So, as you can see, you're not getting rid of me easily, even if I'm not there anymore

in person.

Okay.

Without losing any time, this is work that was done in collaboration with Emre, who wrote

all the software involved, and myself.

And it's all about how we can compute hydrodynamics of mainly proteins, DNA, sugars, biomolecules.

This is what we strive for.

And we came down now because of advancement, either in computer power and in theories,

that we can really represent and calculate for atomic models, the properties.

So what is what we call the Van der Waals bid modeling method in US solar?

One bid for each non-hydrogen atom.

The initial volume of each bid is calculated from the atom's Van der Waals radius, including

the pH, pK dependent bound H atoms.

For instance, acidic residues, they will have the H atoms bound or unbound depends on the

pH of the solution.

The ionization dependent number of bound water molecules are calculated for specific atomic

groups such as hydroxyl, amides and oxygen ions.

We use the Anderson-Hasselbal equation to calculate the percent ionization at the specified

pH.

And we assume that the Kans-Kaufman number of bound water molecules is max at full ionization

and zero at the other end.

So just to remind you what are these hydration numbers, Kans-Kaufman, a long time ago from

NMR freezing experiments, determined how many water molecules were in close proximity with

certain amino acids.

Of course, when you look at these numbers, you realize that one molecule is always present

of the peptide bond because they were studying polypeptides.

And we then assumed that these numbers, which were measured for the entire residues, these

water molecules could be located where exactly there is an interaction with the amino acid.

So for instance, for acidic residues to the COOH terminal and for basic residues to the

amide group.

And so we apply this number directly on the atomic lab.

The volume of the bound water is summoned to the Van der Waal dried volume and a new

bead radius is computed.

The hydrated bead centers can be optionally moved outwardly in respect to the center of

mass by a fraction of the water radius used because you can choose which water radius

you will use for the so-called bound water molecules, which are not really bound.

Of course, we all know that they exchange rapidly, but instantaneously, they will be

always a water molecule in that position.

So it behaves like if it were really bound.

Okay.

Tests are underway to also exclude atoms from dehydration using an accessible surface area

routine that has to be repeated if the outer translation is used because if you move these

atoms, you will get less screening of some other atoms because of their new position.

Okay.

So the way practically it works is through human serum albumin and you convert it into

a bead model where each atom is a source of friction and the hydration you can see

that increases the size of course of certain atoms.

The green are the acidic, the yellow are the basic, the red are polar.

Okay.

Now, let's see what is the effect of the ionization on hydration.