[timtimmy]

You are right, they move insanely fast. The average speed of a medium-sized protein is about 5 m/s. Inside an E. coli, any two proteins will encounter each other at least once a second [0] (this book is incredible).

My simulation is inaccurate in terms of Brownian motion. It is slowed down and smoothed for illustrative purposes. It should be more violent. Nice idea with blurring, I'll think about that. The code is on GitHub. It requires a VR headset, and it is frankly a little clunky and "research code" in terms of the UI. But check it out :D [1]. The next version will support larger simulations on the GPU and a more friendly UI. I have friends at the Scripps institute who work on similar stuff, check them out [2].

[0]: David Goodsell (2009) The Machinery of Life https://www.amazon.ca/Machinery-Life-David-S-Goodsell/dp/038...

[1]: https://github.com/timdecode/LifeBrush

[2]: https://ccsb.scripps.edu/cellpaint/

[DonHopkins]

Thank you for publishing the code as open source! I'll check it out. Do you have any idea how much work it would be to adapt it to Unity3D's ECS (DOTS: Data-Oriented Technology Stack) and shader system, or somehow get it running on WebGL? At least the simulation and rendering part, if not (yet) the VR stuff, so it can reach the widest audience.

https://unity.com/dots

I really love the part in your interactive simulation overview, at 2:58:

LifeBrush - An overview of our illustrative simulation canvas

https://www.youtube.com/watch?v=5LBHRyGxLGI

2:58> The ribosome uses tRNA to match mRNA codons to amino acids. We paint a cloud of tRNA near the ribosome. tRNA, molecular agents, need amino acids. So we paint a cloud of of amino acids nearby. Brownian motion brings tRNA and ribosomes together. But that takes a long time. However, our system is interactive and immersive. So we grab the ribosome and move it around. Now we see how the ribosome marches along the mRNA, with tRNA depositing amino acids onto a growing poly-peptide chain in blue. We reach the end of the mRNA, and the mRNA and poly-peptide chains are released.

So in order to avoid waiting for brownian motion to do its thing over time, you just grabbed the ribosome's lazy ass and dragged him over near the mRNA, then threaded it into his jaws, and waved him around through a cloud of amino acids and tRNA to feed him, so he sucks up the tRNA pasta and mRNA meatballs and amino acid sauce, just like Lady and the Tramp eating spaghetti to Bella Notte, and then he pumps out useful proteins, just like the Golden Goose.

Lady and the Tramp (1955) Scene: 'Bella Notte'

https://www.youtube.com/watch?v=XNQWbZ9sO3Q

The immersive interactivity is (in a good way) like the Libertarian wet dream wish-fulfillment of the invisible hand of unobservable market forces, or the Intelligent Design pseudo-scientific fantasy of God directly intervening in the affairs of molecules! Ribosomes could be the next Tamagotchi! ;) Ribosomegotchi?

You obviously know this stuff well, but I want to mention that your videos "LifeBrush: Discrete element texture synthesis overview" and "LifeBrush: Bunny-planet design session" using Greg Turk's Stanford bunny impress me as an homage to his work on mapping bunnies with 2d textures, and Andy Witkin's work on reaction-diffusion textures, and also looks inspired by the Photoshop smart clone tool.

LifeBrush: Discrete element texture synthesis overview

https://www.youtube.com/watch?v=624F5iaCKco

LifeBrush: Bunny-planet design session

https://www.youtube.com/watch?v=L482dpH9S8o

Greg Turk

https://en.wikipedia.org/wiki/Greg_Turk

Stanford Bunny

https://en.wikipedia.org/wiki/Stanford_bunny

Andy Witkin

https://en.wikipedia.org/wiki/Andrew_Witkin

Andy Witkin's gallery

https://www.cs.cmu.edu/~aw/gallery.html

Reaction Diffusion Textures. (animation) 1991. Nonlinear partial differential equations as a means of artistic expression. Shown at SIGGRAPH '91 electronic theater. mpeg (209K).

https://www.cs.cmu.edu/~aw/mpg/rd.mpg

Reaction Diffusion Textures. 1991, with Michael Kass. Nonlinear partial differential equations as a means of artistic expression. This image won the Prix Ars Electronica '92 grand prix for computer graphics. postscript. pdf. citation.

https://www.cs.cmu.edu/~aw/pdf/texture.pdf

Using Particles to Sample and Control Implicit Surfaces. 1994, with Paul Heckbert. Quasi-physical particles that float on an implicit surface. We use mutual repulsion and fissioning to quickly obtain a good sampling of the surface, and to maintain it as the surface deforms. postscript. pdf. citation. mpeg(23K). BIG mpeg (868K.)

https://www.cs.cmu.edu/~aw/pdf/particles-reprint.pdf