Anthony Salvagno

Repeating Crumley: Seed Growth vs Time

© Salvagno This article is distributed under the terms of the Creative Commons Attribution 4.0 International License, which permits unrestricted use, distribution, and redistribution in any medium, provided that the original author and source are credited. As you know I posted pictures of the seed growth every day. Well a couple of days ago I decided to organize the pictures by sample in one post as opposed to by day. This way you can see the growth of each sample over the 15 day period. The posts are already posted but I figured I would compile the links here with some commentary so you know what’s up.

Recreating Crumley: The setup (Updated)

I’m setting up the Crumley Experiment now that I have most of what I need. I ordered some more tobacco seeds but I have no idea when those are set to arrive so I’ll begin a preliminary experiment with what I have to work out the kinks. If you are too lazy to click the link above then I’ll recall for you that the experiment involved putting tobacco seeds in different percentages of D2O and tracking seed germination.

Open-Source Stochastic Simulation for Modeling Kinesin-1 Kinetics

Kinesin-1 (conventional kinesin) is a homodimeric motor protein important for axonal transport. It has been well studied through ensemble and single-molecule assays. However, the enzymatic stepping cycle is complex, with many rate constants that are modulated by interaction of the two motor domains. This makes it difficult to predict how changes in a given rate constant may affect observable properties such as processivity, velocity, or stall force. We have written a simulation of kinesin walking using a Stochastic Simulation Algorithm. The model allows for interactions between the heads, and includes states that are not considered part of the normal cycle. This adds to the complexity of the model but also allows for probing rare events, such as those that lead to a finite processivity. Also included are rate constant dependencies on force and concentrations of ATP, ADP, and Pi, which may provide insight into other processes under investigation, such as kinesin backstepping. We intend to use the simulation to aid in interpreting our own gliding motility assay results and to place upper and lower limits on values for rate constants. Our source and executable codes will be freely available.Acknowledgements: This work was supported by the DTRA CB Basic Research Program under Grant No. HDTRA1-09-1-008.