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Publications in VIVO

Perkins, Thomas T.

Professor Adjunct, Professor Adjoint


Research Areas research areas


research overview

  • Single molecule studies are increasingly important in biophysics. The Perkins group focuses on developing high precision single-molecule techniques and applying them to answer a range of biological questions, such as: how motor proteins transduce chemical energy into physical motion? And, how does the structure and dynamics of membrane proteins affect their functions? We developed a optical-trapping assay with Ångström-scale stability and resolution in 3D. We are applying these techniques to study DNA-based molecular motors, the folding/unfolding kinetics of RNA structures, and DNA overstretching. We also developed focused-ion beam modified cantilevers for dramatically improved performance of atomic force microscopy and are currently pursuing studies of diverse biological systems (globular proteins, protein-ligand bonds, membrane proteins, structured RNA). We are also leveraging our advances in AFM instrumentation to achieve high-resolution imaging of DNA and protein-DNA complexes.


  • biophysics, single molecule, membrane protein, DNA, RNA, molecule motors,atomic force microscopy, optical trapping,nanotechnology, nanoscience


selected publications


courses taught

  • MCDB 4550 - Cells, Molecules and Tissues: A Biophysical Approach
    Primary Instructor - Spring 2022
    Focuses on the biophysics governing the structure/function of enzymes, cells, extracellular matrix and tissue. Synthesizes ideas from molecular biology, physics, and biochemistry, emphasizing how low Reynolds number physics, not Newtonian physics, is relevant to life inside a cell. Fulfills MCDB scientific reasoning requirement. Recommended prerequisites: MCDB 3135 and MCDB 3145 and PHYS 2010 and PHYS 2020 and CHEM 1133 and MATH 1300 and/or CHEM 3311 (minimum grade C-) or instructor consent required. Same as MCDB 5550 and PHYS 4550 and PHYS 5550.
  • MCDB 4990 - Honors Thesis
    Primary Instructor - Spring 2022
    Involves the preparation and defense of an honors thesis, based on faculty-supervised original research, including final phases of the research project. Recommended prerequisites: MCDB 4840 or MCDB 4980 or comparable research experience, and minimum GPA of 3.3 and approval by the MCDB Honors Committee.


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