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Computational and Theoretical Bioengineering

The computational and theoretical bioengineering group works to explain, model, and provide the means to manipulate medically-related biological systems. Investigations range from biomechanics to protein-protein interactions, to stem cell differentiation and immune system therapies. General areas of interest include bone and cartilage mechanics, stress effects on stem cell differentiation, sequence and structure properties of glycosaminoglycans, nanoelectromechanical transduction in cochlear, outer-hair cell membranes, characterization of molecular imaging markers, structural biology, evolution and immune system therapies, design principles of biochemical circuits, and drug-based inhibition of aberrant protein interactions.

Researchers in the Department of Bioengineering involved in this field include:


Michael Deem 

Michael W. Deem, Ph.D. Click for larger view

  • Newton's laws of biology
  • Physical theories of evolution
  • Physical theories of evolution
  • Structure, nucleation, and function of zeolites

Deem Group

Mike Diehl  

Click for larger viewMichael Diehl, Ph.D.  

  • Regulation of intracellular transport
  • In situ molecular pathway analyses

Macromolecular Systems Bioengineering Group

Jane Grade-Allen_Thumbnail

K. Jane Grande-Allen, Ph.D. Click for larger view

  • Constitutive modeling of the material behavior  of native
    and tissue engineered heart valves
  • Diversity of glycosaminoglycan structures
  • Patient-specific modeling of heart valve disease and surgical repair

Grande-Allen Integrative Matrix Mechanics Lab


Click for larger viewOleg A. Igoshin, Ph.D.

  • Modeling self-organization and pattern formation in cellular systems
  • Deterministic and stochastic models of biochemical networks
  • Systems biology modeling of differentiation and development 

Cellular System Dynamics Group

Jeff Jacot_Thumbnail  

Click for larger viewJeffrey Jacot, Ph.D.

  • Computational finite element modeling of congenital heart defects
  • Voltage mapping of the whole heart

Jacot Laboratory

Jianpeng Ma_Thumbnail  

Jianpeng Ma, Ph.D. Ma_aniso_oct_top

  • Computational simulation of biomolecular dynamics
  • Structural refinement against low-resolution experimental data
  • Structure prediction and folding
  • Structure-based drug design
  • Bioinformatics

 Ma Lab

Amina Qutub  

Amina A. Qutub, Ph.D. Click for larger view

  • Regulation of intracellular hypoxic response in ischemia and cancer
  • Neurogenesis and angiogenesis signaling
  • Algorithm development for cell-level modeling coupled to imaging

Microvascular Systems Biology Laboratory

Rob Raphael  

Robert Raphael, Ph.D.

  • Auditory Systems Biology
  • Micromechanical Biosystems

Membrane and Auditory Bioengineering Group


Ka-Yiu San  

Ka-Yiu San, Ph.D. Click for larger view

  • Metabolic and genetic engineering
  • Systems biotechnology
  • Genetic architecture and phenotype

Metabolic Engineering and Systems Biotechnology Laboratory


David Zhang, Ph.D.

  • DNA and RNA folding parameters and algorithms
  • Predictive quantitative models of nucleic acid reconfiguration kinetics
  • Sequence design and analysis of large scale nucleic acid systems and circuits

Nucleic Acid Bioengineering Laboratory (NABLab)