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- เผยแพร่เมื่อ 16 พ.ค. 2024
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#molecular_dynamics
Patreon:
patreon.com/NanoRooms
The BTS of the videos are here!
Cited articles
The main paper for this video
Boonserm, P., Somsoros, W., Khunrae, P., Charupanit, K., Limsakul, P., & Sutthibutpong, T. (2024). Allosteric Signal within the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein Mediated by a Class 3 Monoclonal Antibody Revealed through Molecular Dynamics Simulations and Protein Residue Networks. ACS omega, 9(4), 4684-4694.
More on the communicability matrix:
Arrigo, F.; Durastante, F. Mittag-Leffler Functions and their Applications in Network Science. SIAM J. Matrix Anal. Appl. 2021, 42 (4), 1581−1601, DOI: 10.1137/21M1407276.
In depth deep dive into molecular dynamics:
manual.gromacs.org/current/in...
a great PCA explanation video:
• StatQuest: Principal C...
@MoBioChem is also a great channel for explaining MD
Molecular Nodes is a 3D animation library created by @BradyJohnston
Here’s a link to the repo: github.com/BradyAJohnston/Mol...
big thanks!
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![🔴 [TRỰC TIẾP] Tứ Xuyên (Trung Quốc) VS U20 Thái Lan | Cúp VTV9 - Bình Điền 2024 | JET STUDIO](http://i.ytimg.com/vi/bguJ41PcW0c/mqdefault.jpg)
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We can help scientists by processing data from Rosetta at home and folding at home ❤
Double posting as backup against stupid TH-cam from arbitrarily DELETING my posts for no reason:
I do differential algebra research, based on my math PhD and math Masters, with a preferred application to bionanotechnology, my chemical engineering BChE degree and my biotechnology A.S. degree.
I attend the weekly KSDA (Kolchin Seminar in Differential Algebra) Zoom meetings.
Here is one from a few weeks ago
"Identifiability from a Few Variables in Biochemical Reaction Networks"
Mercedes S. Perez Millan, University of Buenos Aires
th-cam.com/video/8elQj7h4A6U/w-d-xo.html
"Identifiability and Model Reduction of Pharmacokinetic Models of Carbon Stable Isotope Breath Tests"
Andrew Brouwer, University of Michigan
th-cam.com/video/Rvg0Rrejddw/w-d-xo.html
We DAs seek exact solutions to systems of nonlinear DEs.
Microarrays are superior method to cach molecular drift not simulation
Well made content. Thank you. God bless. Jesus loves you!
Here are several classical contradictions in biology and their potential non-contradictory resolutions from an infinitesimal monadological perspective:
1. Origin of Life Paradoxes
Classical: Paradoxes around abiogenesis, homochirality, first replicators
Non-Contradictory: Infinitesimal protolife monadic transitions
dsi/dt = κ Σjk Γijk(ℓ)[sj, sk] + ξi
ℓ = f(n1...nm) is monad configuration
2. Molecular Binding Paradoxes
Classical: Paradoxes in protein folding, substrate specificity
Non-Contradictory: Nonlinear monadic multiplex resonances
|Φ> = Σn cn Un(Sα) |0> (superposed protolife states)
Wn,m = (monad binding coefficients)
3. Genetic Paradoxes
Classical: Paradoxes like non-viability of certain gene combinations
Non-Contradictory: Pluriverse-valued genetic realizability
⌈Φ⌉ = {Ui(Φ) | i ∈ N} (genotypes as monadic realizations)
Φ ↔ Ψ ⇐⇒ ⌈Φ⌉ = ⌈Ψ⌉ (equivalence over pluriverse)
4. Neurological Binding Paradoxes
Classical: Binding problem paradoxes, separability paradoxes
Non-Contradictory: Relational pluriverse neural geometries
|Ω> = Σn pn Un(Nn) (superposition of neural monad states)
Geodesic[Nn](a,b)→Paths[Σn p(n)Uap →q Ubq] (experience paths)
5. Evolution Paradoxes
Classical: Paradoxes like irreducible complexity, Muller's ratchet
Non-Contradictory: Infinitesimal transitions on fitness landscapes
dfx/dt = Div(∇fxFx) + ξx (monadic exploratory dynamics)
Fx = Γ(x, {xj}) (catalytic fitness relations)
6. Paradoxes in Embryogenesis
Classical: Paradoxes like random determination of chirality
Non-Contradictory: Resonant infinitesimal monadic transitions
dαi/dt = Σj Γij(αi,αj) + ξi (coordinated determinative algebras)
Γij = f(ni, nj, rij) (chiro-isomeric transition charges)
The key themes are using infinitesimal monadic transition processes, relational resonance algebras, pluriverse-valued realizability, and higher-dimensional resonant superpositions to resolve paradoxes stemming from classical separability assumptions, random determinacy, and failure to account for integrated pluralistic structures underlying biological phenomena.
By building models from infinitesimal relational pluralisms as conceptual primitives, the apparent contradictions dissolve into coherent higher-dimensional resonance dynamics between monadic elements and their catalytic interaction algebras across scales.
I'm a burger flipper in the kitchen of McDonald's and this is by far the greatest piece of science education I have ever seen.
So this is why my orders taking so long
Bro is SpongeBob
😂😂😂😂 I liked your joke... But, it is actually amazing (and dangerous) what this knowledge can do..
@@RobertoHernandez-gp3guVery interesting and in depth comment!
You need a raise !!!
I’m a quantum chemistry PhD student, specializing in solid state simulations. One of our laboratory divisions deals with simulations of biological molecules, and for the last four years I thought I was stupid for not understanding what they were talking about. Thank you. This is the most comprehensible introduction to the topic I have ever come across.
As a guy working on the biomolecular side of things in a lab full of material guys, I can reassure you that we feel just as stupid about your stuff as you do about ours 🤣
Hey , how much do quantum chemists make? in $
I am a molecule and this is by far the best description of my family and me
I am a researcher in the field of NMR and theoretical chemistry and this is by far the greatest piece of science education I have ever seen.
In my past I worked as a researcher in MD simulation. I feel kinda sick how everything here is kinda guesswork, heck, mostly just blindly groping. I always wondered if there any way to map these interactions (between side chains and with the solvent) in real time. I heards about Femtosecond X-ray Crystallography, but that's very costly and out of reach for most lab and out of reach for all labs for many proteins.
It's really rare to see this quality of science education outside of a master's degree lecture. You've really mastered the art of presentation
Thanks, I’m flattered! I’m only an undergraduate student.
Most underrated TH-cam channel ever!!!!
facts
I'm a quantum physician from the future and this by far the greatest piece of science education i have ever seen.
Physician
lmao Ic what u did there
I'm a high schooler, and this video single-handedly integrated concepts I learned in Physics, Chemistry, Biology, and Math into something extremely engaging. At my meager level of knowledge, it is rare to enjoy much of the "fun" parts of science while understanding all the concepts and lingo behind it.
I've always wondered why non-competitve inhibitors could affect something on the other side of the compound, and this video inadvertently explained it better than any of study materials I've gone through lol. The best part is that I discovered this while procrastinating, so it doesn't even feel like studying, even though I am learning. This is the joy of learning-- it shouldn't be separated by arbitrary subjects, or between school and life.
Studying doesn't have to be boring. After all, it is just another way of learning. Seeing these interdisciplinary concepts be connected and applied together to help me understand something I want to learn out of my free will is the most satisfying feeling in the world.
I'm only a medical student and a science enthusiast so I can only understand this on surface level, but still quite fascinating to see all the complex methods we have developed to understand how molecules work and interact.
This is the part of science that intrigues me the most. Understanding the most fundamental concepts in biology, chemistry, and physics, understanding what the most basic parts mean, and seeing how these parts all work together to make the bigger things happen
Great comment , I'm interested in this too
I live behind a bin at the back of Walmart on 15th street. This video has changed my life for the better.
"Let's say you're an alien trying to understand how a car works" sounds like something Jerma would start a rant with.
very interesting! my GNN course mentioned how these structures are used to predict timesteps in MD sims, but the course is more focused on epidemiology and interactome matrices.
Amazing... The way he explained and made the concept so beautiful.. Thanks for making these kinda content
This is absolutely amazing... It's so masterfully done that I am genuinely stunned and at a loss for words. If there was an equivalent to the Nobel prize in educational content this should win it. Keep this up man, truly amazing work.
Just 5 mins in, subscribed. Absolutely fantastic content. ❤
11:25 ah the dependency matrix of cyclomatic complexity. oh wait, this is not software.
my goodness, I’m a data scientist working in geoscience research and I’m blown away! I wonder what the network diagrams of the communicability matrices look like..
As big as our universe.
As a cell biologist who has some experience in protein biochemistry, I thought this was an amazing video. I used to do a bit of protein biochemistry a few years back, but now mostly working with imaging and cell biology. I love your videos. So beautifully crafted!
I’m in a PhD for molecular dynamics and this is the video I wish I had when I started. This is amazing!
Thank you for not hiding the equations!
As a pharmacy student - the explanation of molecular modeling is on top!😀
This visualization is perfect. Any body who is good at physics puzzles with the aid known combinations of chemical structures would be good at solving these instabilities. These are puzzles I am really good at.
Apart from the subject itself which is Top Notch as well, This video is an excellent practical demonstration of The Scientific Method.
If TH-cam is Hollywood, This video deserves an Oscar.
Thank you so much for posting this, I have Asperger's and this makes sense ❤❤❤
The visualizations and the style of the video are of very high quality! Incredible work
This video approaches to what I always have wondered about. That was fantastic!
I'm a 50 y-o autodidact and this is by far ONE of the greatest piece of science education I have ever seen.
Incredible video
Man this brings joy to my day as a biology student, thank you
I've always wondered how we studied these interactions, I would have never guessed that it was as clever and interesting as it was shown.Molecular biology is really all about multiple disciplines huh.
Love this! I’m just getting started in structural biology research and think this is a great resource for science education
I study quantitative biology and I have to say you're doing a great job at simplifying complex biological mathematical concepts - continue the great work! I also loved your video on morphogen gradients!
you've really done a very good job mixing between biology and physics in a extremely creative way, keep it up
Im a bioinformatics master's and this just perfectly described a course on structural Bioinformatics I took. Phenomenal work!
2:19 he thinks exactly like me. Thank you for catering my curiosity!
From a standpoint of the molecular biochemistry that constitutes life, these videos are visually and didactically excellent, and I wish I had discovered them when I was studying this. Well, repetitio est mater studiorum, and since I’m of the belief one is never done studying in life, I am very grateful for these audiovisual repetition cards. My autistic brain approves muchly.
I've got to be honest I'm still confused and I can't really grasp how this works, but it's cool to see this
Thank you for making and sharing this.
perfect video! I am doin it with a different Virus, but the workflow is the same. Love it 10/10. If i need to introduce my topic to non sience people, i'm gonna use this kind of introduction.
Maybe a follow up Video would be how to use that together with crystallographie or NMR to advance drug discovery.
Words can't describe how amazingly good this video is. Thanks.
Absolutely masterful video composition and exposition!
How did you create such wonderful animations?
Would like to pursue creating this type of content, if you have some pointers on how/where to start!
Well, I used a combo of blender, manim and keynote. If you want an inside scoop of the very detailed processes, consider becoming a patreon member!
@@Nanorooms keynote?
great ! keep making videos
this is a high quality piece of sciense man. thank you for such a content
Physics makes me appreciate the world
You just proved that there's no free will and we're all just moisture machines.
me when i use basic logic:
my thoughts exactly
M O I S T
Incredibly well put together! Not too simple, not too complex that you can't follow. Not to be picky, but in case it helps future views and outreach, I would recommend turning up the audio as it is pretty quiet, and possibly some quick dynamic range compression so that the volume levels don't vary when you talk a little quieter or louder. Anyways I'm happy I found this channel and will be watching more!!
Really thanks, too much apreciatted that you take this sience ( until now, underrated by the science divulgation community ) and explain even better than i would do it, from a full time MD student... thank you
What an amazing video!
I'm a graduate student in Biological Sciences and I use this method in my undergraduate research! I really enjoyed the video, congratulations!
I realy love your work bro, stay scientific!!!
MOMMMM NEW NANOROOMS JUST DROPPED
wow... just... pure wow..
im so amazed to see this. im currently studying physics, and i hate it, but this inspired me to learn physics and try to understand it better ❤
Unexpected three body problem reference
This was an absolute pleasure to watch
Great explanation 👍
beautiful video. one of the best I have watched. lovely guys. keep going. By next month, probably 100 K subs and soon a million. Amazing!
Somewhere between the scale of the atom and the molecule is where the weird rules of quantum weirdness transition into Newtonian common sense. It's fascinating to see how well the interaction between drugs and proteins actually makes common Newtonian sense.
Yet another incredible video!!
I started studying MD, specifically CGMD this past year and wow man you did an exceptional job with this video, I can only imagine what you've got in the pipeline for the future!!
I was wondering how long does it tend to take you to do your calculations? And what kind of time step are you able to run with?
Thanks and keep it up!
All in my friend’s paper in the description
My physic teacher send me this clip . This is so perfect ❤
So neat, bro. You're so cool! Thanks. Keep making more💛
Fantastic video, one of the best educational videos I've seen. Do you have any book recommendations related to topics similar to this or molecular biology in general? :)
Lehninger Principles of Biochemistry. It was one of the books we had at uni, and it has EVERYTHING you might want to know about the building blocks of life, metabolism, and how it all comes together in an entropy-defying biochemical symphony for the time of life in any being. Don’t let the size scare you away. The book could pass for a murder weapon, but that’s just because it needs to be that big to contain all that knowledge it can convey onto you.
@@TourniquetTwin Thank you so much for the recommendation, I'll definitely check it out!
Lehinger and Stryer are both awesome. I’m using both in my courses.
The location of every amino acid in every protein in this structure is specified by digital information in base 64 encoding, one "digit" per amino acid.
The information came first.
1:42 Newton's laws of motion and molecular dynamics simulations. 3:28 The three body problem.
Can knot thory be used for this application?
I appreciate you’re bringing awareness to the truth that deep down all we are is Lego blocks, mechanical computers, and miniature machines.
Could you please make this a series?
As a senior undergrad molecular neuroscience student, it's crazy how this is the most educational video I have yet to see and it wasn't even from a course or professor. If only orgo professors gave these kinds of videos lol.
That’s funny. I’m actually a Junior undergrad 😂
That's freaking insane dude, is your major neuro as well?@@Nanorooms
Nah. It’s called integrated science. I mixed math biochem and chem
Nice explanations. I like the Taylor series expansion too. Also, the communicability matrix looks a lot like a 2-D FFT. I wonder if any additional information could be obtained by doing an FFT or some other transform on the data? Anyway, nice presentation 👍🏻
❤love it
As a physics major who’s quite passionate to learn about life science as well, I can safely say that biophysics is perhaps the coolest subject you can take. Just such a shame that it’s not offered here in my university because of how few people are taking it
If you study physics and a bit of biology in undergrad, you may be able to do biophysics in grad school.
I'm currently doing a major in physics and a minor in biology. I'm also working in a biophysics lab. You could maybe find one in your university and ask the prof you could work for him. It's a great way to learn biophysics
Soy un estudiante de secundaria colombiano, y espero algún día entender inglés para entender esto
0:56 that is exactly what they do but the. With X-rays to find the structure. I have seen the place where they found the structure of the sars protein at bessy II.
I think your comment got broken.
Incredible video.
i stick currants in buns..
(making currant buns)
nice video 🙂
Consciousness is all there is.
What do you think of RFDiffusion All-Atom? pretty cool right, RFAA too
great video!
Very interesting and those graphics are fantastic. Is this the same tech as in those simulations that hopefully will replace animal testing in the future?
Amazing
Also you just earned a subscriber
I am a student right now and I am in love with this field of study. What college degrees and grad school programs would align with this area, currently I am trying for a biochem degree.
Biochem would fit nicely. An even better option would be bioinformatics.
I’m a molecular biologist and this aligns with a lot of what I do. Molecular biology is a lot of these field wrapped up into one (Biochem, Bioinformatics, pharmacokinetics, genetics, immunology, virology…..) go get a good MCB degree! (Molecular & Cellular Biology)
Awesome video but as a chemist I can’t stop thinking about the 2HN- at 2:00 😖
Do keep it up though! Just not that notation hahah
Is Ochem your nightmare or sumthn? 😩
@@Nanoroomsnah O Chem is my jam I do it for a living! Would just be better to notate it as H2N-. So basically I’m just being a pedantic dork.
Awesome explanation and demonstration of adjacency and communicability matrices btw. It makes the effect of drugs on their drug targets feel really intuitive!
@@Nanoroomsiupac is what he's asking for
Oh yeah lolll I just realized I made a notation mistake
how do you make these videos? I hope you can make some tutorials explaining the process of such videos
Okay yeah man that's like the coolest thing ever
I can’t wait until education is universalized and classes start using info videos and such like this
Great video
Im edging rn and this is greatest piece of sceince education I have ever seen
💀
🤔
What field of science is this, I’d like to get into it
how did you find this video...?
i asked for biology and physics
but is it chemistry??
11:14 exp expansion jumpscare
So we're just a bunch of vibrations? We've been vibin from the start?
Mom! Nanorooms just dropped again!
Nanorooms what is your education background?
Currently, honours in integrated science at UBC
@@Nanorooms that’s dope. Best of luck.
congrats on 100k views, my friend! i know exactly how much work you put into this project, and i am proud to see that it got the results you were hoping for - all that hard work paid off!
here's hoping that this vid will go to the moon and even further! 🚀
Thank you, my friend
Someday we will create a model of the entire cell, and then the entire body. Then it will be possible to do incredible things, including reversing aging.
Maybe even cure cancer!
@@timetraveller2818 curing cancer is much easier than aging
Or simulate life in a computer, simulation theory indeed.
MY GOAT GOT HIS BRILLIANT SPONSORSHIP 🙏🙏🙏🙏 I LOVE YOU
Did you use ChimeraX?
If an alien came to earth he would say, that car must have evolved out of the earth over millions of years.
Yooo a gem
I work in structural biology (wet lab doing x-ray crystallography and cryo-EM) and we don’t trust MD at all. It’s funny to see that different groups of people doing MD can come up with different answers to the same system - yes I’ve even heard a group saying Arieh Warshel’s model is “crude”.
Why? The models are too simple and often can’t take in account of the solvent’s behavior due to computation power limits. Even with QM/MM, the model can only understand what the experimenter puts in, which can miss some serious things.
Also a lot of proteins can have turnover time magnitudes higher than MD could simulate.
In summary, MD is interesting but often quite limited just on its own.