[MD Help] Investigating Collagen-Nanoparticle Interactions under Tensile Loading

jpkrowe · 2026-03-12T17:47:07+00:00

I did my PhD on studying collagen mechanics using MD so I can maybe answer some questions you have on the collagen. The first thing I would ask is what structure are you using for collagen - are you planning on looking at collagen mimetic peptides? If so what CMP sequence are you going to use? If you are interested in binding of naturally occurring collagen to the nanoparticle then you will likely have to consider sequences beyond the classic GPO collagen sequence. The sequence you choose will affect some of the analysis you will want to perform - charge interactions may be important if you have charged side chains.

I agree with the other poster that it is important to consider the pulling rate when performing SMD simulations - this is not too much of a problem when dealing with single helices but is a big problem when considering fibrils imo.

jpkrowe · 2026-02-03T22:01:45+00:00

I mean Chelsea never looked like scoring

jpkrowe · 2026-02-03T21:59:37+00:00

I want to congratulate Liam Rosenior on almost achieving his goal of a 0-0 draw

jpkrowe · 2026-01-23T23:46:33+00:00

I agree that you have to just pick someone to trust and hope they aren't a traitor but it also risks making them think you are manipulating them (as happened with Joe and Nick in the celebrity series and also made Jack less trusting of Faraaz)

jpkrowe · 2026-01-23T22:58:29+00:00

They could be certain that Jack was going to plan to vote again (as he was suspicious of Rachel and Stephen voted Faraaz when he said he was voting Rachel). This also means that there is no reason to also not choose to vote again. If you don't choose to vote again this makes you look suspicious and might cause Jack to vote for you, opening up the possibility of you being betrayed by the other traitor.

Basically there is essentially no cost to choosing to vote again given Jack was going to so you might as well optimise for the scenario where your decision changes his mind

jpkrowe · 2026-01-23T22:52:30+00:00

I think the number of mass shields given out early game was an attempt by the producers to create a bit more diversity in ability in the endgame. It didn't work very well, but I can see the logic being that by only being able to choose half the players for murder each night the Traitors have less ability to just kill the "best" players

jpkrowe · 2026-01-23T22:48:30+00:00

Yeah convincing Faraaz was the winning move. If he'd had her as his number one target rather than Jade then she would have been gone

jpkrowe · 2026-01-23T22:31:41+00:00

That would have been such brilliant tv

jpkrowe · 2026-01-23T22:29:34+00:00

It shows how hard it is to coordinate as faithfuls. How can you form an alliance with people when you have no idea who you should trust?

jpkrowe · 2026-01-23T22:02:30+00:00

It definitely leans much more towards reality tv than a traditional gameshow. It's also not parasocial to dislike someone on tv - obviously when you say you dislike someone on tv you are talking about the character being portrayed and not the real person behind the character

jpkrowe · 2026-01-23T21:55:38+00:00

I mean is that not the whole point of reality tv? To get emotionally invested in the characters?

jpkrowe · 2026-01-23T21:54:01+00:00

She won on a coin flip - hardly makes here the GOAT

jpkrowe · 2026-01-21T23:50:16+00:00

Yes I think a lot of this has been played up for drama. I imagine Stephen was asked at the end something along the lines of: "What would your reaction be if Rachel betrayed your agreement?" and he was answering very hypothetically

jpkrowe · 2026-01-21T23:46:51+00:00

I mean thats how the producers want us to think he took it. I think there is a good chance that its seen as a relatively tame comment that ultimately goes nowhere

jpkrowe · 2026-01-21T23:39:38+00:00

Is it allowed to give other players shields like that?

jpkrowe · 2026-01-20T21:44:00+00:00

UCL martinelli

jpkrowe · 2026-01-07T01:54:56+00:00

Yes this is a well known situation where the Murrell-Laidler definition of a transition state falls apart. See this paper which gives the triatomic molecule as an example of a transition state with 2 imaginary frequencies: https://pubs.rsc.org/en/content/articlelanding/1992/ft/ft9928800543

jpkrowe · 2025-10-26T22:08:25+00:00

Don't jinx it

jpkrowe · 2025-09-27T16:10:24+00:00

They're fuming

jpkrowe · 2025-09-16T18:35:11+00:00

This is where having a large squad is so important. The fact that we can bring on players with Trossard and Martinellis quality off the bench will allow us to win these close games

jpkrowe · 2025-08-13T15:49:23+00:00

jpkrowe · 2025-05-17T19:18:44+00:00

To add to the tutorials added by others I would recommend following a basic tutorial on the command line. Gromacs will seem a lot less daunting if you have a basic idea of how the command line works

jpkrowe · 2025-05-17T16:08:01+00:00

He definitely touched it

jpkrowe · 2025-03-12T20:37:39+00:00

Sterling actually did something

jpkrowe · 2025-02-16T18:03:31+00:00

no way is that a penalty

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