How computer simulations help spy on atoms

Nanoscale objects are so small that they contain just a few thousand atoms. We don’t always have a camera to help us zoom in on a surface and observe how atoms move in real time. That’s where computational science becomes handy. By implementing the basic physics laws into computer programs we can simulate real-life systems and spy on atoms.

Ekaterina Baibuz is a doctoral candidate at the University of Helsinki. She studies physics of materials with computer simulations. The main topic of her research is atomic diffusion on metal surfaces.  Follow her research at  https://www.researchgate.net/profile/Ekaterina_Baibuz

The coolest cartoon scientists have ever made is undoubtedly A Boy and his Atom by IBM. It also hit the Guinness World record for the World's Smallest Film. It was made by moving actual carbon monoxide (CO) molecules one by one, on a surface of copper and photographing each frame with a scanning tunnelling microscope (STM).

When all the frames are combined in a single movie, it looks as if atoms are diffusing on a surface of a substrate by themselves. In fact, the person who controlled the STM machine drove their diffusion. In reality, when no person is involved, the diffusion is driven by the various external conditions: temperature, electric field, laser irradiation etcetera. And we need to know how this happens.

Why? Because small nanoscale objects are everywhere: in your phone, the medicine you take, artificial snow you cruise on during your winter break – you name it! And surface diffusion plays an important role in the production of nanoparticles of different shapes and properties.

EkaterinaBaibuz

Researcher

Ekaterina Baibuz
Twitter:  @katyabaibuz
Instagram: katerina_baibuz

Small nanoscale objects are everywhere: in your phone, the medicine you take, artificial snow you cruise on during your winter break – you name it!”

We can’t always predict how atoms would diffuse at certain conditions, nor is there always an experimental set-up available. Instead we can use computer simulations to help us grasp dynamics of surfaces. By implementing the basic physics laws into computer programs we  can simulate the collective movement of surface atoms and perform virtual experiments.

The tool that is most often used to study surface diffusion is called the Monte Carlo (MC) approach. It allows to simulate up to hours of atomic movement. MC is based on probabilities, hence the gambling name. Probabilities for atomic movements are based on two principle physics rules:

  1. Atoms need to overcome an energy barrier to move from one place to another. We know  how atoms interact with each other, so we can calculate the barriers.
  2. Atoms move faster with higher temperatures MC algorithm “gambles”: it chooses one of the events randomly but so that the jumps with lower barriers are more likely to be chosen. This video shows how A Boy and His Atom looks like in the Monte Carlo simulations at a temperature of 1 000 K. Instead of carbon monoxide molecules, I simulated copper atoms diffusing on a copper substrate. I used the code Kimocs that was recently developed in our group.  
“The Monte Carlo approach is based on probabilities, and it allows us to simulate up to hours of atomic movement.

Sadly, a boy and his atom wouldn’t have such a happy ending in reality, where surface diffusion is controlled by nature: it would take less than a nanosecond (billionth of a second) for a boy to dissolve into several islands of atoms. This example shows only a small system of 20 000 atoms. In fact with a MC approach we can study much bigger and more  complicated structures and reveal many mysteries of a nanoscale world.

Screen Shot 2017-05-29 at 14.54.49

A boy and his atom in the beginning of the Kinetic Monte Carlo simulations (left), and A boy and his atom in the Kinetic Monte Carlo simulations after 10 picoseconds at 1000 K (right). 

formula 1

Γ –  Probability of an atom to make a jump

E – energy barrier,

T – temperature of a system,

k – Boltzmann constant,

v – attempt frequency of a certain type of jumps

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