One example of a web of interrelated facts that I have concerns molecular simulations, with bold/italic denoting things that I have in my anki deck, or would make good cards.
One interesting thing about moleculaes bouncing around is that a nanosecond, which sounds really short, is actually a decently long time. Consider that molecules at room temperature are typically moving at about the speed of sound (340 m/s) and a typical chemical bond length is about 0.1 to 0.2 nanometers. This means that a typical molecule (if nothing bumps into it) will go 1700-3400 bond-lengths in a nanosecond! Of course, molecules in liquid, which are jammed pretty close together, won’t move that far without interruptions- they’ll bump into each other, switch direction and bump into others many times over the course of a nanosecond. This means that the typical timestep (the dt when integrating the differential equations of motion) for a molecular dynamics simulation has to be much shorter. In practice, for a molecular dynamics simulation that simulates all the atoms of a system, dt is about a femtosecond. With these timesteps, it becomes possible to simulate about a microsecond of simulation time per day of all atoms of a medium-sized protein moving around on a modern GPU like an A40. This is a big reason for why we can’t just simulate a protein folding to crack the protein folding problem. Protein folding takes about a second or on the order of a million GPU-days if you were to simulate it.
One example of a web of interrelated facts that I have concerns molecular simulations, with bold/italic denoting things that I have in my anki deck, or would make good cards.
One interesting thing about moleculaes bouncing around is that a nanosecond, which sounds really short, is actually a decently long time. Consider that molecules at room temperature are typically moving at about the speed of sound (340 m/s) and a typical chemical bond length is about 0.1 to 0.2 nanometers. This means that a typical molecule (if nothing bumps into it) will go 1700-3400 bond-lengths in a nanosecond! Of course, molecules in liquid, which are jammed pretty close together, won’t move that far without interruptions- they’ll bump into each other, switch direction and bump into others many times over the course of a nanosecond. This means that the typical timestep (the dt when integrating the differential equations of motion) for a molecular dynamics simulation has to be much shorter. In practice, for a molecular dynamics simulation that simulates all the atoms of a system, dt is about a femtosecond. With these timesteps, it becomes possible to simulate about a microsecond of simulation time per day of all atoms of a medium-sized protein moving around on a modern GPU like an A40. This is a big reason for why we can’t just simulate a protein folding to crack the protein folding problem. Protein folding takes about a second or on the order of a million GPU-days if you were to simulate it.