Particle in a Double well potential: A molecular dynamics toy example using openMM toolkit

in #steemstem2 years ago (edited)
Sort:  

The animated title pic really does a fantastic job of drawing the viewer in. I'll have to try that at some point. Also, very cool introduction to Brownian motion and how coding can help analyze this phenomena.

Wow, and I thought I worked hard on my posts :D

:P I have to improve a lot though.

I don't know if you have to, but everyone can and progress is in big part what life is about I think. :)

Oooo my God...... Interesting things there in your blog and for so many years I never really met most of the things in said in your blog, which simply means, am really educated today. And I enjoyed the class even though I didn't pay an tuition..... Lol
Lovely work in there and every time spent on your blog was really worth it. Great pictures too.
Great work and keep the science and technology spirit up

Posted using Partiko Android

😃

Wow, very nice. But I have to admit I have to read your other publications as well to get further into this subject. Where are these two minima from again? Don't get it!

Regards

Chapper

Hi @chappertron : Thank you for stopping by :) So the minimas are embedded in the potential function which I defined in the beginning.
This is how the function is:

You can see that there are 2 minimas at X=1 and X=-1 in this function.

See this plot(@ Y=0):

You saw the 2 minimas? Our particle toggles between these 2 states.

Oh of course! I have to look closer next time. Reminds me of my biophysics courses at the University used to.

So this equation would explain why the yellow dot moves as it moves in a crowd of smaller particles?

So this equation would explain why the yellow dot moves as it moves in a crowd of smaller particles?

No. If the yellow particle was allowed to move freely, Potential surface would be like a flat plane surface. But now if I compel my particle under this curvy potential with two minimas, that is what I am defining by this equation. Great question btw. I should have been more clear in the article. But I hope people read comment section too. :)

By the way, just defining this potential function won't make things alive. That's what the langevin equation is there. That equation gives life to the particle under whatever potential you define.

Very cool reply!

The langevin equation makes things become alive

That's mathematics at it's best.

Thanks again

Best

Chapper

Hello dexterdev!

Congratulations! This post has been randomly Resteemed! For a chance to get more of your content resteemed join the Steem Engine Team




This post has been voted on by the SteemSTEM curation team and voting trail. It is elligible for support from @curie and @utopian-io.

If you appreciate the work we are doing, then consider supporting our witness stem.witness. Additional witness support to the curie witness and utopian-io witness would be appreciated as well.

For additional information please join us on the SteemSTEM discord and to get to know the rest of the community!

Thanks for having added @steemstem as a beneficiary to your post. This granted you a stronger support from SteemSTEM.

Thanks for having used the steemstem.io app. You got a stronger support!

Hi @dexterdev!

Your post was upvoted by Utopian.io in cooperation with @steemstem - supporting knowledge, innovation and technological advancement on the Steem Blockchain.

Contribute to Open Source with utopian.io

Learn how to contribute on our website and join the new open source economy.

Want to chat? Join the Utopian Community on Discord https://discord.gg/h52nFrV

The animated title pic really does a fantastic job of drawing the viewer in. I'll have to try that at some point. Also, very cool introduction to Brownian motion and how coding can help analyze this phenomena.

Congratulations! This post has been upvoted from the communal account, @minnowsupport, by dexterdev from the Minnow Support Project. It's a witness project run by aggroed, ausbitbank, teamsteem, someguy123, neoxian, followbtcnews, and netuoso. The goal is to help Steemit grow by supporting Minnows. Please find us at the Peace, Abundance, and Liberty Network (PALnet) Discord Channel. It's a completely public and open space to all members of the Steemit community who voluntarily choose to be there.

If you would like to delegate to the Minnow Support Project you can do so by clicking on the following links: 50SP, 100SP, 250SP, 500SP, 1000SP, 5000SP.
Be sure to leave at least 50SP undelegated on your account.

Congratulations @dexterdev! You have completed the following achievement on the Steem blockchain and have been rewarded with new badge(s) :

You received more than 1000 as payout for your posts. Your next target is to reach a total payout of 2000

You can view your badges on your Steem Board and compare to others on the Steem Ranking
If you no longer want to receive notifications, reply to this comment with the word STOP

Do not miss the last post from @steemitboard:

The Steem blockchain survived its first virus plague!
Vote for @Steemitboard as a witness to get one more award and increased upvotes!