ factor, the cold forging can be simulated.

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2013

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Studies on the three-dimensional structures of proteins using X-ray crystallography

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X-ray diffraction is the technique of choice to determine the three-dimensional structures of proteins. In this study it has been applied to solve the structure of the survival motor neuron (SMN) proteins, the Fenna-Mathews-Olson (FMO) from Pelodictyon phaeum (Pld. phaeum)

X-ray diffraction is the technique of choice to determine the three-dimensional structures of proteins. In this study it has been applied to solve the structure of the survival motor neuron (SMN) proteins, the Fenna-Mathews-Olson (FMO) from Pelodictyon phaeum (Pld. phaeum) protein, and the synthetic ATP binding protein DX. Spinal muscular atrophy (SMA) is an autosomal recessive genetic disease resulting in muscle atrophy and paralysis via degeneration of motor neurons in the spinal cord. In this work, we used X-ray diffraction technique to solve the structures of the three variant of the of SMN protein, namely SMN 1-4, SMN-WT, and SMN-Δ7. The SMN 1-4, SMN-WT, and SMN-Δ7 crystals were diffracted to 2.7 Å, 5.5 Å and 3.0 Å, respectively. The three-dimensional structures of the three SMN proteins have been solved. The FMO protein from Pld. phaeum is a water soluble protein that is embedded in the cytoplasmic membrane and serves as an energy transfer funnel between the chlorosome and the reaction center. The FMO crystal diffracted to 1.99Å resolution and the three-dimensional structure has been solved. In previous studies, double mutant, DX, protein was purified and crystallized in the presence of ATP (Simmons et al., 2010; Smith et al. 2007). DX is a synthetic ATP binding protein which resulting from a random selection of DNA library. In this study, DX protein was purified and crystallized without the presence of ATP to investigate the conformational change in DX structure. The crystals of DX were diffracted to 2.5 Å and the three-dimensional structure of DX has been solved.

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2013