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MDsimulator
Добавлен 1 июн 2009
Structure of supercritical water (molecular dynamics simulation)
Molecular dynamics simulation of supercritical water (temperature is 673 K, density is 0.3 g/cm^3). Flexible SPC water model was used.
List of my MD simulation videos: ruclips.net/user/mdsimulator
List of my MD simulation videos: ruclips.net/user/mdsimulator
Просмотров: 4 424
Видео
Oil and water separation by molecular dynamics simulation
Просмотров 60 тыс.11 лет назад
Molecular dynamics simulation of oil (pentane, C5H12) and water separation at 300 K temperature and 1 atm pressure. List of my MD simulation videos: ruclips.net/user/mdsimulator
Helium atom trapped in fullerene (C60) and dodecahedrane (C20H20)
Просмотров 10 тыс.11 лет назад
I simulated the dynamics of a helium atom trapped in fullerene and dodecahedrane. Helium in dodecahedrane was achieved in 1999 (See details in this paper pubs.acs.org/doi/abs/10.1021/ol991037v). List of my MD simulation videos: ruclips.net/user/mdsimulator
![Water vaporization at the water surface [Molecular Dynamics Simulation]](http://i.ytimg.com/vi/B3cXuisH8PI/mqdefault.jpg)
Water vaporization at the water surface [Molecular Dynamics Simulation]
Просмотров 17 тыс.11 лет назад
Molecular dynamics (MD) simulation of water vaporization at the water surface. Temperature is 370 K (97C) and MD speed is 0.6 ps/second. Movie was drawn with VMD 1.9.1 program with the Tachyon module. List of my MD simulation videos: ruclips.net/user/mdsimulator
Molecular Dynamics Simulation of Water
Просмотров 42 тыс.15 лет назад
MD simulation of water List of my MD simulation videos: ruclips.net/user/mdsimulator
teacher how we can conform that the system is equilibrated (from which parameters we can conform aboute the structure is in the stable state) thank you teacher
How Can i get parameters of oil
C00033033-Leishmania tarentolae proteasome 20S subunit (6QM7) Molecular Dynamics Simulation Watch video: ruclips.net/video/JClrPL0IHYg/видео.html
C00033033-Leishmania tarentolae proteasome 20S subunit (6QM7) Molecular Dynamics Simulation Watch video: ruclips.net/video/JClrPL0IHYg/видео.html
Would this simulation be more of an emulsification representation as the oil is aggregating to form a sphere/micelle like structure? like if it was separation there wouldn't be complete surrounding of the oil droplet would there? please correct me if I'm wrong :)
Why is Water Shaped Like That?
A water molecule has only three atoms, so intuitively it should have a linear shape. But because oxygen has free electrons, and the electric charge makes the electrons avoid each other, the molecule shape has to be in a configuration that tries to maximize their distance. So it gives it a bent shape. However, if you are wondering why it doesn't have a spherical shape, that's because it doesn't really affect the simulation.
From Chem H
Why did this video make me laugh?
beautiful visualization
Real time TEM image of liquid-vapor interface structure ruclips.net/video/fiLPDAAEXVo/видео.html
Real-time TEM observation of dynamic structure of liquid-vapor interface at nanometer resolution in electron irradiated sodium chloride crystals (7/7) Paper link: @t Video 1 - liquification: @t Video 2 - Fluid dynamics: @t Video 3 - Brownian motion in liquid: @t Video 4 - Brownian motion in vapor: @t Video 5 - Nanoparticle fusion: @t Video 6 - Nano-motor: @t Video 7 - Interface structure: @t
what software did you use to do this simulation?
its in the description: VMD
can you explain how to do this calculations by programs, what are the required programs please?
XD
I cant understand anything
Hi guys, is it possible to simulate the bioabsorption process by GROMACS or any other MDS apps? it's necessary. Thx
What if science can trap the element 118 in a thing like this? will be a stable one?
It will still desintegrate
How kind of jail do you like? -fullerene ones
Definitely not the dodecahedrane one. Looks unbelievably claustrophobic! 😖
I also want to simulate the water evaporation process. please send your code for me, if its possible.
I want to know what unusual and useful properties they have. I want to know if they are stable and if sigma aldrich could make a bottle of 99% purity stuff.
Aquaman approves this video.
Does it float?
Can I use your video for educational purpose? Thanks.
wow, it took less than 1 ns, so quick~
Hi this is very interesting.Actually I'm trying to make a model of fullerene for an inspection.can you just suggest me how I can make?plz.
@Seth Martinez Thank you very much. But you replied me after two years.
Can you please provide your mail id??
When you find the password to your university’s super computer:
Usually some are open for students but for homework and coursework only 😂
I heard of helium trapped in carbon fullerenes. They said the helium is not just any helium, but a form containing 200 times more of one atom than normal. 1:32 looks like a radiolarian.
Hi professor. I'm currently and undergrad Biochemistry student. What is the computational requirement to simulate a cell or even an organ down to the atomic level? How long will it take to render a few seconds animation on a modern super computer? And on a quantum computer? Thank you.
Probably just 24 of the desktop computers in my computer lab (they are like super fast with graphics and computing) could all do an entire cell. But seriously dude, thats a question for Quora.com
i don't think you could simulate a complete cell atomistic model with current computational machine xd, i simulate 700000 atoms model with most powerful GPU (tesla v100) and 40 CPUs, and it runs 0.5ns simulation-time/day. But the number of atoms in a cell is 100,000,000,000,000 hahaha...not even talk about a organ, btw the computation time of MD is O2. That is why we usually simulate just a little part of cell, like a hole on the membrane, ligand and enzyme.
@@user-lr4rp5ch2e what If we use Quantum computer And AI
Dev do futuro I don’t really know the capability of quantum computer, so I cannot answer you this question. About AI, some people use the AI technique to obtain the meso-scale property of the granular particle, so when they try to simulate the whole cell, the component is no longer atoms but those granular particles, and it reduces lots of computation. I am not sure wether we can call it MD or not, but if you say “can we simulate a cell with particle method?” The answer is yes and just like i mention above. I’ve seen a researcher in APCOM2019 mini symposia who simulates a cell behavior by that.
@@user-lr4rp5ch2e thanks for the answer. Have you seen Google AlphaFold? Can It help in This process? ruclips.net/video/GQH-zWUylPY/видео.html
Does anyone know the name of this song?
I need to know asap.
FUUUCK THIS SONG'S A WOBBLER
If the C60 is like a lobster pot for the Helium. How is the Helium atom getting in there?
We make fulllerene by folding graphite planes into a cage. You first put the Hellium atom on the plane, then fold it around the Hellium atom.
@@wurttmapper2200 Ha, ha, ha
Hmm... could a helium nucleus be trapped in C60-? could multiple? I think it might get pushed out, but I'm not sure.
thanks for nnice and intrsting video.................................
Stability is a concern research and testing needs funding. In the early nineties I also discussed the possibility of he inside C60 I want know exactly what the process is so I can figure out the cheapest way to mass produce this.
Weightless and molecular strength are just 2 interesting measures. Also oscillations will effect microjoules of energy there is so much to learn here anyone that laughed @ the wright brothers will shut down
This has huge potential if we could mass produce it cheaply. Safe space travel without rockets to Nanites with medicine
How would this replace rockets?
Is this demonstrating clathrate hydrate formation?
is there no gravity?
gravity is on the left wall in this simulation
Hi! Can I have the source code of the simulation? I am having a research on driven MD but I'm quite poor in programming.
What I'm wondering is why, sometimes, the oil molecules seem to dissapear/teleport.
This simulation is set in such a way that, when a molecule leaves the box at one side, it enters the box on the opposite side. This is called a 'periodic boundary condition'. It's a trick for simulating large systems
+Cystlib DFT? Ab initio? using planewave basis?
+Yonoodle Hsieh I don't think any quantum mechanical based methods are being in this simulation but instead a force field is being used
@@Cystlib Nice. PBC looks much more weird when the molecule being simulated is larger than the box, like protein molecules. At times its almost hilarious.
Hey guys, I am chemistry undergrad and I want to learn all of this. From the very beginning to possibly simulating cell walls and $hit. Can anyone help me please. Like I don't even have a clue where to begin with ? What is all this DFT Force field Ab initio Amber etc. etc. 😭.... I have pretty good computer. And I wish I knew all this so that I can simulate molecules and reactions, instead of playing games in it. Please can anyone help, where should I begin, how should I begin, I want to be learned like you all guys are in this field. Thanks ❤
How much time an He atom can stay in a C60 cage ? (In air or in water) ?
Time should not be the issue causes of molecular instability is. Avoidance of instabilities requires more research. The potentials are so huge that I am surprised it took so long. We JFK and the moon landing type of motivation to get this done as it should become another giant leap for mankind. So sad to see something like this progress so slowly
which tool was used to perform simulation and visualization ? is the tool serial or supports parallelism ?
This is great. Love to see it done for quarks too
what software do you use for this simulation? thnks
after 10 years, still no answer . . .
Hi! Very nice video. I have two questions: 1) How did you produce the topology? 2) How did you visualize it? VMD? If so, how did you manage to have so high quality video?
+Kobalos the strucutres of fullerenes are produced by a process called nucleation (homogeneus or heterogeneus), google it to find out more ;)
Dosent water form h3o as the oxygen attracts the hydrogen to himself? Great video still, thank you
Not really. What you see (blue dotted line) is a temporary hydrogen bond and not a covalent hydrogen-water bond. Besides, the hydrogen is already attracted by the oxygen is connected to. :)
Can you please share which software is used here for the MD Simulation?
Do you also get a noticeable gas phase at room temperature in your simulations?
How long did it take to compute? on what system
I am intrigued. how did you do it? Can it be done in AMBER or GROMACS? if you have details please?
It's beautiful to see things deeper!