Modelling

Predicting the movement ofsmall molecules inside

a biofilm

Thursday 11/08 Research for modelling purposes was carried out. Relevant information about molecules: Ranaspumin-2, Latherin, Colicin E2 were look for. Required information such as: diffusion coefficient through Biofilm, Molecular weight, length, translation rate, critical concentration. Important data on E. coli was found, such as: total number of ribosomes, total number of translated proteins, aqueous volume of a cell.

Friday 12/08 Research on diffusion equation was carried out for modelling purposes. Derived equation for two-dimensional diffusion was used:

where: A - coefficient to aquire total number of particles in the system

r - distance from the point of origin (mm)D - diffusion coefficientt - time passed from the start of reaction (min)P - number of particles at the certein distance from the origin after the certain amount of

time. Tuesday 16/08 First working model for the DNase Colicin E2 molecule was obtained. Wednesday 17/08 Models for the surfactant molecules Latherin and Ranaspumin-2 were calculated. Thursday 18/08 Model for T4 Endolysin was calculated. Monday 22/08 Models were recalculated to one-dimensional diffusion to decrease complexity and make future estimations easier. One-dimensional diffusion equation is as follows:

where: A - total number of particles in the system

r - distance from the point of origin (mm)D - diffusion coefficientt - time passed from the start of reaction (min)P - number of particles at the certain distance from the origin after the certain amount of

time. Thursday 25/08/ Decay of proteins was taken into consideration. Another equation was included:

where: Pf( r, t) - Number of molecules after the decayλ - Decay coefficient

Friday 2/09 The multi-cell models for Latherin and Colicin E2 were calculated. The models assumed that there are 21 cells of bacteria, laying next to each other in the row, adjacent one to the other, while an average length of a cell is 2 μm.