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ReaDDy Simulations for actin bend/twist coupling figure #5

Open blairlyons opened 2 years ago

blairlyons commented 2 years ago

Use Case

As an author for the actin bend/twist coupling micro-publication, I need data to complete the accompanying figure.

Acceptance Criteria

.simularium trajectories for replicates of all the parameter sets needed for the figure, and plots for pitch and bending for all the replicates of each set.

Details

figure mockup:

164087882-05272a00-1593-4622-9c95-cbbd85cfc2a7

ReaDDy Model:

Model:

Metrics:

Plots (per trajectory):

Reference: https://www.sciencedirect.com/science/article/pii/S0006349510008532

blairlyons commented 2 years ago

@mattakamatsu does this specification for the ReaDDy models look right? Am I forgetting anything?

Actually, which end do we want to displace? If we displace an end, in the current implementation, at least its position is fixed

mattakamatsu commented 2 years ago

Ah right - okay so really we'll have two conditions (the ones you simulated) - move with free rotation or no rotation. I updated the figure mockup accordingly image

mattakamatsu commented 2 years ago

Updated figure mockup showing the output metrics we are looking for:

image

Proxy for filament twist: angular displacement between subunits Proxy for filament bend: displacement between subunits

blairlyons commented 2 years ago

@mattakamatsu (EDIT: I just updated the description above with) what I'm planning to implement, just want to triple check we're on the same page before I get started. lmk if that sounds ok!

mattakamatsu commented 2 years ago

@blairlyons That all looks accurate to me! I like the idea of normalizing bond length to starting or theoretical lengths, and plotting the average ± std at first. I think this should give us enough info to point our way toward a quantitative comparison with Schramm et al.

blairlyons commented 2 years ago

@mattakamatsu here's some initial results! 🎉 I'm not sure the twist metric is useful when there's a lot of bending?

If this looks ok, I can run the replicates in the cloud

mattakamatsu commented 2 years ago

@blairlyons This looks fantastic!! The trending upward of the twist metric is really interesting. I think we'll see more twist if we displace all the way to a 90˚ bend. Which I think is 173 nm? https://www.omnicalculator.com/math/arc-length Otherwise I think it's ready to run replicates. I'm also ready to share with Enrique to help us compare quantitatively to De La Cruz 2010 and Schramm 2017, if that's ok with you!

blairlyons commented 2 years ago

ok I bent the radial ones 90˚, the displacement only gets to 105 nm, but I'm using a radius of 75 nm and it's the euclidean distance on that plot, not the arc length. I also added some vector projection to get only the component of the normal perpendicular to the tangent, thinking this would remove the bending angle from the twist metric. The two metrics diverge in the new runs, we should probably talk about how to calculate this metric. Maybe it's fine without the projection, but when I look at the spatial output it doesn't seem to match...

Those links are updated:

I'm fine with you sharing with Enrique whenever you think it will be useful, probably would be good to know that these are comparable before I run in the cloud. thanks!

mattakamatsu commented 2 years ago

I think it's ready to run replicates in the cloud! And then can look at the twist metric together (maybe with Enrique depending on when he joins the conversation)

On Tue, May 24, 2022 at 1:25 PM Blair Lyons @.***> wrote:

ok I bent the radial ones 90˚, the displacement only gets to 105 nm, but I'm using a radius of 75 nm and it's the euclidean distance on that plot, not the arc length. I also added some vector projection to get only the component of the normal perpendicular to the tangent, thinking this would remove the bending angle from the twist metric. The two metrics diverge in the new runs, we should probably talk about how to calculate this metric. Maybe it's fine without the projection, but when I look at the spatial output it doesn't seem to match...

Those links are updated:

I'm fine with you sharing with Enrique whenever you think it will be useful, probably would be good to know that these are comparable before I run in the cloud. thanks!

— Reply to this email directly, view it on GitHub https://github.com/simularium/vivarium-models/issues/5#issuecomment-1136527023, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD25SOT2JDOPZILH34OC3STVLVQONANCNFSM5PC5Y6HQ . You are receiving this because you were mentioned.Message ID: @.***>

-- Matthew Akamatsu, PhD Assistant Professor @.***> University of Washington Biology https://www.biology.washington.edu/people/profile/matthew-akamatsu

blairlyons commented 2 years ago

ok! I'll get them started

blairlyons commented 2 years ago

TODO: