BIEN Projects: Summer 2008
The BIEN (Biosystems Internships for Engineers) projects that will be offered during the Summer 2008 session are listed below. Project names are linked to their respective descriptions. Faculty members and project directors are linked to their home pages where available.
1. Biosensors for Cell Monitoring
Prof. Pamela Abshire
Interfacing electronics to biological systems leads to the possibility of creating devices that directly monitor the responses of living biological cells. Potential applications include cell-based sensing, medical diagnosis, drug screening, pathogen detection, and scientific research into cellular mechanisms. Students will contribute to ongoing research to develop such bioelectronic and biophotonic interfaces to single cells. Bioelectronic sensors include bioamplifiers and capacitance sensors, detecting weak electrical signals from electrically active cells and cell-substrate interactions which correlate with cell health, respectively. Biophotonic sensors include contact imagers and fluorescence sensors, detecting objects in close physical proximity to an imaging surface and the results of fluorescence assays, respectively. These sensors form the technical basis for applications such as nose-on-a-chip, rapid|throughput screening and microscale fluorescencedetection and lab-on-a-chip. BIEN interns will explore aspects of the technology and applications including sensor characterization and validation in experimental platforms such as the nose-on-a-chip, development of new component technologies such as spectral filters or packaging methods, and development of new functional capabilities such as cell steering or screening.
2. Biometrics and Robotic Control
Prof. Pamela Abshire and Prof. Timothy Horiuchi
It is possible to use a variety of measurements from the human body in order to control the motion of external robotic devices. In this project students will refine methods to control a robotic device using skin-surface signals, i.e. multi-channel electromyography (EMG). Limitations of existing systems are few control channels, slow response time, and limited sensory feedback to the user. Subprojects include circuit design and simulation, characterization of EMG signals, signal classification techniques, design and construction of PC boards and interfaces, and development of robotic interface. This project involves review of electronics and biological literature in addition to design, simulation, testing, and construction.
3. Algorithms on Noisy Speech for Cochlear Impant Users
Prof. Carol Espy-Wilson
The Speech Communication Lab led by Prof. Espy-Wilson is developing a landmark-based approach to speech recognition which involves the explicit extraction Landmark-based Speech Recognition Study and Evaluation of Enhancement of specific linguistic information from the speech signal. A spectro-temporal profile of a speech signal reveals the periodic components that result from quasiperiodic oscillation of the vocal cords and aperiodic components that result from a noisy excitation of the vocal tract. One such noise known as aspiration is generated at the glottis where the vocal folds are fully are partially separated, but close enough to generate enough of a constriction to cause turbulence at the glottis and slightly above as the airflow hits the epiglottis. Another type of noise is generated well above the glottis (in the front half of the vocal tract in American English) by the close proximity of an articulator to the palate or teeth resulting in a narrow constriction that generates noise. For some sounds, this noise is also directed against the teeth that further strengthens the noise. The first part of this speech processing project will study the characteristics of these different types of noises produced by speakers so that we can automatically classify the noise as gstridenth or not, and as gturbulenceh or gaspirationh in order to facilitate robust speech recognition. The speech communication lab has developed an algorithm to increase the signal-to-noise ratio (SNR) of noisy speech signals that does not require an estimate of the noise. Objective measures show that this algorithm does a better job than many other speech enhancement schemes, especially when the noise is fluctuating. The second part of the project aims at determining the effectiveness of speech enhancement algorithms to improve the intelligibility of speech for cochlear implant users for many different noise types including car noise, subway noise, and babble noise.
4. Nanostructured Nickel-Zinc Microbatteries Using Tobacco Mosaic Virus
Prof. Reza Ghodssi
Energy harvesting and on-chip power supply for MEMS devices are essential components in an effort to create efficient and autonomous microsystems. The MEMS Sensors and Actuators Lab (MSAL) led by Prof. Ghodssi is investigating novel approaches for the development of micro-batteries based on the well studied Tobacco Mosaic Virus (TMV). This benign virus can be assembled on a metal surface and coated with another metal, thereby creating a high surface area metallic structure, which can be used as an efficient working electrode in a micro-battery configuration. This promising scheme will be eventually used in already existing sensor and actuator platforms to increase the energy density and allow for more compact devices. This project is in direct collaboration with the Center for Biosystems Research (CBR) at the University of Maryland Biotechnology Institute (UMBI). The objective from biology aspects is to achieve solid surface attachment of the virus particles, investigate the metal coating capabilities (currently nickel and cobalt) and evaluate their electrochemical performance. From the engineering side, REU students will work with Prof. Ghodssi's group to demonstrate the feasibility of the virus assembly in the MEMS and microfluidics domain, make use of the provided chemistry in order to develop the first MEMS-based viral battery and evaluate the cell performance for different electrode configurations. Upon successful completion of the initial goals, the team will be designing self-sustained microfluidic systems for both the TMV assembly and battery operation.
5. Protein Screening Using Aptamer-nanoparticle Complexes
Prof. Mel Gomez
Aptamers are short synthetic nucleic acid sequences, similar to DNA's, that bind to other nucleic acids, peptides, drug or cells. These biomolecules can be engineered to effectively recognize specific targets and to function like antibodies for molecular detection and drug delivery. This project is to develop an optical based system in which aptamers are attached to nanoparticles of gold and suspended in solution. Upon exposure to the target protein, the optical spectrum or the color of the aptamer-nP solution, will change in response to the presence of the target molecule. The mechanism involves the characteristics of the surface plasmon resonance of the nanoparticles. The goal of this project is to develop a prototype of a low cost, fast and easy-to-use system for detecting protein markers for screening for diseases.
6. Feedback Loops in the Behaving Echolocating Bat and Control Systems for Robots
Prof. P. S. Krishnaprasad, Prof. Cynthia Moss, and Prof. Timothy Horiuchi
The echolocating bat Eptesicus fuscus perceives the world around it in the dark, primarily through the information it gathers rapidly and dependably by probing the environment through controlled streams of pulses of frequency modulated ultrasound. The returning echoes from scatterers such as obstacles (cave walls, trees), predators (nocturnal birds such as barn owls) and prey (insects), are captured and transduced into neuronal spike trains by the highly sensitive auditory system of the bat, and processed in the sensori-motor pathways of the brain to steer the bat's flight in purposeful behavior (avoiding obstacles, evading predators, tracking and capturing insect prey). Painstaking laboratory and field studies have begun to yield clues to the exquisite sensitivity of the bat's auditory system, its neural signal processing, and the feedback control systems guiding the flight. The effectiveness of the bat in coping with attenuation and noise, uncertainty of the environment, and sensorimotor delay, makes it a most interesting model system for engineers who have to cope with similar issues in the design of robotic systems. The study of a natural system such as the echolocating bat illuminates questions in engineering, pertaining to effective, goal-directed, and time-constrained information processing - as is needed in robotics. The neural realizations of auditory-motor feedback loops in the bat may serve as models for novel implementations of algorithms in robot designs. Profs. Krishnaprasad, Moss, and Horiuchi plan to leverage their long-time interdisciplinary collaboration to offer students participating in this project a dual-mode experience in learning (a) how laboratory experiments are designed and carried out in the life sciences, specifically in the Auditory Neuroethology Laboratory (ANL); (b) how laboratory Interfacing electronics to biological systems leads to the possibility of creating devices that directly monitor the responses of living biological cells. Potential applications include cell-based sensing. Experiments in robotics are designed and carried out in the context of control system design, specifically in the Intelligent Servosystems Laboratory (ISL); (c) how physical realizations of neural algorithms contribute to system-level behavior through demonstrations on robots, specifically in the Computational Sensorimotor Systems Laboratory (CSSL); and (d) how knowledge and facility with analytical and experimental techniques and discipline in these two different settings can be integrated to: (1) enable bio-inspired design of engineered systems, and (2) guide further hypothesis-driven research in behavioral neurobiology. The dual-mode lab experience will be offered in the form of ISL-Batlab combination or CSSL-Batlab combination. The ISL experience with robotics from will be distinct from the CSSL experience because the former links novel algorithms to higher level software implementations while the CSSL experience will link algorithms to electronic circuit implementations. Students participating in this project will spend nearly equal time in the two different laboratories mentioned, and a final period synthesizing results and reporting on the synthesis of ideas gained through two complementary research experiences. The specific laboratory experiments conducted will study behaviors in nature mirrored in behaviors in robotic systems. Mathematical modeling using differential equations, data gathering and statistical data analysis, and exploitation of software tools for real-time analysis and control will be among the elements of this experience.
7. Ultrasensitive Biodetection and Terahertz Spectroscopy of Protein Molecules
Prof. Tom Murphy
Many methods exist for detecting and quantifying biomolecular interactions, but established techniques are costly, time-consuming, and often require the use of fluorescent or radioactive labels in order to identify and quantify the analyte. The first part of the project will investigate a new label-free biosensor that uses optical waveguides and resonant cavities comprised of nanoporous silicon. Nanoporous silicon is a unique and versatile material with several features that make it especially attractive for biological sensors, including a very high surface area to volume ratio, simple and inexpensive fabrication techniques, and suitability for integration with silicon electronics. The proposed sensor is designed to measure small changes in the refractive index of porous silicon that occur when biological molecules attach to the internal surfaces. REU students will participate in several aspects of the design, fabrication, characterization and evaluation of porous silicon optical waveguides, including electromagnetic analysis of optical waveguides, loss characterization, and bioconjugation of porous materials. The second part of the project focuses on the terahertz region of the electromagnetic spectrum. Lying between the microwave frequencies (100 GHz) and the optical frequencies (30 THz), this region holds tremendous promise not only for identifying and classifying biomolecules, but also for understanding their underlying molecular dynamics and functionality. Potential applications of terahertz spectroscopy include pharmaceutical development, medical imaging, homeland security, and basic scientific studies of protein and DNA structure. Despite recent advances, terahertz spectroscopy of biological material remains challenging, in part because of the practical difficulty in transmitting terahertz signals through aqueous environments. This project seeks to address these fundamental insufficiencies by developing a nanoporous medium to capture, concentrate and isolate biological samples for high-resolution spectroscopy. Students will work on developing porous substrates for capturing biological molecules, evaluating different surface functionalization procedures for porous materials, and performing spectroscopic measurements of samples using terahertz time-domain spectroscopy. Prof. Murphy is a dedicated educator and mentor sought after by undergraduate students.
8. Signal Processing in the Human Brain
Prof. Jonathan Z. Simon
Brain activity is observable via a variety of tools. Most fall into the broad category of brain-imaging (e.g. fMRI) and are too slow to measure real-time neural computations. An alternative is magnetoencephalo-graphy (MEG), which is sensitive to neural processes changing as fast as every millisecond. MEG is related to the more commonly used clinical tool electroencephalography (EEG), but it has key advantages due to its use of neural magnetic fields: the brain is magnetically, but not electrically, transparent. Since the entire brain is active simultaneously, however, the neurally generated magnetic fields become a mix of signals generated in many cortical areas, and they require a variety of signal processing techniques to determine the underlying neural processes performed in individual areas. Summer students will be given the opportunity to apply both traditional and cutting-edge signal processing techniques to neural data acquired via MEG, as well as being able to take part in conducting the experiments in which the MEG data is itself acquired. The goal in conducting these auditory experiments, and their data analysis, is to characterize, understand, and quantify the neural computations performed by the brain.