Lab Meeting
NIH, NIDDK, LBG
Travis Hoppe, Allen Minton, Di Wu
against
Phase separations lead to sudden fundamental changes in liquid structure and local density.
This is usually really important.
Match experimental data with results of computational models.
Classify common protein solution behavior from coarse-grained models.
Predict behavior of mutations and unknown solutions.
is the pairwise interaction of two molecules
is the pairwise interaction of three molecules
...
From the equation of state you can calculate most thermodynamic properties!
For rotationally invariant molecules
but in general...
How do you model a
Need an expression for the Hamiltonian
This is not the free energy, but the enthalpy
Important terms:
How do you model a
What are we ignoring?
Must decide if this approximation is valid for the system.
modeling the
modeling the
Correction for dielectrics?
What to do with the solvent?
First order approximation to screening effects.
Charge strength decays exponentially due to ions.
Describes the electrostatic interaction between a charge distribution and an ionic solution.
Can be linearized and solved on a computer efficiently.
Splits space into regions of discrete .
Crystallized PDB Structure
Typically (in absence of ions)
Electrostatic field
Excluded volume
Spherical Harmonic decomposition
Best fit charges
Monte-Carlo Simulation
Good approximation of the near field, poor up close
Captures the anisotropic field
especially near the isoelectric point
Macrocharge approximations make for reasonable models of large protein solutions
Excluded volume for modeled as a hard sphere.
Representation of the protein electrostatics
in an ionic solution for a given pH.
Our charge distributions are not isotropic anymore,
we must to compute this:
There are many pairwise orientations.
Blind sampling may miss specific interactions.
Need to know at different if we want to scale the model.
counts the number of ways we
can get a particular energy,
If the sampling works, then we should be able to calculate the non-ideality of a protein molecule after subtracting both the excluded volume and the electrostatics portions.
This would allow us to predict phase behaviors in at different pH values, protein concentrations, binary mixtures, and salt concentrations.
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