I wrote a biology paper a few days ago proposing a new mechanism for cognitive enhancement titled “The Eraser Hypothesis”. (Link in bio for full pdf) Now I am running the experiments. The proposal operates at the RNA level instead of neurotransmission, and is focused on an enzyme called FTO that controls whether or not memory related genes get translate into protein. The goal is to partially modulate FTO through a hidden pocket between its two structural domains, restoring the brain’s ability to build memories under metabolic stress without shutting the enzyme down entirely. This is a first draft molecular dynamics simulation of FTO. I ran it on my laptop overnight. It’s of 150,000 atoms (including the full protein, water, and ions). Every frame is computed under a CHARMM36m force field at 310 K in a dodecahedral periodic box with 150 mM NaCl, integrated at 4 femtosecond intervals with hydrogen mass repartitioning via OpenMM on my laptop (m4 max). The bars in the middle are per-residue backbone displacement (which are a live measurement of what is actively moving at each instant) The line drawing on the lower left is backbone RMSD tracking structural drift from the starting conformation. So far because the compute required is just so heavy I’ve only got 30 nanoseconds of data. The target is a cryptic pocket at the interface between FTO’s two domains that only opens transiently during simulation. I’m gonna continue running more sims (should take me around 8-9 days for my goal, I want 200 nanoseconds per replica across 3 independent runs) then map its dynamics, druggability, and pharmacophore in a new paper. Music is my piece “Reverie Overture”. #biology