# Simulation Ions in water (abstract model)

Ions in water may show strange behavior due to their hydration shell. This is a early draft using current web technologies with a python back end to calculate the first mineral nucleus. The scientific side is described in my blog post water-proteins-ions. I welcome any ideas to this project, please post them in my blog.

## Simulation Parameter

Choose Parameter and click calculate. The effects are obvious in the threshold graph:
 Damping Weight Relative weight between log and square function. Small value (0.01): log function; big value (1.8): square function value: 0 to 2 Sinus Frequency Threshold cycles during reactionvalue: 0 to 100 Sinus Amplitude Increases or decreases the sinus amplitude. Fractions like 0.01 are possible. Greater 1 = boost, smaller 1 = damping, 1 means plain sinus. value: 0 to 10 Loops Representing time (more or less)value: 0 to 20000 Ions Start number of Ions in the clustervalue: 0 to 10 000

## Plot Calculated Data

X = loops (=time) ;
Here: Loops (or time)
Y = Number of ions Here: number of ions in the cluster

To get the data, click in the text field and copy the values (Crtl + a)

In this little simulation a random number is generated and compared to a threshold. Ions are added or removed from the cluster, depending whether the random number is above or below the threshold. The threshold changes with the time (=loops).

## Threshold Graph

X = loops ;
Here: Loops (or time)
Y = threshold functions Here: strength of the damping function

Try plotting a second time if it doesn't work the first time (press "clear all", then "plot data")
The tool plotting the data is called JSXGraph and was developed by the Universty of Bayreuth.
The threshold function is a sum of three functions:
x2 *w +
+ ln x *(2-w) +
+ sin x *u

These functions are summed up and normalized to 1. The dominance of each function can be adjusted with the simulation parameters, e. g.: w is the damping weight, u is the sinus amplitude.