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Kinetic Monte Carlo simulations for the diffusion of molecules on a substrate

The hexaiodobenzene molecule shown in the image, when deposited on a noble metal substrate such as Cu(111) , Ag(111) or Au(111), at room temperature looses the I atoms and starts diffusing. The relative probability of diffusion and of binding to a neighboring molecule determine the shape of the network that will be obtained. The experiments performed at Empa [ http://dx.doi.org/10.1021/ja107947z J. AM. CHEM. SOC. 2010, 132, 16669–16676 ] shows that on a Cu substrate dendrites will form while on a Au substrate 2D networks will form.

The python program KMC.py will allow you to simulate the diffusion and binding of molecules once the energy barriers for the diffusion event and for the binding event as well as the simulation temperature will be defined.

During the execution the program shows snapshots of the positions of the molecules. Molecules free to diffuse will be represented via blue dots. Molecules that irreversibly formed a bond with a neighboring molecule will be represented by red dots. At the end of the execution a snapshot of the final configuration of the system is saved an image file. The program asks you for some input:

 
coverage
update graph each steps
temperature in K
diffusion barrier
binding barrier

TASK 1 execute the program with the following parameters:

coverage 0.1
update graph each steps 10
number of steps 100000
temperature in K 300
diffusion barrier 0.1
binding barrier 0.1

Observe how events occurr. Did the job perform all the 100000 steps? Why? Observe the patterns obtained.

execute the program with the following parameters:

coverage 0.1
update graph each steps 100
number of steps 100000
temperature in K 300
diffusion barrier 0.1
binding barrier 0.1

TASK 2