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author | bnewbold <bnewbold@robocracy.org> | 2014-04-22 22:01:56 -0400 |
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committer | bnewbold <bnewbold@robocracy.org> | 2014-04-22 22:01:56 -0400 |
commit | 822bd0b04d1cce54c2fff57c4b206c51d1dcb940 (patch) | |
tree | e3cd895f9b54b7d44ff249dea3c50dda927304cc /lectures/lec06_intro1 | |
parent | 222292b3aa9d967557c3165cce5cc7f5773c20ab (diff) | |
download | dmmsb2014-822bd0b04d1cce54c2fff57c4b206c51d1dcb940.tar.gz dmmsb2014-822bd0b04d1cce54c2fff57c4b206c51d1dcb940.zip |
rename notes -> lectures
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-rw-r--r-- | lectures/lec06_intro1 | 44 |
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diff --git a/lectures/lec06_intro1 b/lectures/lec06_intro1 new file mode 100644 index 0000000..97b2f39 --- /dev/null +++ b/lectures/lec06_intro1 @@ -0,0 +1,44 @@ + +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 + |