I have some suggestions for books related to the topics you mentioned. There's a pretty good section on cognitive ergonomics in Wickens' Introduction to Human Factors Engineering that is a clear introduction to the topic, and mentions some examples of design issues that can arise from human beings' cognitive limitations and biases.
Also, Chris Eliasmith's book Neural Engineering: Computation, Representation, and Dynamics in Neurobiological Systems shows some of the technical approaches people have taken to modelling what happens in the brain.
I'm not sure if either of those is what you're looking for, but I found them interesting.
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