In a peer reviewed article — "Universal Approach to FRAP Analysis of Arbitrary Bleaching Patterns" — we leveraged a computational simulation to simplify diffusion coefficient estimate in a cell membrane (FRAP experiments). The work also resulted in an open source tool for ImageJ.

By leveraging Total Internal Reflection Fluorescence Microscopy (TIRFM) we were able to measure the binding rate of a model protein to a microfabricated binding site. Binding site was fabricated using a Nano Fountain Pen (NFP) on treated glass slides. NFPs can paint/print features down to the nanoscale, thus potentially facilitating addressable, single viewfield multiplexed sensing. In our experimental system, TIRFM lets us to reject unbound fluorescent molecules due to rapid decay of the TIR evanescent wave. Consequently, the brightness off the feature is proportional to the concentration of bound analyte. Measuring the dynamics of the change in brightness lets us directly measure the binding rate and infer the desorption rate and binding coefficient (Kd) for the system. Our results closely match previously reported values in the literature.

Micrograph of a Nano Fountain Pen

Binding dynamics of a fluorescent Avidin tracer to a biotinylated-BSA feature fabricated on a treated glass slide. Brightness is proportional to concentration of bound Avidin

comparison of bBSA-Avidin binding rate to previously reported values for similar systems

leveraging deep learning techniques for large scale cell segmentation and studying dynamics of near-confluent proliferating cells. Developed a tool for streamlining analysis of FUCCI experiments. Currently working on a manuscript for peer-review.

Large scale (~3k cells in viewfield) analysis of FUCCI cells. Tracking information color coded based cells that are not dividing (red), just divided (green) & about to divide (yellow)

Schematic of a FUCCI experiment. (A) proliferating cells (B) a cell cycle for FUCCI cells that fluoresce red during their G0/G1 and green during S/G2/M. Imaging these cells in two channels would localize them as per (C). (D) shows the fluorescent intensity for each channel. The presence of both fluorophores indicates cells about to divide