Biomedical Engineering Research Laboratories

Auditory Neurophysiology Laboratory, Professor Voigt.

  • Experimental and theoretical studies of the neuronal circuitry in the cochlear nucleus.
  • Single- and multi-unit recording and analysis techniques used to study the responses of neurons and neural nets to acoustic stimulation.
  • Intracellular recording and marking techniques associate specific neurons to their physiology.
  • Computational neural models test hypotheses of cochlear nucleus function.

Auditory Neuroscience Laboratory, Professor Shinn-Cunningham. Projects in the Auditory Neuroscience Laboratory explore how we perceive sound sources in ordinary listening environments that contain multiple competing sources, echoes, and reverberation. A variety of methods are employed, including psychophysics, modeling, EEG, acoustical measurement and single-unit recording.

Binaural Hearing Laboratory, Professor Colburn. The Binaural Hearing Laboratory is focused on studies of binaural interaction, including phenomena such as sound localization for which monaural processing also plays a major role. The goal of these studies is an integrated understanding of binaural interaction and its role in human sound perception including the interpretation of acoustic cues in complex sound environments (e.g., multiple sources in reverberant spaces). Specific projects range from signal processing models of physiological activity to empirical measurements of the hearing abilities of listeners with hearing losses and/or neurological lesions. In the neural modeling area, we are evaluating the abilities of simple neural models to generate firing patterns equivalent to those seen in binaural cells in brainstem nuclei such as the MSO, LSO, and IC. In psychophysical studies of normal listeners, current interests include interaural discrimination and binaural detection, especially detection with reproducible noise maskers. In studies of listeners with hearing impairments, we are trying to relate listeners’ abilities on a variety of binaural tests to a primary set of psychophysical measures. In studies of sound localization and recognition, we are studying and simulating the cues that lead to externalization, localization, and separation of sources.

Biomedical Microdevices & Microenvironments Laboratory, Professor Klapperich. The Biomedical Microdevices & Microenvironments Laboratory is focused on the interactions between biological molecules and cells and synthetic microenvironments. Specifically, we are interested in building microenvironments in vitro that mimic the physiological environment. These synthetic microenvironments are intended for use in diagnostics, high throughput drug screening, and to enable previously impossible basic science studies. Currently we have projects aimed at recapitulating the microenvironments of the breast, cochlea and motor neurons. We are also engaged in the design and engineering of manufacturable disposable microfluidic systems for low-cost point-of-care molecular diagnostics. We are currently working on devices for the detection of C. difficile, influenza and C-Reactive Protein, an inflammatory marker in heart disease.

Biomedical Optics Laboratory, Professor Bigi. The focus of our research is the development of minimally invasive diagnostics and therapeutics based on optical and photonic technologies. We often collaborate with clinical researchers who test the new technologies on animals or human subjects. With noninvasive optical measurements there is minimal risk to the patient, but significant medical benefits are possible. Some of our ongoing projects include:

  • “Optical biopsy”: development of fiber-optic probes that perform spectroscopic measurements on tissue in vivo and noninvasively to instantly diagnose cancer and other pathologies in specific organ areas.
  • “Optical pharmacokinetics”: fiber-optic probes designed to measure drug concentrations in tissue, dramatically reducing the number of animals required for drug studies. This can also be used to determine the optimum type and dosage of novel (light-activated) chemotherapy agents for individual patients.
  • Sensors to monitor the response of tumors to specific treatments.
  • Optical methods for noninvasive imaging of neuronal activation and brain function.
  • Optical methods for identifying different types of infectious agents.

Biomicroscopy Laboratory, Professor Mertz. The Biomicroscopy Lab focuses on the development of new optical microscopy techniques and on their applications to biological imaging. Our aim is to invent new techniques or to improve on existing techniques, usually for the purpose of high resolution imaging in thick tissue. We have built several experimental setups, three of which are based on femtosecond laser sources. Our current research areas include multiphoton microscopy, second harmonic generation, autoconfocal microscopy, graded field microscopy, and dynamic speckle illumination microscopy. Our goal is to apply these techniques to biological imaging, in particular brain tissue imaging, either in vitro (slice) or in vivo (anesthetized animal).

Biomimetic Materials Engineering Laboratory, Professor Wong. Dr. Wong’s research focuses on the development of biomaterials to probe how structure, material properties and composition of the cell-biomaterial interface affect fundamental cellular processes. Her current research interests include tissue engineering of small diameter blood vessels for bypass and intravascular pharmacology (e.g. stents); development of targeted nano- and micro-particle contrast agents for multi-modal (magnetic resonance, ultrasound, and optical) detection of atherosclerotic and vulnerable plaque; and engineering biomimetic systems to study restenosis and breast cancer.

Biomimetic Systems Laboratory, Professors Mountain and Hubbard. The long range goal of the Auditory Systems Laboratory is to develop large-scale biophysically-based models of the auditory pathways. The purpose of these models is to aid the interpretation of and the design of physiological and psychophysical experiments as well as to study auditory models for their usefulness as preprocessors for automated recognition of acoustic signals. Experimental approaches range from single-unit recordings to auditory evoked potentials obtained from the scalp and modeling approaches range from computational approaches to electronic hardware implementations. This laboratory is also engaged in the study of natural acoustic signal sources and acoustic environments. The purpose of this effort is to develop a better understanding of the evolutionary pressures which have shaped the auditory pathway as well as to develop computer simulations of natural environments for use as input to the auditory models. Other current projects include the use of auditory models for the acoustic transients and development of models for processing temporal sequences.

Biomolecular Systems Laboratory, Professor DeLisi. The Bimolecular Systems Laboratory develops and applies computational/mathematical methods, and high throughput experimental methods, to analyze changes in gene and protein expression profiles of cells in response to various endogenous and exogenous signals. In collaboration with the Fraunhofer Center for Manufacturing Innovation, and the departments of Chemistry and Physics, we are developing and applying new DNA and peptide microarray technologies for fingerprinting the complete molecular state of a cell. Examples include the response to ligands (drugs, toxins, hormones etc), and changes that occur as normal cells mature, differentiate, progress toward disease. The long-range goal is to relate expression patterns to pathways, pathways to networks and networks to function.

BioRobotics Laboratory, Professor Dupont. The BioRobotics Research Group (BRG) solves theoretical and practical problems in minimally invasive surgery. They specialize in medical robot and instrument design, development of imaging techniques for surgical guidance, modeling tool-tissue interaction; and teleoperation/automation of instrument motion. They utilize analytical tools from robotics, dynamics and control together with innovative design techniques to create successful solutions. The team members come from diverse backgrounds with degrees in mechanical/biomedical/electrical engineering and medicine. Their specialties range from biomedical robotics, clinical practice and imaging to product design and many areas in between.

Brain & Vision Laboratory, Professor Vaina. Fundamental and applied research of visual information processing and perceptual learning in humans:

  • Eye-movements and visual-perceptual abilities of neurological patients: measurement and rehabilitation.
  • Structural and functional neuroimaging for functional-anatomical mapping of the visual motion system in humans.
  • Functional plasticity in the human visual system: characteristics, computational models, and applications to rehabilitation.
  • Computational methods for aiding visually guided navigation in visually impaired patients

The Broude Laboratory, Professor Broude.

  • Development of mass spectrometry of nucleic acid chips as a new general diagnostic platform for genetic diseases, cancer, and infectious disease.
  • Molecular engineering of streptavidin, a general prototyping system for solid state biochemistry, DNA and antibody-based assays.
  • Development of high-contrast methods for detecting nucleic acids in living cells and manipulating cells expressing specific MRNAs.

Cell & Tissue Mechanics Laboratory, Professor Stamenovic. Fundamental and applied research of soft tissue rheology and mechanical properties of cells:

  • Measuring and modeling mechanical properties of the cytoskeleton of living cells and its interactions with the extracellular matrix.
  • Measuring and modeling rheological behaviors of living cells.
  • Modeling of pneumatic osteoarthritis knee brace.
  • Measurements and nonlinear modeling of the dynamic stress-strain relationship of soft tissues, in particular, of lung tissues. Image processing of fluorescently labeled components (such as collagen and elastin fibers) of tissues.
  • Nonlinear dynamic modeling of various physiological phenomena such as avalanche mechanism of airway reopening.

Cellular & Subcellular Mechanics Laboratory, Professors Dembo and Evan. Experiments use extremely sensitive mechanical probes, novel materials and advanced optical microscopy to expose the physical actions and material properties of single cells and of the ultra-fine macro molecular machines sensors and transducers that drive and control cellular and subcellular processes. Advanced computational methods are needed for data processing to obtain solutions for equations and for the final physical analysis used to establish definitive mechanistic interpretations of experimental data. A core teaching laboratory for training in nano-to-micro mechanical instrumentation has been set up to enable students and faculty to develop new research projects in biomedical engineering.

  • We have a goal of achieving force measurements with resolution on the scale of the thermal energy divided by a molecular dimension (approximately 10E-10 gm wt). We are also trying to develop noninvasive detectors that will be capable of measuring displacements with resolution of a few nanometers at very high temporal rates.
  • We are conducting studies to investigate the role of structural mechanics in regulating biochemical pathways, biological adhesion phenomena, cytoskeletal deformation and active cellular motility.
  • We are developing novel materials that mimic the interfacial properties of natural biomaterials and we are studying the interactions of cells with such artificial substrata.
  • We are developing novel biomaterials as substrata for control of cell adhesion and cell motility. For example, materials with patterned surface modifications are used to investigate the effect of their physical, chemical, and mechanical properties on interactions with living cells.

Cochlear Biophysics Laboratory, Professors Mountain and Hubbard. The long-range goal of the Boston University Cochlear Biophysics Laboratory is to improve understanding of the hearing process through a synergistic combination of engineering and physiological techniques:

  • Identify, quantify, and model the mechanisms responsible for mechanical sensitivity and frequency selectivity of the mammalian cochlea (inner ear). Recent experimental evidence suggests that the outer hair cells of the cochlea act as electromechanical amplifiers which increase hearing sensitivity one-hundred fold. Our efforts are directed towards confirming this hypothesis and clarifying our understanding of the underlying mechanisms.
  • As a byproduct of their normal function, the outer hair cells also produce acoustic energy which can be measured in the external ear canal (otoacoustic emissions). These otoacoustic emissions have provided scientists and clinicians with a unique noninvasive tool to study cochlear function. In spite of hundreds of studies on otoacoustic emissions, the details of their production and their propagation back to the ear canal are not well understood. Our research, which builds on extensive experience with otoacoustic emissions, cochlear electrophysiology and biomechanics, and computer simulation, is expected to shed new light on this important clinical tool.

Collins Lab, Professor Collins. The Collins Lab focuses on developing nonlinear dynamical techniques and devices to characterize, improve and mimic biological function. Our specific interests include: (1) systems biology—reverse engineering naturally occurring gene regulatory networks, and (2) synthetic biology—modeling, designing and constructing synthetic gene networks.

Computational Genomics Laboratory, Professor Kasif. The research we pursue in partnership with major genomic centers and several other laboratories involves the development of new biotechnology and computational frameworks for the analysis, computational representation, measurement and modeling of biological systems. We are interested in:

  • Human cells (e.g., insulin signaling networks) as well as bacterial genomics
  • Computational functional genomics: new gene identification, functional classification and gene expression analysis
  • Computational comparative genomics: methods for comparing complete genomic sequences at different levels of detail
  • Discovery and modeling of biological pathways using probabilistic networks
  • Genomic biotechnology: new computer-assisted genomic and proteomic technologies
  • Clinical research focusing on Diabetes and Cancer.

Ehrlich Laboratory, Professor Ehrlich. The emerging view is that cancer shares an analogy to contagious disease. Under healthy systemic control, or with the intervention of drugs, an evolving balance is developed between healthy and potentially malignant rare progenitor cell types. Therefore, “baseline” genomic data is insufficient, and averaged genomic data or averaged expression patterns are very indirect and blunt as a diagnostic. Our laboratory is developing the new methods and instruments needed to gather sufficiently detailed molecular snapshots from sufficiently specific rare-cell phenotypes for both drug development and clinical diagnosis. To some extent, the technology that can fill the gap can be assembled from high-speed microscopy and microfluidics; however, the instruments and work flow need to be redesigned, and other elements, such as efficient cost-effective quantitative expression analysis, need to be re-thought in format.

Fields & Tissues Laboratory, Professor Eisenberg. Research in the area of electrically mediated phenomena in tissues and biopolymers:

  • Computational modeling of current distributions in the heart and thorax during electrical defibrillation
  • Finite element modeling of magnetically induced currents in inhomogeneous anisotropic tissues and bodies
  • Microcontinuum and microstructural models of electromechanical interactions in connective tissues; tissue mechanics

Frank-Kamenetskii Laboratory, Professor Frank-Kamenetskii. Experimental and theoretical studies of DNA structure and function. New principles of DNA-drug interactions, equilibrium and kinetic specificity of DNA-ligand interaction, complexes of a DNA mimic, peptide nucleic acid (PNA), with duplex, modulation of activity of proteins working on DNA using PNAs, molecular beacons and their applications, DNA nanostructures based on PNA, applications of the PNA technology for genome analysis and DNA detection.

Grinstaff Laboratory, Professor Grinstaff. The Grinstaff group pursues highly interdisciplinary research in the areas of biomedical engineering and macromolecular chemistry.

  • designing, synthesizing, and characterizing novel biodendrimers. Ongoing evaluations for the repair of corneal lacerations, anti-cancer drug delivery, DNA delivery, and temporary biodegradable scaffolds for cartilage repair.
  • creating novel polymeric coatings termed “interfacial biomaterials” that control biology on plastic, metal, and ceramic surfaces.
  • designing electrochemical-based sensors/devices using conducting polymer nanostructures and specific DNA structural motifs.

Medical Acoustics Laboratory, Professor Porter. Research in the Medical Acoustics Laboratory is directed towards developing new and exciting medical applications of ultrasound. Studies conducted in this laboratory combine acoustics, fluid dynamics, chemistry, biology, and biomedical engineering for:

  • fabricating targeted ultrasound contrast agents for molecular imaging of diseases
  • designing ultrasound-triggered drug delivery systems
  • evaluating the underlying mechanisms for ultrasound-induced cellular uptake of drugs, genes, and proteins
  • studying the mechanisms responsible for ultrasound-enhanced drug activity

Molecular Biotechnology Laboratory, Professor Cassandra Smith. Research in the Molecular Biotechnology Research Laboratory brings novel approaches and tools from the interface of genomics, genetics and biotechnology to complex disease studies. A major focus is on preventing schizophrenia by understanding how monozygotic (identical) twins can be discordant for disease. Another project focuses on the specific delivery of DNA therapeutic reagents (called aptamers) to cancer cells. Here, the goal is to develop effective targeted therapies for cancer treatment and diagnosis that minimize damage to bystander cells. Other projects focus on the development of novel DNA and RNA detection and analysis methods.

Motor Unit Laboratory, Professor De Luca. Research in this lab investigates how the brain and spinal cord control the activation of muscle cells to produce muscle force. The Precision Decomposition Technique, which has received international recognition, was developed here. It is used to identify all electrical action potentials of several concurrently active muscle fibers from the complex myoelectric signal detected during a muscle contraction.

  • Knowledge gained through research in this lab is expected to be transferred into the clinical environment to improve the ability of the neurologist to categorize and quantify neurological dysfunction

Multi-Dimensional Signal Processing Laboratory, Professor W. Clement Karl. Research in the general areas of multidimensional and multiresolution signal and image processing and estimation and geometric-based estimation. The development of efficient methods for the extraction of information from diverse data sources in the presence of uncertainty including:

  • Enhanced resolution image reconstruction for Cardiac Computerized Tomography
  • Multisource data fusion
  • Nanoscale optical microscopy
  • Biological interface estimation and tracking

Natural Sounds & Neural Coding Laboratory, Professor Sen. How do neurons in the brain encode complex natural sounds? What are the neural substrates of selectivity and discrimination of different categories of natural sounds? How are these substrates shaped by learning? The Natural Sounds & Neural Coding Laboratory investigates these questions in the model system of the songbird. Electrophysiological techniques are used to record neural responses from hierarchical stages of auditory processing. Theoretical methods from areas such as statistical signal processing, systems theory, probability theory, information theory and pattern recognition are applied to characterize how neurons in the brain encode natural sounds. Computational models are constructed to understand the processing of natural sounds both at the single neuron and the network level, to model neural selectivity and discrimination, and to explore the role of learning in shaping the neural code.

Olfactory Systems Laboratory, Professor Wachowiak. We study how the nervous system encodes odor information, and how the brain processes this information. In other words, how does the brain identify smells? This is a tough problem because most smells are complex mixtures of different odor molecules, because the number of different smells that an animal must detect and identify is huge, and because the olfactory environment is highly varied over time and space. Our focus is on understanding how patterns of neural activity encode odor information and how this code changes as a result of neural processing. A major interest of the lab is in understanding olfaction as an active sense in which the detection, encoding and processing of odor information is shaped by the animal’s behavior at all levels of the nervous system. We use optical imaging as a primary tool to directly visualize neural activity as an animal smells an odor, and also to investigate how neurons process olfactory information using reduced preparations. We image activity in the earliest stages of the olfactory pathway—among olfactory receptor neurons, which detect odorants, and neurons in the olfactory bulb, the first stage of olfactory processing in the brain.

Optical Characterization & Nanophotonics Laboratory, Professors Golberg, Ünlü, and Swan. Research in Optical Characterization & Nanophotonics (OCN) Laboratory focuses on developing and applying advanced optical characterization techniques to the study of solid-state and biological phenomena at the nanoscale. Under the direction of Professors Goldberg, Swan and Ünlü, we have a interdisciplinary group of faculty, graduate and undergraduate students, and visitors including guest faculty, students, and often high school students and teachers working on a broad range of research projects. Our laboratory has a vertically integrated structure where researchers ranging from high school students to senior professors work together on truly interdisciplinary research topics.

Organogenesis Laboratory, Professor Tien. Research applying techniques adopted from microlithography, self-assembly, microfluidics, and developmental biology to develop methods of assembling cells into ordered three-dimensional aggregates and use these aggregates as artificial tissue and as in vitro models of disease. Current work focuses on the fabrication of branched networks such as vasculature and pulmonary trees, and spatially complex organoids such as liver acini. This laboratory is a part of the Micro and Nano Biosystems Research facilities.

Orthopaedic & Developmental Biomechanics Laboratory, Professor Morgan. This laboratory uses experimental and computational methods to explore the relationships between structure, mechanical function, and biological function of tissues at multiple length scales. Principles of engineering mechanics, materials science, and cell and molecular biology are employed to investigate how the deformation and failure behavior of biological tissues depend on the tissue microstructure; and conversely, how differentiation and adaptation of tissues and cells are modulated by their local mechanical environment. Current research projects include quantification of functional loading conditions for trabecular bone, the effects of mechanical stimulation on bone and cartilage development, and the biomechanical consequences of damage in bone. The laboratory houses a complete wet lab as well as a separate computational facility for image processing and modeling.

Pulmonary Physiology & Dynamics Laboratory, Professor Suki

  • Roles of collagen remodeling and network breakdown in pulmonary emphysema
  • Role of mechanotransduction in pulmonary emphysema
  • Measurements and nonlinear modeling of the rheological properties of soft tissues including lung tissues and tissue engineered constructs
  • Imaging of the extracellular matrix components such as collagen and elastin fibers and cell during stretching
  • Statistical mechanical modeling of various physiological phenomena such as avalanches in airway reopening and fluctuations in cellular contraction in recurrent airway diseases
  • Surfactant secretion in epithelial cells induced by dynamic stretching
  • Noise-enhanced life-support systems including mechanical ventilation

Respiratory Research Laboratory, Professor Jackson. The Respiratory Research Laboratory’s major research objectives are: using engineering and scientific principles to provide insight into the function of the respiratory system; developing methods of non-invasively quantifying changes in lung function resulting from disease or pharmacological interventions. Specific activities include:

  • Measurement of the mechanical impedance of the respiratory and pulmonary systems. Measurement and analysis of the underlying microscopic and macroscopic properties of the pulmonary tissues and cells. Development of instrumentation for measurements of pulmonary function in adults, infants, and patients in intensive care units
  • Prediction of the system’s behavior through detailed morphometrically based computer models that include the acoustic properties of the branching airways, nonlinear visco- and plasto-elastic properties of the tissues
  • Develop constitutive descriptions of the respiratory tissues based on their molecular, cellular, and systems structure and function
  • Use of systems identification techniques to extract physiologically relevant parameters from complex mechanical impedance data
  • Computer modeling of gas transport and mixing in the lung

Respiratory & Physiological Systems Identification Laboratory, Professor Lutchen. Development of novel linear and nonlinear systems identification approaches for probing mechanisms associated with healthy and diseased physiological systems. Principal applications in respiratory physiology. Research efforts include:

  • Development of measurement, monitoring, and signal processing techniques that provide new insights on the structural airway and tissue conditions of the healthy and diseased lung
  • Advanced application of mechanistic and morphometrically based models for interpreting the structure-function relations in the lung with emphasis on the mechanisms that compromise breathing capability and ventilation
  • Advancing linear and nonlinear systems identification science, sensitivity analysis, and optimal experiment design to evaluate the efficacy of applying models to physiological data with emphasis on structural lung models and cardiovascular dynamics
  • Understanding the origins of linear and nonlinear properties of physiological systems

Ritt Laboratory, Professor Ritt. Current projects employ electrophysiological, behavioral, optogenetic and theoretical methods applied to the rodent whisker system, a highly refined tactile sensory system. Experiments combine multi-electrode recording of brain activity; high-speed videography of behavior and development of automated image analysis algorithms; and optical stimulation of specific cell types (e.g., excitatory vs. inhibitory neurons) using genetically targeted expression of light-sensitive ion channels. Parallel modeling uses tools from dynamical systems, control theory and decision theory. Augmenting experiments with model-driven, real-time feedback forms a basis for development of brain-machine interfaces, with an emphasis on sensory neural prosthetics, in addition to providing state-of-the-art tools to address basic questions of neural function.

Segre Laboratory, Professor Segre. Metabolic networks are among the most-conserved and best-understood networks in biological systems. Yet, deciphering how metabolism at the cellular level responds to genetic (e.g., gene deletion) and environmental (e.g., nutrient shift) perturbations is an open challenge, relevant both to understanding physiological regulation and evolutionary adaptation. In our group, we approach these questions using kinetic and flux balance models of metabolic networks. In flux balance models, metabolic networks are treated as steady state systems, whose reaction rates (fluxes) can span a space of solutions constrained by fundamental mass conservation laws. Efficient optimization algorithms can search this space for flux arrangements that optimize a given objective function, such as maximization of cellular growth, or minimization of the deviation of fluxes with respect to a previously achieved state. Using these approaches, we can perform large-scale computer experiments of single and double gene deletions, generate global maps of predicted epistatic interactions between genes, and study the interplay between physiological and evolutionary adaptation in different organisms.

Sensory Signal Processing Laboratory, Professor Teich. Work carried out in the Sensory Signal Processing Laboratory centers on the statistical behavior and signal processing of biological signals. Particular projects include:

  • Encoding of acoustical and optical stimuli into sequences of action potentials at various locations in auditory and visual systems.
  • Using the wavelet transform of the electrocardiogram to distinguish patients with heart disease from normal ones.
  • The study of neural-based psychophysical models that consider ascending sensory pathways as amplifying neural networks.
  • The development of a quantum-optical microscope that should be useful for carrying out high-resolution fluorescence studies in the neurosciences.

Single Molecule Biophysics & 
Nano-biotechnology Laboratory, Professor Meller. Research is directed toward the development of novel experimental techniques for the study of biomolecular interactions and dynamics, at the single molecule or at the single complex level. In particular, his research is focused on:

  • Employing nanopore force spectroscopy to study RNA unfolding and re-folding kinetics
  • DNA switches and transcription initiation kinetics
  • RNA helicases activity
  • Mapping of transcription factors interactions with DNA
  • Ultra-fast DNA sequencing
  • Development of novel optical methods for single molecule detection in biomedical applications

Steffen Laboratory, Professor Steffen. Our efforts in the area of technology development aim at identifying protein interactions using mass spectrometry. We are developing two methods: (1) for identifying strong, stable interactions in complexes, such as those that might be found in a ribosome, polymerase or other multi-subunit complex; (2) for identifying weak, transient interactions, such as those that are involved in signal transduction. Our efforts in bioinformatics revolve around pathway and network identification. We have developed an algorithm for automated modeling of pathways in yeast, based only on two-hybrid protein interaction and microarray data. No prior knowledge of the pathway is needed. We now wish to extend this method to C. elegans and drosophila, and will explore application of this algorithm to mouse and human. Other computational efforts involve integrating known pathway and network data with proteomic and microarray experiments.

Structural BioInformatics Laboratory, Professor Vajda. The focus of this laboratory is the development and application of computational tools for the analysis of protein structure and protein-ligand interactions. Some of the particular problems we currently study are the evaluation of binding free energy in protein-protein complexes, development of efficient docking algorithms, computational solvent mapping of proteins using molecular probes to identify the most favorable binding positions, method development for fragment-based drug design, construction of an enzyme binding site database, and improving the prediction of protein active sites by homology modeling.

Szabo Laboratory, Professor Szabo. Professor Szabo’s research goals are overcoming present limitations in imaging the body using ultrasound and other imaging modalities and finding new ways of extracting diagnostically useful information about tissue structure, health and function noninvasively. His work involves the following: multi-modal and 3D digital imaging and beamforming, signal processing, ultrasound-induced bioeffects, simulation and measurement of mechanical tissue properties, and scanning acoustic microscopy.

Vascular Interface & Microhemofluidics Laboratory, Professor Damiano. One of the major thrusts of our research is to investigate cellular and molecular interactions at the interface between blood and the vascular endothelium in order to advance our understanding of cardiovascular health and disease. Specific interests include (1) studying the role of the endothelial surface layer (ESL) in inflammation, (2) determining the extent of the ESL on endothelial-cell monolayers in vitro and throughout the vasculature in vivo, (3) analyzing the implications of the ESL for microvascular hemodynamics, and (4) studying the role of the ESL in atherosclerosis and in the vascular complications of hyperglycemia. Our research is also centered around designing, testing, and implementing a closed-loop control system for regulating blood glucose in type 1 diabetes. Based on results from our pre-clinical studies in diabetic pigs, we have recently received FDA approval to test our blood-glucose control system in subjects with type 1 diabetes. Clinical trials have begun in the Mallinckrodt General Clinical Research Center at the Massachusetts General Hospital.

Visual Information Processing Laboratory, Professor Passaglia. The Visual Information Processing Lab investigates the computational strategies employed by the nervous system to process and encode a visual scene. Behavioral, electrophysiological, histological, theoretical, and computer modeling techniques are applied to animals with visual systems of varying complexity in order to gain a broad spectrum of insights into the neural basis of visual perception. The research efforts of the lab are primarily directed at the retinal network of the eye and its synaptic contacts in the brain. The aim is to understand how visual images are represented in the retinal output and how the representation changes as ocular diseases, such as glaucoma, inflict damage to the network.

Xia Laboratory, Professor Xia. Research in the lab is focused on computational structural and systems biology. We develop computational techniques to model the structure, function, and evolution of complex biomolecular systems, such as proteins and protein networks. Specific projects include: modeling and simulation of proteins and protein networks; comparative and evolutionary analysis of proteins and protein networks; protein sequence-structure-function relationships; prediction of protein structure and function.

Zhang Lab, Professor Zhang. Professor Zhang’s current research projects are in the characterization of the biomechanical behavior of microstructural components in native and engineered blood vessels using an integrative approach of mechanical testing combined with multi-scale modeling, understanding of the inelastic deformation mechanisms in micro- and nano-electromechanical systems and relations of these behaviors to design, analysis, and device performance.

Instructional Laboratories

BioInterface Technologies (BIT) Facility. The BioInterface Technologies Facility is located in room 501 at 44 Cummington Street. It is a central teaching and research facility with a focus on biomaterial and tissue engineering. It offers instrumentation and service in biomaterial synthesis, property (chemical, physical, mechanical) analysis and biological assessment.

Biomedical Engineering Data-Acquisition Laboratory. The Biomedical Engineering Data-Acquisition Laboratory is a biomedical instrumentation facility located at 48 Cummington Street, rooms 209 and 211. These Windows workstations are equipped with data acquisition cards connected to signal measurement and analysis instrumentation, and are available for classroom instruction, homework, and research involving data capture and recording.

Biomedical Engineering Computational Simulation Facility. The Biomedical Engineering Computational Simulation Facility is a high-performance computing laboratory located at 24 Cummington Street, basement rooms B03 and B04, with a smaller laboratory located at 48 Cummington Street, basement room B11. The facility consists of high-performance Linux workstations at each seat and rack-mounted computational nodes in a separate server room. The facility is available for classroom instruction, homework and research requiring high computational power, and all machines are clustered together as part of a parallel computing grid for remote access to regular scientific applications and for processing long, computationally intensive jobs.

Micro/Nano Biosystems Fabrication Facilities. The Micro/Nano Biosystems Fabrication Facilities are located in rooms 712 and 718 at 44 Cummington Street. The facilities are intended for the processing of micro- and nano-scale features in 4” and smaller diameter Silicon wafers. They consist of temperature and humidity controlled class 100 and class 1000 clean rooms suitable for photolithography

Micro/Nano Imaging (MNI) Facility. The Micro and Nano Imaging (MNI) Facility suite is a central teaching and research facility with a focus on imaging biological materials ranging from tissues to individual molecules. Instrumentation includes Confocal, TIRF and multiple Widefield systems with the ability to maintain cells and tissues under appropriate conditions. It is located on the 5th floor of 44 Cummington Street.