summaryrefslogtreecommitdiffstats
path: root/lectures/lec06_intro1
blob: 97b2f393e62f3efb4e42d40b622cd172ef7fee56 (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44

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