BIEN Projects: Summer 2009
The BIEN (Biosystems Internships for Engineers) projects that will be offered during the Summer 2009 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 Implant 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. Microfluidic Devices for Studying Bacterial Films
Prof. Reza Ghodssi
EBacterial infections are the leading cause of disease worldwide, and the development of antimicrobial drugs has been one of the highest priorities of biomedical research. It was recently shown that certain types of bacteria communicate with each other through small signaling molecules. This capability, called quorum sensing, allows the bacteria to perform population-coordinated actions and to overcome the host's immune system. They start to aggregate and form a pathogenic matrix known as a biofilm, which is impenetrable to conventional antibiotics. A promising new approach for combating bacteria is to develop drugs that disable their communications, making them less pathogenic and more susceptible to antibiotics. Researchers at the MEMS Sensors and Actuators Lab (MSAL) in the ECE department are developing microfluidic devices with integrated sensors for studying bacterial quorum sensing and testing potential drugs. The growth of E. coli biofilms within the devices is monitored optically, and its growth is correlated with factors in the environment. The use of microfluidic technology will ultimately allow large numbers of potential drugs to be tested rapidly with small sample volumes. This project is a collaborative effort involving groups in the Bioengineering and Materials Engineering departments and the University of Maryland Biotechnology Institute (UMBI). It offers interdisciplinary learning opportunities to MERIT students. The student will use advanced bioengineering equipment, a microfluidic test station and an optical characterization setup. The goal of the project will be to perform measurements of biofilm growth using standard laboratory tools. The results of this study will be used to validate the microfluidics-based experiments and to further refine the microfluidic devices.
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. Bat-Inspired Robot Navigation Using Echolocation
Prof. P. S. Krishnaprasad 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 sensorimotor 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 and Horiuchi plan to offer students participating in this project a dual-mode experience in learning (a) how artificial sonar systems are constructed and operated, (b) what information these signals provide, (c) what we understand about how bats integrate spatial information into the control of movement, and (d) how to design a navigation system based on these ideas. Experiments in robotics are designed and carried out in the context of control system design, specifically in the Intelligent Servosystems Laboratory (ISL) and physical realizations of neural algorithms that contribute to system-level behavior through demonstrations on robots will be done specifically in the Computational Sensorimotor Systems Laboratory (CSSL)
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. 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. Fabrication and Characterization of Nanoporous Waveguides for Optical Biosensing
Prof. Tom Murphy
In this project, we will investigate using nanoporous optical waveguides as a new method for ultrasensitive, label-free sensing of biomolecules. The student will work together with the faculty member and graduate students to fabricate and measure porous optical waveguides, and possibly develop a simple microfluidic assembly to enable on-chip sensing.
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.
9. Security and Privacy Protection of Electronic Collections of Medical Data
Prof. Min Wu
With the proliferation of the digital and networking technologies, a large amount of health care and medical diagnostic information are now acquired and archived in digital form. These electronic collections of medical data can not only provide readily available medical data to facilitate clinical diagnosis in the new e-Healthcare paradigm, but also provide rich body of data to advance medical research. Ensuring the security and privacy of sensitive medical information is critical in order for the full potential of these electronic medical data to be realized.
Prof. Wu's research group has been investigating a broad range of information security issues, including access control, data integrity verification, tracking data origin source of information leak, and secure search and retrieval. The algorithm and software prototypes developed by previous REU students, such as a digital fingerprinting toolbox and a non-intrusive imaging forensic system, have played an important role in advancing innovative research.
Through the proposed REU project, Prof. Wu plans to leverage the research expertise of her group and focus on security and privacy protection in challenging medical applications. Some of the challenges include large data volume associated with medical data, which calls for computationally efficient algorithms; the low contrast/signal-to-noise-ratio of many types of medical data as well as high integrity requirement, whereby directly applying many existing media security algorithms designed for photographic images and music becomes insufficient. Mentored by experienced graduate students, the REU students will first learn the state-of-the-art security and protection techniques, and work as a team to identify issues unique to biomedical data. The undergraduate team will then develop algorithms and software toolboxes to provide efficient encryption, secure search, authentication, and digital fingerprinting of medical images and other 1-D and multidimensional biomedical data. Given the adversarial nature of many security applications, students will be divided into two sub-teams to encourage their creativity and critical thinking and to perform attacks and counter-attacks on the algorithms and system.