Digital Commons Network^™

Non-Boltzamann Sampling For The Accurate Calculation Of Peptide-Surface Adsorption Free Energy, Feng Wang

All Dissertations

%Abstract
The objectives of this project are 1) the setup and refinement of peptide-SAM surface model systems with explicit water using CHARMM and 2) the development of up-to-date simulation protocols for the accurate calculation of adsorption free energy by incorporating the recent development of non-Boltzmann sampling methods in molecular dynamics and applying it for the calculation of adsorption free energy of short peptides onto well-characterized self-assembled monolayers, which is important for understanding protein/surface interactions.
A software package called the Simulation Template Engine for Peptides at Surfaces (STEPS) was developed for the fulfillment of the first objective. It facilitates the automatic …

Control Techniques For Robot Manipulator Systems With Modeling Uncertainties, David Braganza

All Dissertations

This dissertation describes the design and implementation of various nonlinear control strategies for robot manipulators whose dynamic or kinematic models are uncertain. Chapter 2 describes the development of an adaptive task-space tracking controller for robot manipulators with uncertainty in the kinematic and dynamic models. The controller is developed based on the unit quaternion representation so that singularities associated with the otherwise commonly used three parameter representations are avoided. Experimental results for a planar application of the Barrett whole arm manipulator (WAM) are provided to illustrate the performance of the developed adaptive controller.
The controller developed in Chapter 2 requires the …

Biodiesel Forming Reactions Using Heterogneous Catalysis, Yijun Liu

All Dissertations

Biodiesel synthesis from biomass provides a means for utilizing effectively renewable resources, a way to convert waste vegetable oils and animal fats to a useful product, a way to recycle carbon dioxide for a combustion fuel, and production of a fuel that is biodegradable, non-toxic, and has a lower emission profile than petroleum-diesel. Free fatty acid (FFA) esterification and triglyceride (TG) transesterification with low molecular weight alcohols constitute the synthetic routes to prepare biodiesel from lipid feedstocks. This project was aimed at developing a better understanding of important fundamental issues involved in heterogeneous catalyzed biodiesel forming reactions using mainly model …

Nonlinear Vibration And Frequency Response Analysis Of Nanomechanical Cantilever Beams, Seyed Nima Mahmoodi

All Dissertations

Microcantilevers are one the most commonly utilized microelectromechanical systems in a variant of the ultra-precise scanning and characterization application. Of particular interest, the problem of vibrations of microcantilevers has recently received considerable attention due to its application in several nanotechnological instruments such as atomic force microscopy, nanomechanical cantilever sensors and friction force microscopy. For applications such as these, the problem of coupled flexural-torsional nonlinear vibrations of a piezoelectrically-actuated microcantilever beam is considered in this dissertation. The actuation and sensing are both facilitated through bonding a piezoelectric layer (here, ZnO) on the microcantilever surface. The beam is considered to have simultaneous …

In Situ Photopolymerized Hydrogels For Enhancing Protein Delivery, Chien-Chi Lin

All Dissertations

In recent years, there has been immense interest in the utilization of photopolymerized hydrogels as carriers for controlled protein delivery and cell scaffolds for tissue engineering applications. Although poly(ethylene glycol) (PEG)-based hydrogels formed from mild photopolymerization methods have been suggested as biocompatible matrices that allow for safely encapsulating biomolecules including proteins, peptides, DNA, and cells, the adverse effects of photopolymerization reactions on the encapsulated proteins have largely been overlooked. In addition, conventional hydrophilic hydrogels fail to effectively control protein delivery rates due to their high permeability. These two problems are critical since the delivery of protein therapeutics from hydrogel matrices …

Differentiation Modulation Of Adult Stem Cells In An Adipose System, Aditya Chaubey

All Dissertations

The need for soft tissue reconstruction or augmentation has increased continuously over the years. This need is compounded by patients suffering from post-traumatic repair and congenital soft-tissue deformities. All the current options available to treat the soft tissue deformities have inherent difficulties associated with them. Hence, more research is needed to come up with a better solution to this problem which is only going to increase in magnitude. Tissue engineering is a relatively new technique which has the potential to deliver a cell-based device which can overcome the problems associated with traditional therapies. However, before it becomes clinically viable we …

Activation Of Systemic Adhesion Molecules And C Reactive Protein In Response To Biomaterial Particle Induced Cytokine Production, Robin Graham

All Dissertations

Chronic inflammation has been identified as a major contributor to many diseases including, atherosclerosis, osteoporosis, dementia, Alzheimer's disease and type 2 diabetes, to name a few. Many of the same markers of inflammation found in the diseases listed above, including IL-1, IL-6, TNF-α, NF-B and adhesion molecules, have also been found in wear debris induced osteolysis. While the local response to biomaterial wear debris has been characterized quite extensively, very little is known about the systemic effect of biomaterial wear debris on the inflammatory system. The objectives of this study were to evaluate the in vitro and in vivo inflammatory …

Flight Physician - August, 2007, Civil Aviation Medical Association

Browse all Civil Aviation Medical Association Newsletters

A sixteen page newsletter of the Civil Aviation Medical Association. The newsletter provided news about civil aviation medicine and information related to the organization.

Using Reconstructability Analysis For Input Variable Reduction: A Business Example, Stephen Shervais, Martin Zwick

Complex Systems Faculty Publications and Presentations

We demonstrate the use of reconstructability analysis (RA) on the UCI Australian Credit dataset to reduce the number of input variables for two different analysis tools. Using 14 variables, an artificial neural net (NN) is able to predict whether or not credit was granted, with a 79.1% success rate. RA preprocessing allows us to reduce the number of independent variables from 14 to two different sets of three, which have success rates of 77.2% and 76.9% respectively. The difference between these rates and that of the 14-variable NN is not statistically significant. The three-variable rulesets given by RA achieve success …

Anwendung Von Interferenz- Und Ir-Mikroskopie Zur Charakterisierung Und Untersuchung Des Stofftransportes In Nanoporösen Materialien, Lars Heinke, Christian Chmelik, Pavel Kortunov, Sergey Vasenkov, Douglas M. Ruthven, Dhananjai B. Shah, Jörg Kärger

Chemical & Biomedical Engineering Faculty Publications

Die Anwendung der Interferenz-Mikroskopie bedeutet einen entscheidenden Durchbruch in der Untersuchung des Stofftransports von Gastmolekülen in nanoporösen Wirtsmaterialien. Diese Technik ermöglicht die Beobachtung der zeitaufgelösten intrakristallinen Konzentrationsprofile, die durch eine Änderung des umgebenden Gasdruckes entstehen. Dieser Ansatz wurde zur Untersuchung von Adsorptions- und Desorptionsprozessen in verschiedenen Zeolithsystemen verwendet. Die Vorteile dieser Technik, vor allem wenn sie mit Infrarotabsorptionsmessungen kombiniert wird, werden an Hand der experimentellen Resultate des Methanol-in-Ferrierit-Systems illustriert.

Applications Of Diffusion Maps In Gene Expression Data-Based Cancer Diagnosis Analysis, Rui Xu, Donald C. Wunsch, Steven Damelin

Electrical and Computer Engineering Faculty Research & Creative Works

Early detection of a tumor's site of origin is particularly important for cancer diagnosis and treatment. The employment of gene expression profiles for different cancer types or subtypes has already shown significant advantages over traditional cancer classification methods. One of the major problems in cancer type recognition-oriented gene expression data analysis is the overwhelming number of measures of gene expression levels versus the small number of samples, which causes the curse of dimension issue. Here, we use diffusion maps, which interpret the eigenfunctions of Markov matrices as a system of coordinates on the original data set in order to obtain …

Shift Work In The Long-Termcare Industry : An Examination Of Organizational And Individual Factors That Influence Employee Outcomes, Kristin Elizabeth Charles

Dissertations and Theses

The long-term care (LTC) industry provides medical and social services in facility-based settings to the elderly, chronically ill, and disabled. With the aging of the United States population, the need for LTC workers is expected to drastically increase in the next decade. However, the industry faces a significant staffing shortage. One potential cause of staffing problems in LTC is working non-standard work schedules. Because of the need to provide around the clock care, LTC employees often work non-standard shifts, long hours, night work, and over weekends and holidays. Although many studies have examined health and sleep-related outcomes associated with non-standard …

A Time-To-First-Spike Cmos Image Sensor, Xiaochuan Guo, Xin Qi, John G. Harris

Electrical and Computer Engineering Faculty Research & Creative Works

A time-to-first spike (TTFS) imager was designed such that each pixel outputs a single digital pulse whose timing encodes pixel illumination. For still image applications, this time representation provides a tremendous increase in dynamic range, similar to that of other existing time-based imagers. However, a major advantage of the TTFS imager is that this wide dynamic range can be achieved even for 30 frames/s video applications. A prototype 32x32 TTFS image sensor was fabricated in AMI 0.5 μm CMOS technology. The prototype chip demonstrates a 104 dB dynamic range (limited by the optical equipment), 42 μV/electron conversion gain, 1.25 nA/cm …

Nitrogen And Phosphorus Concentrations Of Runoff As Affected By Moldboard Plowing, John E. Gilley, Bahman Eghball, David B. Marx

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The excessive application of manure on cropland areas can cause nutrients to accumulate near the soil surface. This study was conducted to measure the effects of moldboard plowing on the redistribution of nutrients within the soil profile and nutrient transport by overland flow. Composted beef cattle manure was applied at dry weights of 0, 68, 105, 142, and 178 Mg ha^-1 to a silty clay loam soil and then incorporated by disking. Selected plots were moldboard plowed 244 days later to a depth of approximately 23 cm. Soil samples for analysis of water‐soluble phosphorus, Bray and Kurtz No. 1 …

Nutrient Concentrations Of Runoff During The Year Following Manure Application, John E. Gilley, Bahman Eghball, D. B. Marx

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Little information is currently available concerning temporal changes in nutrient transport following the addition of manure to cropland areas. This study was conducted to measure nutrient transport in runoff as affected by tillage and time following the application of beef cattle or swine manure to a site on which corn (Zea mays L.) was grown. Rainfall simulation tests were initiated 4, 32, 62, 123, and 354 days following land application. Three 30 min simulated rainfall events, separated by 24 h intervals, were conducted at an intensity of approximately 70 mm h-1. Dissolved phosphorus (DP), particulate phosphorus (PP), total phosphorus …

Optimal Scheduling Of Generator Maintenance Using Modified Discrete Particle Swarm Optimization, Yusuf Yare, Ganesh K. Venayagamoorthy

Electrical and Computer Engineering Faculty Research & Creative Works

This paper presents a modified discrete particle swarm optimization (PSO) based technique for generating optimal preventive maintenance schedule of generating units for economical and reliable operation of a power system while satisfying system load demand and crew constraints. While GA and other analytical methods might suffer from premature convergence and the curse of dimensionality, heuristics based swarm intelligence can be an efficient alternative. PSO is known to effectively solve large scale multi-objective optimization problems. Here, a modified discrete PSO approach is proposed for the GMS optimization problem in order to overcome the limitations of the conventional methods and come up …

Sheep Updates 2007 - Part 4, Dean Thomas, Dominique Blache, Dean Revell, Hayley Norman, Phil Vercoe, Zoey Durmic, Serina Digby, Di Mayberry, Megan Chadwick, Martin Sillence, David Masters, R. Silberstein, F. Byrne, P. G. H. Nichols, J. Young, L. Aitkins, M. G. Wilmot, A. J. Rintoul, T. Lambert, D. R. Mcclements, P. Raper, P. Ward, C. Walton, T. York, David Pethick, David Hopkins, Malcolm Mcphee, D. B. Savage, J. V. Nolan, I. R. Godwin, A. Aoetpah, T. Nguyen, N. Baillie, C. Lawler, Ken Geenty, John Smith, Darryl Smith, Tim Dyall, Grant Uphill, John Young, Michael Paton, John Dorrian

Sheep Updates

This session covers eight papers from different authors:

GRAZING

1. The impact of high dietary salt and its implications for the management of livestock grazing saline land, Dean Thomas, Dominique Blache, Dean Revell, Hayley Norman, Phil Vercoe, Zoey Durmic, Serina Digby, Di Mayberry, Megan Chadwick, Martin Sillence and David Masters, CRC for Plant-based Management of Dryland Salinity, Faculty of Natural & Agricultural Sciences, The University of Western Australia, WA.

2. Sustainable Grazing on Saline Lands - outcomes from the WA1 research project, H.C. Norman^1,2, D.G. Masters^1,2, R. Silberstein^1,2, F. Byrne^2,3, P.G.H. Nichols …

49th Rocky Mountain Conference On Analytical Chemistry

Rocky Mountain Conference on Magnetic Resonance

Final program, abstracts, and information about the 49th annual meeting of the Rocky Mountain Conference on Analytical Chemistry, co-endorsed by the Colorado Section of the American Chemical Society and the Rocky Mountain Section of the Society for Applied Spectroscopy. Held in Breckenridge, Colorado, July 22-26, 2007.

Space Suit Concepts And Vehicle Interfaces For The Constellation Program, D. M. Klaus, J. Metts, R. Kobrick, M. Mesloh, T. Monk, Et Al.

Publications

In carrying out NASA’s Vision for Space Exploration, a number of different environments will be encountered that will require the crew to wear a protective space suit. Specifically, four suited mission phases are identified as Launch, Entry & Abort profiles, Contingency 0g (orbital) Extravehicular Activity (EVA), Lunar Surface EVA and Martian Surface EVA. This study presents conceptual design solutions based on a previous architecture assessment that defined space suit operational requirements for four proposed space suit configuration options. In addition, a subset of vehicle interface requirements are defined for enabling umbilical and physical connections between the suits and the various …

Ultrasonically-Assisted Drug Delivery In Rats Reduces Tumor Growth, William G. Pitt, Beverly L. Roeder, G. Bruce Schaalje, Bryant J. Staples

Faculty Publications

Previously we have shown that nanosized drug carriers called Plurogels™ sequestered Doxorubicin (Dox) and partially released this drug with application of ultrasound (US) (Fig. 1)1. The application to chemotherapy was successfully demonstrated in a rat tumor model2. However previous studies did not examine the distribution of Dox in the insonated and control tissue. This recent work investigated the effect of two US frequencies and examined the Dox distribution in the insonated and control tumors to determine if US was depositing more Dox at the insonated site.

Development Of Deployable Wings For Small Unmanned Aerial Vehicles Using Compliant Mechanisms, Steven D. Landon

Theses and Dissertations

Unmanned Air Vehicles (UAVs) have recently gained attention due to their increased ability to perform sophisticated missions with less cost and/or risk than their manned counterparts. This thesis develops approaches to the use of compliant mechanisms in the design of deployable wings for small UAVs. Although deployable wings with rigid-link mechanisms have been used in the past to maintain flight endurance while minimizing required storage volume, compliant mechanisms offer many advantages in manufacturability and potential space savings due to function sharing of components. A number of compliant, deployable wing concepts are generated and a classification system for them is formed. …

Detection Of Ultrathin Biological Films Using Vacuum Ultraviolet Spectroscopic Ellipsometry, Dileep K. Goyal, Greg K. Pribil, John A. Woollam, Anuradha Subramanian

Anuradha Subramanian Publications

Spectroscopic ellipsometry (SE) is a non-contact and a non-destructive optical technique used in characterization of thin films. It is widely used to determine optical constants, thickness in multilayer stacks and microstructure (voids, alloy fraction, or mixed phase composition). This paper reports on a systematic investigation of the optical properties of two different kinds of silane compounds: 3-aminopropyltriethoxysilane (APTES) and 3-glycidoxypropyltriethoxy-silane (GPS) as well as for immunoglobulin G (IgG) attached to these modified samples using vacuum ultraviolet spectroscopic ellipsometry (VUV-SE). VUV-SE is a newly developed technique and used to evaluate the strength and energy of the interband electronic excitations/transitions in these …

Physisorption Of Nucleobases On Graphene: Density-Functional Calculations, Gowtham S, Ralph H. Scheicher, Rajeev Ahuja, Ravindra Pandey, Shashi P. Karna

Data Science Publications

We report the results of our first-principles investigation on the interaction of the nucleobases adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U) with graphene, carried out within the density-functional theory framework, with additional calculations utilizing Hartree-Fock plus second-order Møller-Plesset perturbation theory. The calculated binding energy of the nucleobases shows the following hierarchy: G>A≈T≈C>U, with the equilibrium configuration being rather similar for all five of them. Our results clearly demonstrate that the nucleobases exhibit significantly different interaction strengths when physisorbed on graphene. The stabilizing factor in the interaction between the base molecule and graphene sheet is …

Extended Abstract Rotopod: A Novel Approach To Efficient Legged Locomotion, Damian M. Lyons

Faculty Publications

A number of attempts have been made to integrate the efficiency of wheeled locomotion with the terrain versatility of legged locomotion, e.g., Univ.Michigan’s Rhex platform and Case Western’s Whegs. Those platforms cast legs as rotating spokes placed traditionally at the corners of a rectangular platform. In this paper, we present an alternate approach, with three legs radiating down from a central hub. The energy to move the platform is generated by a rotating reaction mass mounted at the hub and, at rest, rotating parallel to the ground plane.

Our approach is to construct a platform whose natural, uncontrolled motion is …

Precipitation And Fouling In Heavy Oil–Diluent Blends, E Hong, A. Paul Watkinson

Heat Exchanger Fouling and Cleaning VII

Heavy oil fractions rich in asphaltenes were mixed with diluents containing from 0.6-25% aromatics, and the resulting blends subjected to batch precipitation experiments at 85°C, and thermal fouling tests at surface temperatures in the range 230-310ºC. Deposit compositions were determined, and are compared with suspended asphaltene composition. When the heavy oils were blended with the most aromatic diluents, precipitation and fouling were negligible. As the aromaticity of the diluents was decreased, the extent of asphaltene precipitation and the fouling rates increased. The solubility parameter of the blends, δmix, and the flocculation solubility parameter for asphaltenes, δf , were determined from …

Formation Of Gum And Deposits In An Oxygenated Naphtha Stream, Yonghua Li, Paul Watkinson, Patricio Herrera, Feridoun Fahiminia, Morgan James

Heat Exchanger Fouling and Cleaning VII

Gums formed when organic fluids are in contact with air can cause fouling of process equipment. The oxidation and formation of gum in a naphtha stream was studied in a stirred batch reactor as a function of temperature (96 to 130ºC) and at a total pressure of 584 kPa. Mixtures of air and nitrogen in the pressurizing gas gave dissolved oxygen contents in the range 10-270 ppm wt. Peroxide and existent (dissolved) gum contents were measured over periods of up to 80 hours. Rates of reaction were low, with maximum concentrations of peroxide typically below 4 meq/L, and gum formation …

Observation Of An Isokinetic Temperature And Compensation Effect For High Temperature Crude Oil Fouling, C. A. Bennett, R. S. Kistler, K. Nangia, W. Al-Ghawas, N. Al-Hajji, A. Al-Jemaz

Heat Exchanger Fouling and Cleaning VII

The initial fouling rates of four crude oils were determined at a nominal bulk temperature of 315 °C, an initial heated wall shear stress of 13 Pa, and initial surface temperatures between 375 and 445 °C. These initial fouling rates ranged from 1.3(10-6) to 7.8(10-5) m2 K/kJ. Corresponding Arrhenius plots were linear with the initial fouling rates passing through an isokinetic temperature of 407.5 °C. A plot of the natural logarithm of the preexponential factors (7.6(104) – 5.2(1015) m2 K/kJ) versus the apparent activation energies (128 – 269 kJ/mol) was also linear, confirming the validity of the isokinetic temperature and …

Milk Protein Fouling In A Tubular Heat Exchanger: Effect Of Milk Temperature And Reynolds Number, D.H.G. Pelegrine, K.F. Oliveira, M.T.M.S. Gomes

Heat Exchanger Fouling and Cleaning VII

In the present work, β-lactoglobulin fouling phenomenon was studied, when milk flowed in a tubular heat exchanger, where hot water was used to raise milk temperature. Experiments have been carried out to determine the effect of Reynolds number and fluid temperature in whey protein fouling, in a tubular heat exchanger and the results showed that fouling increases as the fluid temperature increases. In addition, as the Reynolds number increases, the total amount of fouling (obtained by integrating the whole amount of deposit down the tube dividing by the total area) decreased.

Simulation Of Calcium Phosphate Deposition On Stainless Steel Surfaces: A New Approach Based On Cellular Automata, F. G. Martins, T. Campos, R. Rosmaninho, L. F. Melo

Heat Exchanger Fouling and Cleaning VII

Fouling caused by calcium phosphate upon heating is basically a crystallization/precipitation process, which starts with the formation of stable clusters of ions or molecules in a process called nucleation that occurs either in the bulk liquid or at the surface. The cellular automata are useful tools to model complex systems of the universe. They could be considered as a good alternative to differential equations and have been used to model many physical/biological systems. In this preliminary work, a two dimensional space was considered where the cellular automata lattice was represented as a grid of squares, with each square representing a …

A Real Time Monitoring Model Of The Calcium Carbonate Fouling Induction Period Based On The Conductance Titration, S.R. Yang, S.X. Cao, L.J. Chen, Z.M. Xu, M.L. Yu, W.H. Sun, K.L. Zheng

Heat Exchanger Fouling and Cleaning VII

A new method has been developed to monitor the calcium carbonate fouling induction period (CCFIP) in real time. Based on the conductance titration, this paper investigated the forming process of CCFIP by a staticdynamic combined simulation experiment unit. With the help of titration analysis (that is titrimetry), an accurate definition of CCFIP and the corresponding real time monitoring model were built up. The investigation results show that the proposed model applies not only to measure the CCFIP in real time, but also applies to an investigation of the influence of various factors on the CCFIP.