I too have been studying Zimbardo's work and this area of research is still in its infancy at the moment, so, although those here who are more knowledgeable on neuroscience may be able to correct me if I am wrong, I believe from the lack of information I have seen that it is too early for any conclusive neurological basis to the formation of evil.
Whilst Dr. Philip Zimbardo's work, on the subject is in his book you mentioned — The Lucifer Effect — (Zimbardo, 2007) [See also: lucifereffect.com] there is also has an accompanying video at TED Talks (Zimbardo, 2008). In this video he highlights the basis of his book. There are also other similar works by other people.
The whole area of research on evil and heroism started, although not originally to study origins of evil, around 1950 with Solomon Asch and his Conformity experiment known as the Asch Experiment, which led to a further experiment by Stanley Milgram known as the Milgram Experiment.
Asch’s experiment was essentially benign in nature but Stanley Milgram’s experiment had a macabre nature to it. This made Milgram’s experiment particularly famous after he published his results as it made newspaper headlines and caused many people to sit up and really examine human nature, and the social requirement to conform to peers and authority figures.
[Stanley Milgram] asked the question, "Could the Holocaust happen here, now?" People say, "No, that's Nazi Germany, Hitler, you know, that's 1939." He said, "Yeah, but suppose Hitler asked you, 'Would you electrocute a stranger?' 'No way, I'm a good person.'" He said, "Why don't we put you in a situation and give you a chance to see what you would do?" (Zimbardo, 2008)
The movie The Wave (2008) was based on teacher Ron Jones's "Third Wave" experiment, which took place at a Californian school in 1967 to explain how the German population could accept the actions of the Nazi regime during the Second World War. Because his students did not understand how something like national socialism could even happen, he founded a totalitarian, strictly-organized "movement" with harsh punishments that was led by him autocratically. The intricate sense of community led to a wave of enthusiasm not only from his own students, but also from students from other classes who joined the program later. Jones later admitted to having enjoyed having his students as followers. To eliminate the upcoming momentum, Jones aborted the project on the fifth day and showed the students the parallels towards the Nazi youth movements.
What is interesting with the Milgram Experiment is that it doesn't seem that the root of evil is always related to the parts of the brain related to empathy. You cannot just put those who "failed" the test into the category of those who lack empathy because when you watch the 1962 documentary about the experiment on YouTube (PSU, 1962) which showed the experiment in action, an example is at 22 minutes into the documentary, where the "teacher" was showing signs of distress and wanted to check that the "learner" was okay before continuing. When the "teacher" was told he must continue he reluctantly did so, but he grew more agitated.
Stanley Milgram’s experiment seemed to inspire Dr. Philip Zimbardo with his studies into evil and heroism. Philip Zimbardo conducted the notorious Stanford Prison Experiment in 1971 and was an expert witness at Abu Grahib
I became an expert witness for one of the guards, Sergeant Chip Frederick, and in that position, I had access to the dozen investigative reports. I had access to him. I could study him, have him come to my home, get to know him, do psychological analysis to see, was he a good apple or bad apple.
Milgram's study is all about individual authority to control people. Most of the time, we are in institutions, so the Stanford Prison Study is a study of the power of institutions to influence individual behavior. Interestingly, Stanley Milgram and I were in the same high school class in James Monroe in the Bronx, 1954. (Zimbardo, 2008)
With his work, Dr. Philip Zimbardo came to the following psychological definition of evil:
Evil is the exercise of power. And that's the key: it's about power. To intentionally harm people psychologically, to hurt people physically, to destroy people mortally, or ideas, and to commit crimes against humanity.
The power is in the system. The system creates the situation that corrupts the individuals, and the system is the legal, political, economic, cultural background. And this is where the power is of the bad [apple] barrel makers. (Zimbardo, 2008)
PSU, 1962. Obedience - Films in the Behavioral Sciences [Video] University Park, PA:Pennsylvania State University
Online Stream at: https://cas.byu.edu/cas
Zimbardo, P. G., 2007. The Lucifer Effect: How Good People Turn Evil New York:The Random House Publishing Group
Zimbardo, P. G., 2008. The Psychology of Evil. [Online]
Available at: http://www.ted.com/talks/philip_zimbardo_on_the_psychology_of_evil