Projects
Signal Relay
Model
To study how white blood cells (specifically neutrophils) coordinate motion, I programmed a model in Python that accounts for how signaling molecule secretion, diffusion, and removal, as well as cell response to those molecules.
Results
Some of the signaling molecules are released in containers called exosomes. Model results show that exosomes help by stabilizing the signals. This figure shows about 100,000 data points.
For more information, see,
Alex C. Szatmary, Ralph Nossal, Carole A. Parent*, Ritankar Majumdar*, Modeling neutrophil migration in dynamic chemoattractant gradients: assessing the role of exosomes during signal relay”. Molecular Biology of the Cell 28:23, 3457–3470 (2017). (Abstract and PDF)
Shaft Design Tool
Geometry of shaft and parts on it (gear, coupling, bearings, keys)
Factor of safety along the shaft
In mechanical design courses, students are often given "calculators" (Excel worksheets) that ease rote calculations. However, students struggle to design shafts because doing so requires information on all the other machine parts and math that is heavier than Excel handles well. Previously, users would manually edit a Matlab script that a colleague had shared with me; that process was difficult and tedious. I refactored my calculators and Matlab script so that users could fill in an Excel template by making cell references to their other calculators; those cells automatically generated the needed Matlab code. In this example, a user could see that the factor of safety is low at the coupling seat so the shaft should be made thicker there.
Ruffle Citation Graph
To see clusters of ideas on a biological process (morphogenesis) I made a Python tool called Ruffle. I took notes on articles in plain text files and tracked which other articles were cited. From those files, Ruffle translated the data to JSON, constructed a bidirectional graph (shown here), and generated an annotated bibliography as a hyperlinked PDF.
White Blood Cell Rolling Adhesion
Some white blood cells (namely neutrophils) stick to blood vessel walls and roll on them on their way to inflammation sites. Adhesion molecules are present in patches on the blood vessel walls, some of them as dimers (pairs). I programmed a model in Python that accounts for fluid forces, cell deformation, and stochastic bond formation and rupture. The figure shows histograms of where the cells were, for different distributions of adhesion molecules. The model shows that even a little non-uniformity in the distribution can control cell position, and that this effect is disrupted if the adhesion molecules are present as dimers.
For more information see,
Alex C. Szatmary. The Effect of P-Selectin Dimers on Neutrophil Rolling on Endothelium. Biophysical Society Annual Meeting. Baltimore, MD. February 2015. (Abstract and PDF)