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diff --git a/notes/lec06_intro1 b/notes/lec06_intro1 deleted file mode 100644 index 97b2f39..0000000 --- a/notes/lec06_intro1 +++ /dev/null @@ -1,44 +0,0 @@ - -Background: - -Ligands are little molecules (which could be proteins or chemicals or whatever) -which bind to a larger biomolecule (eg, a protein or DNA) called the receptor. -"Receptor/ligand" binding affinity refers to how strongly different ligands -want to attach to different receptors. Both binding (association) and -un-binding (dissociation) is happening all the time, so you get a (dynamic, or -possibly steady state) distribution of binding probability. - -ref: https://en.wikipedia.org/wiki/Ligand_(biochemistry) - -ODEs (ordinary differential equations) are those involving only a single -independent variable; eg, solving for x in terms of t, only having derivatives -dx/dt, (d^2 x / d x^2), etc. the order of the ODE is the highest order of -derivative. - -PDEs (partial differential equations) are those involving multiple independent -variables, and thus partial derivatives. Eg, x in terms of t and r, having -derivatives del x / del t, del x / del r, and del^2 x / (del t * del r). - -ref: https://en.wikipedia.org/wiki/Differential_equation#Ordinary_and_partial ---------- - -Law of mass action: rate of a reaction involving two quantities is proportional -to the product of the densities of both. - -Michaelis-Menten: approximation to solution of enzyme-catalyzed reaction -equation: - - d [S] / dt = (max reaction rate) * [S] / (Km + [S]) - - [S] is concentration of substrate S - Km is Michaelis constant, which is a specific substrate concentration - - (max reaction rate) =~ k_2 [E]_total - Km =~ (k_-1 + k_2) / (k_1) - - all assuming that enzyme E catalizes S into P with rates k_n: - - -> k_1 - [E] + [S] [ES] -> k_2 [E] + [P] - <- k_-1 - |