Read the article. They accurately modeled the biological neuron's behavior with about 1000 'neurons'. They didn't need quintillions of neurons. So clearly the computational complexity is vastly lower than the number of atoms or molecules.
I believe they modeled the behavior of a model of a neuron, not an actual neuron. Models are intrinsically simplifications of the reality.
But that model represented the input/output behavior of the neuron. Of course it doesn't represent the behavior of every single atom of the neuron itself, but that isn't relevant to its computational behavior.