DeniseKirschner

Denise Kirschner

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Denise Kirschner is a Professor in the Department of Microbiology and Immunology.  She serves as founding co-director of the Center for Systems Biology, is affiliated with both the Center for the Study of Complex Systems and  the Center for Computational Medicine and Bioinformatics. Her research involves the modeling of immunological responses in infectious diseases, focusing on questions related to host-pathogen interactions. The pathogens she studies include both bacteria (Mycobacterium tuberculosis) and HIV-1. Such pathogens have evolved strategies to evade or circumvent the host-immune response and the lab’s goal is to understand the complex dynamics involved and develop optimal treatment and vaccine strategies.

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Karl Grosh

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Professor Grosh research spans various aspects of structural acoustics, mechanics, biomechanics and linear/nonlinear vibrations. Current research involves Cochlear mechanics (experiments and modeling of the mechanics of soft tissue and tissue growth), electroacoustic transducers, and computational and analytic methods for solving interior viscous fluid-structure interaction problems.

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C. Alberto Figueroa

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Alberto Figueroa is an Associate Professor with a joint appointment in Biomedical Engineering and Surgery. He works on computational methods for patient-specific cardiovascular simulation.figueroa_image-264x300

Modeling the function of the cardiovascular system in health and disease represents a fascinating scientific challenge. This challenge can only be addressed by combining a deep understanding of the physiologic, biologic, engineering and mathematical principles involved.Our lab uses medical image processing, high performance computational fluid dynamics simulation, and multi-scale modeling to simulate blood flow in the human body. Our specific areas of interest are surgical planning, disease research, arterial growth and remodeling, and medical device design and performance evaluation.

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Jeff Fessler

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Jeff Fessler is a Professor in the Department of Electrical Engineering and Computer Science – Electrical and Computer Engineering Division. His research interests include numerical optimization, inverse problems, image reconstruction, computational imaging, tomography, magnetic resonance imaging.  Most of these applications involve large problem sizes and parallel computing methods (cluster, cloud, GPU, SIMD, etc.) are needed.

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Jennifer Linderman

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The Linderman group works in the area of computational biology, especially in developing multi-scale models that link molecular, cellular and tissue level events.   Current areas of focus include: (1) hybrid multi-scale agent-based modeling to simulate the immune response to Mycobacterium tuberculosis and identify potential therapies, (2) models of signal transduction, particularly for G-protein coupled receptors, and (3) multi-scale agent-based models of cancer cell chemotaxis.

Hybrid multi-scale model of the immune response to Myobacterium tuberculosis in the lung. Selected immune cell behaviors and interactions captured by the model are shown. Not shown are single cell receptor/ligand dynamics involving the pro-inflammatory cytokine tumor necrosis factor (TNF) and the anti-inflammatory cytokine interleukin 10 (IL-10).

Hybrid multi-scale model of the immune response to Myobacterium tuberculosis in the lung. Selected immune cell behaviors and interactions captured by the model are shown. Not shown are single cell receptor/ligand dynamics involving the pro-inflammatory cytokine tumor necrosis factor (TNF) and the anti-inflammatory cytokine interleukin 10 (IL-10).

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David Sept

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David Sept is a Professor in the Department of Biomedical Engineering, and he is affiliated with the Center for Computational Medicine and Bioinformatics. The Sept lab works in the area of computational biology and we use a wide array of computational techniques to study protein, drug and cellular systems.  In addition to “standard” simulation techniques like molecular dynamics, we are developing new simulation and analysis methods for application in more complex systems.

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Cynthia Chestek

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Cynthia Chestek is an Assistant Professor of Biomedical Engineering, Electrical Engineering – Electrical and Computer Engineering Division, and the Neurosciences Graduate Program.

The Chestek lab focuses on brain machine interface (BMI) systems using 100 channel arrays implanted in motor and pre-motor cortex. The goal of this research is to eventually develop clinically viable systems to enable paralyzed individuals to control prosthetic limbs, as well as their own limbs using functional electrical stimulation and assistive exoskeletons. The lab apply a variety of machine learning algorithms to large-scale neural datasets obtained from spiking activity or field potentials in order to decode the motor commands. This is done both offline, and in real-time during experiments. Other computational challenges include mitigating non-stationarities in neural recordings over time. Over the next few decades, the size of these datasets is most likely to increase with the development of larger electrode arrays, and novel surgical techniques for implanting them.
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Ronald Larson

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Ronald Larson is the A.H. White and G.G. Brown Professor of Chemical Engineering. He is affiliated with the departments of Chemical Engineering, Macromolecular Science, Biomedical Engineering, and Mechanical Engineering. He currently serves as interim Chair of Biomedical Engineering. Larson’s research interests include theory and simulations of the structure and flow properties of viscous or elastic fluids, sometimes called “complex fluids,” which include polymers, colloids, surfactant-containing fluids, liquid crystals, and biological macromolecules such as DNA, proteins, and lipid membranes. He also studies computational fluid mechanics, including microfluidics, and transport modeling, using mesoscopic and macroscopic simulation methods.  He has written numerous scientific papers and two books on these subjects, including a 1998 textbook, “The Structure and Rheology of Complex Fluids.”

Simulated three dimensional self assembly of spherical “Janus” particles with attractive faces (blue, on far left and red on far right) and non-attractive faces (white). The far left shows packing in the “rotator” phase, where the attractive faces have not ordered orientationally, which occurs at lower temperature. Other images show single sphere, or groups of spheres, indicating hexagonal ordering. Surrounding points show positions of surrounding spheres, at multiple time points, indicating motions about crystal lattice points.

Simulated three dimensional self assembly of spherical “Janus” particles with attractive faces (blue, on far left and red on far right) and non-attractive faces (white). The far left shows packing in the “rotator” phase, where the attractive faces have not ordered orientationally, which occurs at lower temperature. Other images show single sphere, or groups of spheres, indicating hexagonal ordering. Surrounding points show positions of surrounding spheres, at multiple time points, indicating motions about crystal lattice points.