Engineering Commons^™

Mobility Of A Semiflexible Chain Confined In A Nanochannel, Douglas R. Tree, Yanwei Wang, Kevin D. Dorfman

Faculty Publications

The classic results of de Gennes and Odijk describe the mobility of a semiflexible chain confined in a nanochannel only in the limits of very weak and very strong confinement, respectively. Using Monte Carlo sampling of the Kirkwood diffusivity with full hydrodynamic interactions, we show that the mobility of a semiflexible chain exhibits a broad plateau as a function of extension before transitioning to an Odijk regime, and that the width of the plateau depends on the anisotropy of the monomers. For the particular case of DNA in a high ionic strength buffer, which has highly anisotropic monomers, we predict …

Fiber Optic Monitoring Of Subsea Equipment, David Brower, John Hedengren, Cory Loegering, Alexis Brower, Karl Witherow, Karl Winter

Faculty Publications

Bass Lite deepwater field in the Gulf of Mexico, at water depths of approximately 2,050 m (6,750 feet), commenced operation in February 2008. Natural gas is produced from Bass Lite via a 90-km (56-mile) subsea tieback to the Devils Tower Spar. This project involved several innovations, one of which was the incorporation of a fiber optic sensing system that measures realtime temperature, pressure and strain along the pipeline length. This is a first of its kind innovation that is in actual operation.

Visualizing Evolution In Real-Time Method For Strain Engineering, Luis Reyes, James Winkler, Katy Kao

Faculty Publications

The adaptive landscape for an industrially relevant phenotype is determined by the effects of the genetic determinants on the fitness of the microbial system. Identifying the underlying adaptive landscape for a particular phenotype of interest will greatly enhance our abilities to engineer more robust microbial strains. Visualizing evolution in real-time (VERT) is a recently developed method based on in vitro adaptive evolution that facilitates the identification of fitter mutants throughout the course of evolution. Combined with high-throughput genomic tools, VERT can greatly enhance the mapping of adaptive landscapes of industrially relevant phenotypes in microbial systems, thereby expanding our knowledge on …

Multiple Structure Alignment With Mstali, Paul Shealy, Homayoun Valafar

Faculty Publications

Background

Multiple structure alignments have received increasing attention in recent years as an alternative to multiple sequence alignments. Although multiple structure alignment algorithms can potentially be applied to a number of problems, they have primarily been used for protein core identification. A method that is capable of solving a variety of problems using structure comparison is still absent. Here we introduce a program msTALI for aligning multiple protein structures. Our algorithm uses several informative features to guide its alignments: torsion angles, backbone C^α atom positions, secondary structure, residue type, surface accessibility, and properties of nearby atoms. The algorithm allows …

A Pressure Gauge Based On Gas Density Measurement From Analysis Of The Thermal Noise Of An Atomic Force Microscope Cantilever, Dongjin Seo, Mark R. Paul, Willian A. Ducker

Faculty Publications

We describe a gas-density gauge based on the analysis of the thermally-driven fluctuations of an atomic force microscope (AFM) cantilever. The fluctuations are modeled as a ring-down of a simple harmonic oscillator, which allows fitting of the resonance frequency and damping of the cantilever, which in turn yields the gas density. The pressure is obtained from the density using the known equation of state. In the range 10–220 kPa, the pressure readings from the cantilever gauge deviate by an average of only about 5% from pressure readings on a commercial gauge. The theoretical description we use to determine the pressure …

Relative Navigation And Control Of A Hexacopter, Timothy Mclain, Randal W. Beard, Robert C. Leishman, John Macdonald

Faculty Publications

This paper discusses the progress made on developing a multi-rotor helicopter equipped with a vision-based ability to navigate through an a priori unknown, GPS-denied environment. We highlight the backbone of our system, the relative estimation and control. We depart from the common practice of using a globally referenced map, preferring instead to keep the position and yaw states in the EKF relative to the current map node. This relative navigation approach allows simple application of sensor updates, natural characterization of the transformation between map nodes, and the potential to generate a globally consistent map when desired. The EKF fuses view …

Mesh Adaption For Efficient Multiscale Implementation Of One-Dimensional Turbulence, D. O. Lignell, A. R. Kerstein, G. Sun, E. I. Monson

Faculty Publications

One-Dimensional Turbulence (ODT) is a stochastic model for turbulent flow simulation. In an atmospheric context, it is analogous to single-column modeling (SCM) in that it lives on a 1D spatial domain, but different in that it time advances individual flow realizations rather than ensemble-averaged quantities. The lack of averaging enables a physically sound multiscale treatment, which is useful for resolving sporadic localized phenomena, as seen in stably stratified regimes, and sharp interfaces, as observed where a convective layer encounters a stable overlying zone. In such flows, the relevant scale range is so large that it is beneficial to enhance model …

One-Dimensional-Turbulence Simulation Of Flame Extinction And Reignition In Planar Ethylene Jet Flames, David O. Lignell, Devin Rappleye

Faculty Publications

A series of three simulations of temporally evolving, planar, nonpremixed ethylene jet flames are performed using the one-dimensional-turbulence (ODT) model. The simulations are performed at a fixed Reynolds number, but varying Damköhler numbers, under conditions that result in significant flame extinction and reignition. Results are compared to corresponding direct numerical simulations (DNSs), which exhibit 40, 70, and nearly 100% peak flame extinction among the three cases. The planar, temporal configuration is ideal for comparison and validation of the ODT model, and identical thermodynamic, transport, and kinetic models were used. The ODT model captures the jet evolution and heat …

Chemical Potential Perturbation: Extension Of The Method To Lattice Sum Treatment Of Intermolecular Potentials, Stan G. Moore, Dean R. Wheeler

Faculty Publications

The recently developed chemical potential perturbation (CPP) method [S. G. Moore and D. R. Wheeler, J. Chem. Phys. 134, 114514 (2011) https://doi.org/10.1063/1.3561865.] is extended to the lattice (Ewald) sum treatment of intermolecular potentials. The CPP method predicts chemical potentials for a range of composition points using the local (position-dependent) pressure tensor of an inhomogeneous system. When computing the local pressure tensor, one can use the Irving-Kirkwood (IK) or Harasima (H) contours of distributing the pressure. We compare these two contours and show that for a planar interface, the homogeneous pressure and resulting chemical potential can be approximated with …

State Of Charge And Loss Of Active Material Estimation Of A Lithium Ion Cell Under Low Earth Orbit Condition Using Kalman Filtering Approaches, Saeed Khaleghi Rahimian, Sean Rayman, Ralph E. White

Faculty Publications

The state of charge (SOC) and the loss of active material of the electrodes of a Li ion cell under Low Earth Orbit condition (LEO) have been estimated using Kalman filtering methods, by means of the physics-based single particle (SP) model. Zero mean Gaussian noise was added to the charge-discharge curves obtained by the SP model to generate synthetic data. Afterwards, nonlinear Filtering approaches including Extended Kalman Filtering (EKF) and Unscented Kalman Filtering (UKF) were applied to predict the true SOC and the electrodes’ degradation, by minimizing the measurement residuals between the model prediction and the synthetic data. The results …

Getting It Right The First Time: Predicted Performance Guarantees From The Analysis Of Emergent Behavior In Autonomous And Semi-Autonomous Systems, Ronald C. Arkin, Damian M. Lyons, Shu Jiang, Prem Nirmal, Munzir Zafar

Faculty Publications

A crucially important aspect for mission-critical robotic operations is ensuring as best as possible that an autonomous system be able to complete its task. In a project for the Defense Threat Reduction Agency (DTRA) we are developing methods to provide such guidance, specifically for counter-Weapons of Mass Destruction (C-WMD) missions. In this paper, we describe the scenarios under consideration, the performance measures and metrics being developed, and an outline of the mechanisms for providing performance guarantees.

Navigation Of Uncertain Terrain By Fusion Of Information From Real And Synthetic Imagery, Damian M. Lyons, Prem Nirmal, D. Paul Benjamin

Faculty Publications

We consider the scenario where an autonomous platform that is searching or traversing a building may observe unstable masonry or may need to travel over unstable rubble. A purely behaviour-based system may handle these challenges but produce behaviour that works against long-terms goals such as reaching a victim as quickly as possible. We extend our work on ADAPT, a cognitive robotics architecture that incorporates 3D simulation and image fusion, to allow the robot to predict the behaviour of physical phenomena, such as falling masonry, and take actions consonant with long-term goals.

We experimentally evaluate a cognitive only and reactive only …

Using A Virtual World For Robot Planning, D. Paul Benjamin, John V. Monaco, Yixia Lin, Christopher Funk, Damian M. Lyons

Faculty Publications

We are building a robot cognitive architecture that constructs a real-time virtual copy of itself and its environment, including people, and uses the model to process perceptual information and to plan its movements. This paper describes the structure of this architecture. The software components of this architecture include PhysX for the virtual world, OpenCV and the Point Cloud Library for visual processing, and the Soar cognitive architecture that controls the perceptual processing and task planning. The RS (Robot Schemas) language is implemented in Soar, providing the ability to reason about concurrency and time. This Soar/RS component controls visual processing, deciding …

Aircraft Route Optimization For Heterogeneous Formation Flight, Jia Xu, Andrew Ning, Geoffrey Bower, Ilan Kroo

Faculty Publications

We examine the value of extended formation flight in the context of airline operations. The study is based on a bi-level route optimization framework. The aircraft performance model includes the effects of rolled-up wakes, formation heterogeneity, and formation-induced compressibility effects. We incorporate airline economics to understand the trade-off between speed and drag savings in the context of formation flight. The application of formation flight to a representative South African Airlines (SAA) long-haul route network can reduce fuel burn by over 4.6% or reduce direct operating cost by 2.1%. The savings increase to 6.8% in fuel or 2.4% in cost when …

Low-Loss Meta-Atom For Improved Resonance Response, Derrick Langley, Ronald Coutu Jr., Peter J. Collins

Faculty Publications

Measurements of a meta-atom integrated with a low noise amplifier into the split-ring resonator are presented. A comparison is made between baseline meta-atoms and one integrated with a GaAs low noise amplifier. S-parameter measurements in a RF strip-line show the resonant frequency location. The resonance null is more prominent for the integrated meta-atom. Biasing the low noise amplifier from 0 to 7 VDC showed that the resonant null improved with biasing voltage. As the biasing voltage increases, the transmission null reduced from -11.82 to -23.21 dB for biases from 0 to 7 VDC at resonant frequency.

Sr2Fe1.5Mo0.5O6-Δ – Sm0.2Ce0.8O1.9 Composite Anodes For Intermediate-Temperature Solid Oxide Fuel Cells, Beibei He, Ling Zhao, Shuxiang Song, Tong Liu, Fanglin Chen, Changrong Xia

Faculty Publications

Sr₂Fe_1.5Mo_0.5O_6−δ (SFM) perovskite is carefully investigated as an anode material for solid oxide fuel cells with LaGaO₃-based electrolytes. Its electronic conductivity under anodic atmosphere is measured with four-probe method while its ionic conductivity is determined with oxygen permeation measurement. Samaria doped ceria (SDC) is incorporated into SFM electrode to improve the anodic performance. A strong relation is observed between SDC addition and polarization losses, suggesting that the internal SFM-SDC contacts are active for H₂ oxidation. The best electrode performance is achieved for the composite with 30 wt% SDC addition, resulting …

A Ceramic-Anode Supported Low Temperature Solid Oxide Fuel Cell, Hanping Ding, Junjie Ge, Xingjian Xue

Faculty Publications

We report the fabrication and evaluation of a ceramic-anode supported button cell LSCM-SDC/SDC/PBSC (thickness 400 μm/20 μm/20 μm). The anode/electrolyte assembly LSCM-SDC/SDC was co-fired at low temperature of 1250°C, where a slight amount of CuO was mixed with LSCM. The CuO (20.3 wt%) were impregnated into the porous substrate to enhance current collecting effect. The cell exhibited power density of 596 mWcm−2 and 381 mWcm−2 at 700°C with wet hydrogen and methane as the fuel respectively, where the silver paste was used as current collectors, the highest performance up to date for the cells with metal oxide anodes at this …

Power Spectral Densities Of Baseband Signals In Epc Class-1 Gen-2 Uhf Rfid Systems, Robert H. Morelos-Zaragoza

Faculty Publications

The power spectral densities (PSD) of baseband signals in EPC Class-1 Gen-2 UHF RFID systems are shown. PSD are obtained using Matlab as the Fourier transform (via the FFT algorithm) of the autocorrelation function of random pulse sequences. The PSD of PIE, FM0 and Miller subcarrier for M=2, 4 and 8 are shown for both unipolar (for 100% ASK or OOK modulation) and polar (PSK modulation) waveforms.

Novel On-Demand Droplet Generation For Selective Fluid Sample Extraction, Melinda Simon, Jeffrey Fisher, Melinda Simon, Abraham Lee

Faculty Publications

 A novel microfluidic device enabling selective generation of droplets and encapsulation of targets is presented. Unlike conventional methods, the presented mechanism generates droplets with unique selectivity by utilizing a K-junction design. The K-junction is a modified version of the classic T-junction with an added leg that serves as the exit channel for waste. The dispersed phase fluid enters from one diagonal of the K and exits the other diagonal while the continuous phase travels in the straight leg of the K. The intersection forms an interface that allows the dispersed phase to be controllably injected through actuation of an elastomer …

Sparsening Filter Design For Iterative Soft-Input Soft-Output Detectors, Raquel G. Machado, Andrew G. Klein, Richard K. Martin

Faculty Publications

A large body of research exists around the idea of channel shortening, where a prefilter is designed to reduce the effective channel impulse response to some smaller number of contiguous taps. This idea was originally conceived to reduce the complexity of Viterbi-based maximum-likelihood equalizers. Here, we consider a generalization of channel shortening which we term "channel sparsening". In this case, a prefilter is designed to reduce the effective channel to a small number of nonzero taps which do not need to be contiguous. When used in combination with belief-propagation-based maximum a posteriori (MAP) detectors, an analogous complexity reduction can be …

A New Approach For The Preparation Of Variable Valence Rare Earth Alloys From Nano Rare Earth Oxides At A Low Temperature In Molten Salt, Milin Zhang, Yongde Yan, Wei Han, Xing Li, Zhiyao Hou, Yang Tian, Ke Ye, Lihong Bao, Xiaodong Li, Zhijian Zhang

Faculty Publications

The solubility of RE₂O₃ (RE = Eu, Sm, and Yb) with variable valence in molten salts is extremely low. It is impossible to directly obtain variable valence metals or alloys from RE₂O₃ using electrolysis in molten salts. We describe a new approach for the preparation of variable valence rare earth alloys from nano rare earth oxide. The excellent dispersion of nano–Eu₂O₃ in LiCl–KCl melts was clearly observed using a luminescent feature of Eu³⁺ as a probe. The ratio of solubility of nano-Sm₂O₃/common Sm₂O_{3 …}

A Laplace Pressure Based Microfluidic Trap For Passive Droplet Trapping And Controlled Release, Melinda Simon, Robert Lin, Jeffrey Fisher, Abraham Lee

Faculty Publications

Here, we present a microfluidic droplet trap that takes advantage of the net Laplace pressure force generated when a droplet is differentially constricted. Mathematical simulations were first used to understand the working range of the component; followed by finite element modeling using the CFDsoftware package to further characterize the behavior of the system. Controlled release of the trapped droplets is also demonstrated through both a mechanical method and a chemical method that manipulates the total pressure exerted on the trapped droplet. The unique design of this trapping device also provides the capability for selection of a single dropletfrom a train, …

Temperature Dependence Of Current Conduction In Semi-Insulating 4h-Sic Epitaxial Layer, P. G. Muzykov, Ramesh Madhu Krishna, K. C. Mandal

Faculty Publications

No abstract provided.

Resolution Limit For Dna Barcodes In The Odijk Regime, Yanwei Wang, Wes F. Reinhart, Douglas R. Tree, Kevin D. Dorfman

Faculty Publications

We develop an approximation for the probability of optically resolving two fluorescent labels on the backbone of a DNA molecule confined in a nanochannel in the Odijk regime as a function of the fluorescence wavelength, channel size, and the properties of the DNA (persistence length and effective width). The theoretical predictions agree well with equivalent data produced by Monte Carlo simulations of a touching wormlike bead model of DNA in a high ionic strength buffer. Although the theory is only strictly valid in the limit where the effective width of the nanochannel is small compared with the persistence length of …

An Approach To Stereo-Point Cloud Registration Using Image Homographies, Damian M. Lyons, Stephen D. Fox

Faculty Publications

No abstract provided.

Defining, Teaching, And Assessing Engineering Design Skills, Nikos J. Mourtos

Faculty Publications

The paper discusses a systematic approach for defining, teaching, and assessing engineering design skills. Although the examples presented in the paper are from the field of aerospace engineering, the principles apply to engineering design in general. What makes the teaching of engineering design particularly challenging is that the necessary skills and attributes are both technical and non-technical and come from the cognitive as well as the affective domains. Each set of skills requires a different approach to teach and assess. Implementing a variety of approaches for a number of years at SJSU has shown that it is just as necessary …

Influence Of Personality On A Senior Project Combining Innovation And Entrepreneurship, Jinny Rhee, David W. Parent, Clifton M. Oyamot

Faculty Publications

No abstract provided.

Characterizing Performance Guarantees For Real-Time Multiagent Systems Operating In Noisy And Uncertain Environments, Damian M. Lyons, Ronald Arkin, Stephen Fox, Shu Jiang, Prem Nirmal, Munzir Zafar

Faculty Publications

Autonomous robots offer the potential to conduct Counter-Weapons of Mass Destruction (C-WMD) missions in an efficient and robust manner. However, to leverage this potential, a mission designer needs to be able to determine how well a robot system will operate in the noisy and uncertain environments that a C-WMD mission may require. We are developing a software framework for verification of performance guarantees for C-WMD missions based on the MissionLab software system and a novel process algebra approach to representing robot programs and operating environments.

In this paper, we report on our initial research for the Defense Threat Reduction Agency …

Design Optimization Of Transistors Used For Neural Recording, E J. Basham, David W. Parent

Faculty Publications

Neurons cultured directly over open-gate field-effect transistors result in a hybrid device, the neuron-FET. Neuron-FET amplifier circuits reported in the literature employ the neuron-FET transducer as a current-mode device in conjunction with a transimpedance amplifier. In this configuration, the transducer does not provide any signal gain, and characterization of the transducer out of the amplification circuit is required. Furthermore, the circuit requires a complex biasing scheme that must be retuned to compensate for drift. Here we present an alternative strategy based on the design approach to optimize a single-stage common-source amplifier design. The design approach facilitates in circuit characterization of …

Identification Of Influential Social Networkers, Magdalini Eirinaki, S. P. Singh Monga, S. Sundaram

Faculty Publications

Online social networking is deeply interleaved in today's lifestyle. People come together and build communities to share thoughts, offer suggestions, exchange information, ideas, and opinions. Moreover, social networks often serve as platforms for information dissemination and product placement or promotion through viral marketing. The success rate in this type of marketing could be increased by targeting specific individuals, called 'influential users', having the largest possible reach within an online community. In this paper, we present a method aiming at identifying the influential users within an online social networking application. We introduce ProfileRank, a metric that uses popularity and activity characteristics …