Engineering Commons^™

Genome3d: A Viewer-Model Framework For Integrating And Visualizing Multi-Scale Epigenomic Information Within A Three-Dimensional Genome, Thomas M. Asbury, Matt Mitman, Jijun Tang, W. Jim Zheng

Faculty Publications

Background
New technologies are enabling the measurement of many types of genomic and epigenomic information at scales ranging from the atomic to nuclear. Much of this new data is increasingly structural in nature, and is often difficult to coordinate with other data sets. There is a legitimate need for integrating and visualizing these disparate data sets to reveal structural relationships not apparent when looking at these data in isolation.

Results
We have applied object-oriented technology to develop a downloadable visualization tool, Genome3D, for integrating and displaying epigenomic data within a prescribed three-dimensional physical model of the human genome. In order …

Experimental Measurements During Combustion Of Moist Individual Foliage Samples, Brent M. Pickett, Carl Isackson, Rebecca Wunder, Thomas H. Fletcher, Bret Buitler, David R. Weise

Faculty Publications

Individual samples of high moisture fuels from the western and southern United States and humidified aspen excelsior were burned over a flat-flame burner at 987◦ ±12 C and 10±0.5 mol% O2. Time-dependent mass and temperature profiles of these samples were obtained and analysed. It was observed that significant amounts of moisture remained in the individual samples after ignition occurred. Temperature histories showed a plateau at 200◦–300 C at the leaf perimeter rather than at 100 C, with a plateau of 140 C for the leaf interior. Implications are that classical combustion models should be altered to reflect the behaviour of …

A Sub-Grid, Mixture–Fraction-Based Thermodynamic Equilibrium Model For Gas Phase Combustion In Firetec: Development And Results, Michael M. Clark, Thomas H. Fletcher, Rodman R. Linn

Faculty Publications

The chemical processes of gas phase combustion in wildland fires are complex and occur at length-scales that are not resolved in computational fluid dynamics (CFD) models of landscape-scale wildland fire. A new approach for modelling fire chemistry in HIGRAD/FIRETEC (a landscape-scale CFD wildfire model) applies a mixture–fraction model relying on thermodynamic chemical equilibrium to predict combustion flame temperatures and product species compositions. The mixture–fraction approach is common in combustor modelling applications. However, since individual flame sheets are not resolved in HIGRAD/FIRETEC, application of the mixture–fraction approach requires the development of a sub-grid model, which is based on the two assumptions …

Characterization Of Electrowetting Processes Through Force Measurements, Nathan B. Crane, Pradeep Mishra, Alex A. Volinsky

Faculty Publications

A new method of characterizing electrowetting is presented in which the forces applied to a modified nanoindenter tip by a test water droplet are measured. A droplet is trapped between the flat nanoindenter tip and the test substrate containing the necessary electrodes. When voltage is applied to the electrodes in the substrate, lateral and normal forces are exerted on the tip and measured by the nanoindenter transducer. Proper selection of the tip geometry permits direct prediction of the resulting in-plane lateral forces using analytical formulas derived from the Young-Lippmann equation. Experimental results show good agreement with both analytical and numerical …

Investigation Of Nitrogen Release During Coal Pyrolysis In An Oxy-Fuel Combustion Process, John M. Sowa, Kolbein K. Kolste, Thomas H. Fletcher

Faculty Publications

Three coals were studied in a flat flame burner (FFB) to determine nitrogen release during pyrolysis as a function of the temperature from 1600 to 1900 K in an oxy-fuel environment. The oxy-fuel environment was created by replacing the background N2 with CO2 in the FFB experiments. Both types of experiments were conducted under fuel-rich conditions, with no O2 present in the postflame gases. The oxy-fuel results were compared to previous results from FFB experiments in a N2 atmosphere. A bituminous coal showed no difference in mass and nitrogen release between the two environments. The sub-bituminous coal exhibited higher mass …

Improved Method For The Determination Of Kinetic Parameters From Non-Isothermal Thermogravimetric Analysis (Tga) Data, Thomas H. Fletcher, James L. Hillier, Trent Bezzant

Faculty Publications

Thermogravimetric analysis (TGA) at a constant heating rate is a popular technique for characterizing reaction behavior. Determination of kinetic coefficients from suchTGAdata has given rise to a large range of reported activation energies for similar samples. In general, rate coefficients are determined using either a linearized integral method or a derivative method. A new method incorporating several well-known techniques is presented that avoids the problems with the linearized techniques as they are generally used. This paper compares results from the new method with results using either the integral or derivative method. Mathematically generated data were used with known kinetic parameters …

Incentive Mechanisms In P2p Media Streaming Systems, Xiao Su, Suchreet Dhaliwal

Faculty Publications

This paper highlights the need to curb free-riding in P2P media streaming systems and discusses the mechanisms by which this could be accomplished. Free riding, whereby a peer utilizes network resources, but does not contribute services could have a huge impact on the efficacy of blue streaming systems, leading to scalability issues and service degradation. We discuss why BitTorrent-like tit-for-tat mechanisms cannot be simply tailored and used in streaming. Even though the problem of free riding is more severe in P2P media streaming than in file sharing, the deployed systems still lack incentive schemes. In this paper, we categorize, analyze, …

The Surface Characteristics And Reactivity Of Residual Carbon In Coal Gasification Slag, Xianglong Zhao, Cai Zeng, Yanyan Mao, Wenhua Li, Yun Peng, Tao Wang, Boris Eiteneer, Vladimir Zamansky, Thomas H. Fletcher

Faculty Publications

In a slagging entrained-flow coal gasifier, a large portion of the inorganic matter will form liquid slag that may have strong physical and chemical interactions with char. Understanding the char-slag interaction is important for improving the modeling and design of gasifiers. This paper reports the characteristics of residual carbon in both coarse and fine slag from a typical entrained-flow coal water slurry gasifier. The surface characteristics of slag and residual carbon in slag were evaluated by scanning electron microscopy and energy dispersive X-ray spectroscopy. The reactivity of the residual carbon in slag was compared through thermal gravimetric analysis. It was …

Thermal Analog To Afm Force-Displacement Measurements For Nanoscale Interfacial Contact Resistance, Brian D. Iverson, John E. Blendell, Suresh V. Garimella

Faculty Publications

Thermal diffusion measurements on PMMA-coated Si substrates using heated AFM tips were performed to determine the contact resistance between an organic thin film and Si. The measurement methodology presented demonstrates how the thermal contrast signal obtained during a force-displacement ramp is used to quantify the resistance to heat transfer through an internal interface. The results also delineate the interrogation thickness beyond which thermal diffusion in the organic thin film is not affected appreciably by the underlying substrate.

Wireless Sensor Network Radio Power Management And Simulation Models, Michael I. Brownfield, Theresa Nelson, Scott Midkiff, Nathaniel J. Davis Iv

Faculty Publications

Wireless sensor networks (WSNs) create a new frontier in collecting and processing data from remote locations. The IEEE 802.15.4 wireless personal area network-low rate (WPAN-LR) WSNs rely on hardware simplicity to make sensor field deployments both affordable and long-lasting without maintenance support. WSN designers strive to extend network lifetimes while meeting application-specific throughput and latency requirements. Effective power management places sensor nodes (or motes) into one of the available energy-saving modes based upon the sleep period duration and the current state of the radio. The newest generation of WPAN-LR-based sensor platform radios operates at a 250 kbps data rate and …

Thermal And Mechanical Multistate Folding Of Rnase H, Thomas A. Knotts, Terry J. Schmitt, Jonathan E. Clark

Faculty Publications

Two different classes of experimental techniques exist by which protein folding mechanisms are ascertained. The first class, of which circular dichroism is an example, probes thermally-induced folding. The second class, which includes atomic force microscopy and optical tweezers, measures mechanically-induced folding. In this article, we investigate if proteins fold/unfold via the same mechanisms both thermally and mechanically. We do so using Ribonuclease H, a protein that has been shown to fold through a three-state mechanism using both types of experimental techniques. A detailed, molecular-level description of the states involved in thermal and mechanical folding shows that mechanisms for both types …

Enhance Diamond Coating Adhesion By Oriented Interlayer Microcracking, Habio Guo, Xingcheng Xiao, Yue Qi, Zhi-Hui Xu, Xiaodong Li

Faculty Publications

In this paper, we report a microcrack toughening mechanism for enhancing the adhesion of diamondcoating. The oriented microcracks were formed within the TiC interlayer to dissipate strain energy and accommodate deformation via the crack opening-closing mechanism, thus enhancing the coating/substrate interfacial toughness. The delamination of diamondcoating was effectively prevented when the parallel microcracks were confined within the interlayer and arrested at interfaces of coating/interlayer/substrate. Density functional theory calculations revealed that the highly anisotropicfracture strength of the TiC phase energetically favors crack initiation and propagation along (100) planes only, which are 54.7° away from the interface. These microcracks are constrained inside …

Using Artificial Neural Networks And Model Predictive Control To Optimize Acoustically Assisted Doxorubicin Release From Polymeric Micelles, Ghaleb A. Husseini, Farouq S. Mjalli, William G. Pitt, Nabil M. Abdel-Jabbar

Faculty Publications

We have been developing a drug delivery system that uses Pluronic P105 micelles to sequester a chemotherapeutic drug - namely, Doxorubicin (Dox) - until it reaches the cancer site. Ultrasound is then applied to release the drug directly to the tumor and in the process minimize the adverse side effects of chemotherapy on non-tumor tissues. Here, we present an artificial neural network (ANN) model that attempts to model the dynamic release of Dox from P105 micelles under different ultrasonic power intensities at two frequencies. The developed ANN model is then utilized to optimize the ultrasound application to achieve a target …

Compact Trench-Based Silicon-On-Insulator Rib Waveguide Ring Resonator With Large Free Spectral Range, Seunghyun Kim, Gregory P. Nordin, Weisheng Hu, Yusheng Qian, Jiguo Song, Gregory L. Wojcik

Faculty Publications

We demonstrate a compact trench-based silicon-on-insulator (SOI) rib waveguide ring resonator comprised of trench-based bends and splitters. It has a perimeter of 50 μm and occupies an area of only 25×25 μm. The measured free spectral range (FSR) is 13.2 nm, which the largest reported for an SOI rib waveguide ring resonator. The measured FSR, full width at half maximum, and quality factor match reasonably well with analytical calculations. Further calculation shows that a FSR of 50.8 nm is achievable for an SOI rib waveguide ring resonator with a perimeter of 15 μm.

Energy Efficiency Of Hydrogen Sulfide Decomposition In A Pulsed Corona Discharge Reactor, Morris D. Argyle, Sanil John, Jerry C. Hamann, Suresh S. Muknahallipatna, Stanislaw Legowski, John F. Ackerman

Faculty Publications

A novel pulsed corona wire-in-tube reactor with quartz view-ports allowed visual observation of the effect of charge voltage and gas composition on the corona distribution. The H2S conversion and energy efficiency of H2S decomposition in this pulsed corona discharge reactor varied at constant power due to the selected values of the electrical parameters of pulse forming capacitance, charge voltage, and pulse frequency. Low pulse forming capacitance, low charge voltage, and high pulse frequency operation produce the highest energy efficiency of H2S conversion at constant power. H2S conversion is more efficient in Ar-N2 gas mixtures than in Ar or N2. these …

Structured P2p Technologies For Distributed Command And Control, Daniel R. Karrels, Gilbert L. Peterson, Barry E. Mullins

Faculty Publications

The utility of Peer-to-Peer (P2P) systems extends far beyond traditional file sharing. This paper provides an overview of how P2P systems are capable of providing robust command and control for Distributed Multi-Agent Systems (DMASs). Specifically, this article presents the evolution of P2P architectures to date by discussing supporting technologies and applicability of each generation of P2P systems. It provides a detailed survey of fundamental design approaches found in modern large-scale P2P systems highlighting design considerations for building and deploying scalable P2P applications. The survey includes unstructured P2P systems, content retrieval systems, communications structured P2P systems, flat structured P2P systems and …

Improved Implementation Of Kirkwood-Buff Solution Theory In Periodic Molecular Simulations, Joseph W. Nichols, Stan G. Moore, Dean R. Wheeler

Faculty Publications

Kirkwood-Buff (KB) solution theory is a means to obtain certain thermodynamic derivatives from knowledge of molecular distributions. In actual practice the required integrals over radial distribution functions suffer inaccuracies due to finite-distance truncation effects and their use in closed systems. In this work we discuss how best to minimize these inaccuracies under traditional KB theory. In addition we implement a method for calculating KB quantities in molecular simulations with periodic boundary conditions and particularly within the canonical ensemble. The method is based on a finite-Fourier-series expansion of molecular concentration fluctuations and leads to more reliable results for a given computational …

In-Plane All-Photonic Transduction With Differential Splitter Using Double-Step Rib Waveguide For Photonic Microcantilever Arrays, Ryan Anderson, Seunghyun Kim, Gregory P. Nordin, Jong Wook Noh, Weisheng Hu

Faculty Publications

We report a differential splitter consisting of an asymmetric double-step multimode rib waveguide and a Y-branch splitter for in-plane photonic transduction of photonic microcantilever deflection. Arrays of photonic microcantilevers are integrated with differential splitters and an optical waveguide network to demonstrate uniformity and sensitivity of transduction. Measurement results from multiple arrays indicate a sensitivity of 0.32 x 10-3 nm-1 and minimum detectable deflection of 141 pm for a 3.5 Hz measurement bandwidth.

Sharing Landmark Information Using Mixture Of Gaussian Terrain Spatiograms, Damian M. Lyons

Faculty Publications

In this paper we evaluate the use of a novel spatial histogram called the terrain spatiogram as a common representation for exchanging landmark information between robots working as a team to map an area. Individual robots use range sensors to provide the spatial dimension of the spatiogram and video for the image dimension. We have previously shown that terrain spatiograms can be shared between robots in a heterogeneous team to recognize landmarks and to fuse observations from multiple sensors or multiple platforms. A terrain spatiogram using a mixture of Gaussians (MOG) model is introduced and a corresponding normalized spatiogram similarity …

Combining Multiple Scoring Systems For Target Tracking Using Rank-Score Characteristics, Damian M. Lyons, D. Frank Hsu

Faculty Publications

Video target tracking is the process of estimating the current state, and predicting the future state of a target from a sequence of video sensor measurements. Multitarget video tracking is complicated by the fact that targets can occlude one another, affecting video feature measurements in a highly non-linear and difficult to model fashion. In this paper, we apply a multisensory fusion approach to the problem of multitarget video tracking with occlusion. The approach is based on a data-driven method (CFA) to selecting the features and fusion operations that improve a performance criterion. Each sensory cue is treated as a scoring …

Application Of Systems Engineering To Rapid Prototyping For Close Air Support, John M. Colombi, Richard G. Cobb

Faculty Publications

Twenty-first century military operations have brought forth many new challenges for the Armed Forces of the United States. One such challenge is with new operating environments, where current systems are not always effective. While it is desirable to apply a systems engineering approach to best meet critical user needs, there may be a misconception that systems engineering requires a lengthy and detailed process not nimble enough for a rapid prototyping effort. This article describes how a classic systems engineering methodology was successfully tailored to the rapid development of potential material solutions to meet a critical operational need. Key observations are …

Phage-Induced Alignment Of Membrane Proteins Enables The Measurement And Structural Analysis Of Residual Dipolar Couplings With Dipolar Waves And Lambda-Maps, Sang Ho Park, Woo Sung Son, Rishi Mukhopadhyay, Homayoun Valafar, Stanley J. Opella

Faculty Publications

At pH > 6 added filamentous bacteriophage fd is compatible with many of the detergents used to solubilize membrane proteins for solution NMR studies of membrane proteins and, therefore, serves as an alignment media. In combination with strained polyacrylamide gel alignment, Dipolar Waves can be used to directly assess the secondary structure and a λ-map extracts the order tensors for de novo structure calculation of membrane proteins without distance restraints.

New Low-Complexity Equalizers For Offset Qpsk, Qiang Lei, Michael D. Rice

Faculty Publications

Reduced-complexity linear and decision-feedback equalizers for use with offset QPSK are described and analyzed. The analysis and simulations show that reduced-complexity equalizers have 1/4 the complexity and achieve this at a loss that depends on the channel. As an example, the loss for the “Proakis B” channel is 2.7 dB for the linear equalizer and 0.8 dB for the decision feedback equalizer.

3510-V 390-M Omega . Cm(2) 4h-Sic Lateral Jfet On A Semi-Insulating Substrate, Chih-Fang Huang, Cheng-Li Kan, Tian-Li Wu, Meng-Chia Lee, Yo-Zthu Liu, Kung-Yen Lee, Feng Zhao

Faculty Publications

The performance of high-voltage 4H-SiC lateral JFETs on a semi-insulating substrate is reported in this letter. The design of the voltage-supporting layers is based on the charge compensation of p- and n-type epilayers. The best measured breakdown voltage is 3510 V, which, to the authors' knowledge, is the highest value ever reported for SiC lateral switching devices. The R-on of this device is 390 m Omega . cm(2), in which 61% is due to the drift-region resistance. The BV2/R-on is 32 MW/cm(2), which is typical among other reported SiC lateral devices.

Performance Flight Testing Of Small Electric Powered Unmanned Aerial Vehicles, Jon N. Ostler, W. Jerry Bowman, Deryl O. Snyder, Timothy W. Mclain

Faculty Publications

Flight testing methods are developed to find the drag polar for small unmanned aerial vehicles powered by electric motors with fixed-pitch propellers. Wind tunnel testing was used to characterize the propeller-motor efficiency. The drag polar was constructed using data from flight tests. This drag polar was then used to find the following performance parameters: maximum velocity, minimum velocity, velocity for maximum range, velocity for maximum endurance, maximum rate of climb, maximum climb angle, minimum turn radius, maximum turn rate, and maximum bank angle. The developed flight testing methods are used to characterize the performance of a small UAV.

Abstracting Gis Layers From Hyperspectral Imagery, Torsten E. Howard, Michael J. Mendenhall, Gilbert L. Peterson

Faculty Publications

The spectral-spatial relationship of materials in a hyperspectral image cube is exploited to partially automate the creation of Geographic Information System (GIS) layers. The topological neighborhood preservation property of the Self Organizing Map (SOM) is clustered into six (partially overlapping) neighborhoods that are mapped into the image domain to locate in-scene structures of similar material type. GIS layers are abstracted through spatial logical and morphological operations on the six image domain material maps and a novel road finding algorithm connects road segments under significant tree-occlusion resulting in a contiguous road network. It is assumed that specific knowledge of the scene …

X-Ray Photoemission Analysis Of Chemically Treated Gate Semiconductor Surfaces For Radiation Detector Applications, A. J. Nelson, A. M. Conway, B. W. Sturm, E. M. Behymer, C. E. Reinhardt, R. J. Nikolic, S. A. Payne, G. Pabst, K. C. Mandal

Faculty Publications

No abstract provided.

Lamina Emergent Torsion (Let) Joint, Joseph O. Jacobsen, Guimin Chen, Larry L. Howell, Spencer P. Magleby

Faculty Publications

Part of the challenge in designing compliant mechanisms is finding suitable joints that provide the needed motion and force-deflection characteristics. The Lamina Emergent Torsional (LET) Joint is presented as a compliant joint suited for applications where large angular rotation is desired, but high off-axis stiffness is not as critical. The joint is introduced and the equations necessary for determining the force-deflection characteristics are presented. Since the LET Joint can be fabricated from a single planar layer, it is well suited for macro and micro applications. Illustrative examples are provided with devices fabricated from materials as diverse as steel, polypropylene, and …

Developing And Assessing A Case Study For Teaching Engineering Entrepreneurship At San Jose State University, Anuradha Basu, Minnie Patel

Faculty Publications

In this paper the authors share their experience of developing a case study for teaching engineering entrepreneurship and subsequently developing assessment and instructional material for the case. We also present the lessons learned from that experience. The authors developed the case study in question on the basis of a survey of engineering students’ perceptions of entrepreneurship6. Our survey showed that many students were interested in entrepreneurship, but were hesitant about starting their own business. We proposed two complementary approaches to learning, namely, case studies and active learning, to enhance the engineering students’ understanding of the entrepreneurial process and dispel some …

A Miniature Implanted Inverted-F Antenna For Gps Application, Mohammed Z. Azad, Mohammod Ali

Faculty Publications

A miniature implanted Hilbert inverted-F antenna design at the 1.575 GHz; global positioning system (GPS) frequency is proposed, which can be used to track the location of its user, e.g., the elderly with declining mental capacity (alzheimer's disease). A detailed parametric study of the antenna design is performed by considering it to be implanted within a human muscle model. The effects of the substrate, superstrate, and the nearby muscle tissue on antenna performance are carefully investigated. A laboratory prototype of the antenna was built and tested within a muscle equivalent fluid indicating good VSWR performance. Finally the said antenna when …