Digital signal processing and digital system design using discrete cosine transform [student course]

The discrete cosine transform (DCT) is an important functional block for image processing applications. The implementation of a DCT has been viewed as a specialized research task. We apply a micro-architecture based methodology to the hardware implementation of an efficient DCT algorithm in a digital design course. Several circuit optimization and design space exploration techniques at the register-transfer and logic levels are introduced in class for generating the final design. The students not only learn how the algorithm can be implemented, but also receive insights about how other signal processing algorithms can be translated into a hardware implementation. Since signal processing has very broad applications, the study and implementation of an extensively used signal processing algorithm in a digital design course significantly enhances the learning experience in both digital signal processing and digital design areas for the students.

Computational Design and Experimental Discovery of an Anti-estrogenic Peptide Derived from Alpha-Fetoprotein

Breast cancer is the most common cancer among women, and tamoxifen is the preferred drug for estrogen receptor-positive breast cancer treatment. Many of these cancers are intrinsically resistant to tamoxifen or acquire resistance during treatment. Consequently, there is an ongoing need for breast cancer drugs that have different molecular targets. Previous work has shown that 8-mer and cyclic 9-mer peptides inhibit breast cancer in mouse and rat models, interacting with an unsolved receptor, while peptides smaller than eight amino acids did not. We show that the use of replica exchange molecular dynamics predicts the structure and dynamics of active peptides, leading to the discovery of smaller peptides with full biological activity. Simulations identified smaller peptide analogues with the same conserved reverse turn demonstrated in the larger peptides. These analogues were synthesized and shown to inhibit estrogen-dependent cell growth in a mouse uterine growth assay, a test showing reliable correlation with human breast cancer inhibition.

Computational approaches for the design of peptides with anti-breast cancer properties

Background: Breast cancer is the most common cancer among women. Tamoxifen is the preferred drug for estrogen receptor-positive breast cancer treatment, yet many of these cancers are intrinsically resistant to tamoxifen or acquire resistance during treatment. Therefore, scientists are searching for breast cancer drugs that have different molecular targets. Methodology: Recently, a computational approach was used to successfully design peptides that are new lead compounds against breast cancer. We used replica exchange molecular dynamics to predict the structure and dynamics of active peptides, leading to the discovery of smaller bioactive peptides. Conclusions: These analogs inhibit estrogen-dependent cell growth in a mouse uterine growth assay, a test showing reliable correlation with human breast cancer inhibition. We outline the computational methods that were tried and used along with the experimental information that led to the successful completion of this research.

Thin-Film Sparse Boundary Array Design for Passive Acoustic Mapping During Ultrasound Therapy

A new 2-D hydrophone array for ultrasound therapy monitoring is presented, along with a novel algorithm for passive acoustic mapping using a sparse weighted aperture. The array is constructed using existing polyvinylidene fluoride (PVDF) ultrasound sensor technology, and is utilized for its broadband characteristics and its high receive sensitivity. For most 2-D arrays, high-resolution imagery is desired, which requires a large aperture at the cost of a large number of elements. The proposed array's geometry is sparse, with elements only on the boundary of the rectangular aperture. The missing information from the interior is filled in using linear imaging techniques. After receiving acoustic emissions during ultrasound therapy, this algorithm applies an apodization to the sparse aperture to limit side lobes and then reconstructs acoustic activity with high spatiotemporal resolution. Experiments show verification of the theoretical point spread function, and cavitation maps in agar phantoms correspond closely to predicted areas, showing the validity of the array and methodology.

Engineering Design: the Information Component

The curriculum of the Bucknell University Chemical Engineering Department includes a required senior year capstone course titled Process Engineering, with an emphasis on process design. For the past ten years library research has been a significant component of the coursework, and students working in teams meet with the librarian throughout the semester to explore a wide variety of information resources required for their project. The assignment has been the same from 1989 to 1999. Teams of students are responsible for designing a safe, efficient, and profitable process for the dehydrogenation of ethylbenzene to styrene monomer. A series of written reports on their chosen process design is a significant course outcome. While the assignment and the specific chemical technology have not changed radically in the past decade, the process of research and discovery has evolved considerably. This paper describes the solutions offered in 1989 to meet the information needs of the chemical engineering students at Bucknell University, and the evolution in research brought about by online databases, electronic journals, and the Internet, making the process of discovery a completely different experience in 1999.

Hierarchical Approach for Survivable Network Design

A central design challenge facing network planners is how to select a cost-effective network configuration that can provide uninterrupted service despite edge failures. In this paper, we study the Survivable Network Design (SND) problem, a core model underlying the design of such resilient networks that incorporates complex cost and connectivity trade-offs. Given an undirected graph with specified edge costs and (integer) connectivity requirements between pairs of nodes, the SND problem seeks the minimum cost set of edges that interconnects each node pair with at least as many edge-disjoint paths as the connectivity requirement of the nodes. We develop a hierarchical approach for solving the problem that integrates ideas from decomposition, tabu search, randomization, and optimization. The approach decomposes the SND problem into two subproblems, Backbone design and Access design, and uses an iterative multi-stage method for solving the SND problem in a hierarchical fashion. Since both subproblems are NP-hard, we develop effective optimization-based tabu search strategies that balance intensification and diversification to identify near-optimal solutions. To initiate this method, we develop two heuristic procedures that can yield good starting points. We test the combined approach on large-scale SND instances, and empirically assess the quality of the solutions vis-à-vis optimal values or lower bounds. On average, our hierarchical solution approach generates solutions within 2.7% of optimality even for very large problems (that cannot be solved using exact methods), and our results demonstrate that the performance of the method is robust for a variety of problems with different size and connectivity characteristics.

An integrated environment for filter design

Analog filters and direct digital filters are implemented using digital signal processing techniques. Specifically, Butterworth, Elliptic, and Chebyshev filters are implemented using the Motorola 56001 Digital Signal Processor by the integration of three software packages: MATLAB, C++, and Motorola's Application Development System. The integrated environment allows the novice user to design a filter automatically by specifying the filter order and critical frequencies, while permitting more experienced designers to take advantage of MATLAB's advanced design capabilities. This project bridges the gap between the theoretical results produced by MATLAB and the practicalities of implementing digital filters using the Motorola 56001 Digital Signal Processor. While these results are specific to the Motorola 56001 they may be extended to other digital signal processors. MATLAB handles the filter calculations, a C++ routine handles the conversion to assembly code, and the Motorola software compiles and transmits the code to the processor

Investigation of the Design of a Bistable Micro-Chemical-Mechanical Device Utilizing Lateral Buckling

The Gracias Laboratory at Johns Hopkins University has developed microgrippers which utilize chemically-actuated joints to be used in micro-surgery. These grippers, however, take up to thirty minutes to close fully when activated biochemicals in the human body. This is very problematic and could limit the use of the devices in surgery. It is the goal of this research to develop a gripper that uses theGracias Laboratory's existing joints in conjunction with mechanical components to decrease the closing time. The purpose of including the mechanical components is to induce a state of instability at which time a small perturbation would cause the joint to close fully.The main concept of the research was to use the lateral buckling of a triangular gripper geometry and use a toggle mechanism to decrease the closure time of the device. This would create a snap-action device mimicking the quick closure of a Venus flytrap. All developed geometries were tested using finite element analysis to determine ifloading conditions produced the desired buckled shape. This research examines lateral buckling on the micro-scale and the possibility ofusing this phenomenon in a micro-gripper. Although a final geometry with the required deformed shaped was not found, this document contains suggestions for future geometries that may produce the correct deformed shape. It was determined through this work that in order to obtain the desired deformed shape, polymeric sections need to be added to the geometry. This simplifies the analysis and allows the triangular structure to buckle in the appropriate way due to the added joints. Future work for this project will be completed by undergraduate students at Bucknell University. Fabrication and testing of devices will be done at Johns Hopkins University in the Gracias Laboratory.

DESIGN OF A LIQUID FUEL INJECTOR FOR ALTERNATIVE FUEL STUDIES IN AN ATMOSPHERIC MODEL GAS TURBINE COMBUSTOR

A new liquid-fuel injector was designed for use in the atmospheric-pressure, model gas turbine combustor in Bucknell University’s Combustion Research Laboratory during alternative fuel testing. The current liquid-fuel injector requires a higher-than-desired pressure drop and volumetric flow rate to provide proper atomization of liquid fuels. An air-blast atomizer type of fuel injector was chosen and an experiment utilizing water as the working fluid was performed on a variable-geometry prototype. Visualization of the spray pattern was achieved through photography and the pressure drop was measured as a function of the required operating parameters. Experimental correlations were used to estimate droplet sizes over flow conditions similar to that which would be experienced in the actual combustor. The results of this experiment were used to select the desired geometric parameters for the proposed final injector design and a CAD model was generated. Eventually, the new injector will be fabricated and tested to provide final validation of the design prior to use in the combustion test apparatus.

The Design of XML-Based Model and Experiment Description Languages for Network Simulation

The Simulation Automation Framework for Experiments (SAFE) is a project created to raise the level of abstraction in network simulation tools and thereby address issues that undermine credibility. SAFE incorporates best practices in network simulationto automate the experimental process and to guide users in the development of sound scientific studies using the popular ns-3 network simulator. My contributions to the SAFE project: the design of two XML-based languages called NEDL (ns-3 Experiment Description Language) and NSTL (ns-3 Script Templating Language), which facilitate the description of experiments and network simulationmodels, respectively. The languages provide a foundation for the construction of better interfaces between the user and the ns-3 simulator. They also provide input to a mechanism which automates the execution of network simulation experiments. Additionally,this thesis demonstrates that one can develop tools to generate ns-3 scripts in Python or C++ automatically from NSTL model descriptions.

Design, Construction, and Validation of an Atmospheric Combustor for Alternative Fuel Studies

An atmospheric combustion apparatus was designed through several iterations for Bucknell University's combustion laboratory. The final design required extensive fine-tuning of the fuel and air systems and repeated tests to arrive at a satisfactory procedure to transfer from gaseous to liquid fuel operation. Measurement of exhaust emissions were obtained under tests of gaseous methane and liquid heptane were operation in order to validate the functionality of the combustion apparatus, the fuel transition procedure, and emissions analyzer systems. The emission concentrations of CO, CO2, NOx, 02, S02, and unburned hydrocarbons from a multianalyzer and HFID analyzer were obtained for a range of equivalence ratios. The results verify the potential for future alternative fuel tests and illuminate necessary alterations for further liquid fuel studies.

FPGA BASED DESIGN FOR ACCELERATED FAULT-TESTING OF INTEGRATED CIRCUITS

In the past few decades, integrated circuits have become a major part of everyday life. Every circuit that is created needs to be tested for faults so faulty circuits are not sent to end-users. The creation of these tests is time consuming, costly and difficult to perform on larger circuits. This research presents a novel method for fault detection and test pattern reduction in integrated circuitry under test. By leveraging the FPGA's reconfigurability and parallel processing capabilities, a speed up in fault detection can be achieved over previous computer simulation techniques. This work presents the following contributions to the field of Stuck-At-Fault detection: We present a new method for inserting faults into a circuit net list. Given any circuit netlist, our tool can insert multiplexers into a circuit at correct internal nodes to aid in fault emulation on reconfigurable hardware. We present a parallel method of fault emulation. The benefit of the FPGA is not only its ability to implement any circuit, but its ability to process data in parallel. This research utilizes this to create a more efficient emulation method that implements numerous copies of the same circuit in the FPGA. A new method to organize the most efficient faults. Most methods for determinin the minimum number of inputs to cover the most faults require sophisticated softwareprograms that use heuristics. By utilizing hardware, this research is able to process data faster and use a simpler method for an efficient way of minimizing inputs.

Design and Development of an FPGA-based Distributed Computing Processing Platform

This thesis presents two frameworks- a software framework and a hardware core manager framework- which, together, can be used to develop a processing platform using a distributed system of field-programmable gate array (FPGA) boards. The software framework providesusers with the ability to easily develop applications that exploit the processing power of FPGAs while the hardware core manager framework gives users the ability to configure and interact with multiple FPGA boards and/or hardware cores. This thesis describes the design and development of these frameworks and analyzes the performance of a system that was constructed using the frameworks. The performance analysis included measuring the effect of incorporating additional hardware components into the system and comparing the system to a software-only implementation. This work draws conclusions based on the provided results of the performance analysis and offers suggestions for future work.

A Method for Assessing the Sustainability of Design in Developing World Projects

Projects for the developing world usually find themselves at the bottom of an engineer’s priority list. There is often very little engineering effort placed on creating new products for the poorest people in the world. This trend is beginning to change now as people begin to recognize the potential for these projects. Engineers are beginning to try and solve some of the direst issues in the developing world and many are having positive impacts. However, the conditions needed to support these projects can only be maintained in the short term. There is now a need for greater sustainability. Sustainability has a wide variety of definitions in both business and engineering. These concepts are analyzed and synthesized to develop a broad meaning of sustainability in the developing world. This primarily stems from the “triple bottom line” concept of economic, social, and environmental sustainability. Using this model and several international standards, this thesis develops a metric for guiding and evaluating the sustainability of engineering projects. The metric contains qualitative questions that investigate the sustainability of a project. It is used to assess several existing projects in order to determine flaws. Specifically, three projects seeking to deliver eyeglasses are analyzed for weaknesses to help define a new design approach for achieving better results. Using the metric as a guiding tool, teams designed two pieces of optometry equipment: one to cut lenses for eyeglasses and the other to diagnose refractive error, or prescription. These designs are created and prototyped in the developed and developing worlds in order to determine general feasibility. Although there is a recognized need for eventual design iterations, the whole project is evaluated using the developed metric and compared to the existing projects. Overall, the success demonstrates the improvements made to the long-term sustainability of the project resulting from the use of the sustainability metric.