There are a number of different mechanisms. The initial injury causes a cascade of chemical events plus cellular events. The brain identifies the damaged cells and after a brief effort to allow for healing/metabolic correction, tRNA (transmitting RNA) is released causing the damaged cells to die. This continues until there are clean margins, so to speak, taking a term from cancer surgery.

The nutritional therapy many of us recommend helps basically in two ways. It provides the substances that allow and/or encourage the cells to function properly. The B-12, folic acid, D3 and some other supplements help the blood-brain barrier to strengthen.

The complexity of the metabolic processes in vitro ( live cells in a test tube or petri dish) are understood to a point. The specific in vivo (in the living body) process malfunctions are hard to identify. They can identify the metabolites of malfunctioning processes and the proteins (tau and others) that are problematic and erroneous neurotransmitters but not tie these malfunctions to an individual patient's brain. This is part of the reason for the 'Try this drug and see if it helps' treatment.

The software problem, so to speak, is due to either axonal or other cellular damage limiting the proper transmission of signals or failure of neurotransmitters to properly transmit the signals. The 'code' is directly written into the neurons. It is not loadable code that can be unloaded like computer code. It does get moved as the brain reorganizes and consolidates the data.

If you have ever watched a hard disk defragment and compress data, this happens each night during sleep. Information goes from immediate memory to short term memory to long term memory.

The processing of this data can get messed up by excessive adrenaline/epinephrine-norepinephrine causing the cellular processes to speed up. This data can also get messed up by faulty gating. Think of this as a traffic cop telling the data where to go and at a particular speed. In some injuries, different areas of the brain will operate at different speeds due to cellular damage or inadequate blood flow.

For example, my neuro can see that my brain processes incoming stimuli at a very slow rate and allows this data to pass through the gating process with haphazard controls. This means that I do best by limiting the amount of stimuli that my brain has to process. Think of this as if I am artificially gating or limiting the information so that it does not need to rely on the brain's gating mechanism to keep the processes under control.

There are many permutations of the various malfunctions that make it next to impossible to fully diagnose the brain's struggles.

Anybody who tries to make a definitive diagnosis is just making educated guesses. That is why individual symptoms are treated individually. There are not global treatments that can effect the many different injuries with a single therapy.

The CBT (Cognitive Behavioral Therapy) can be effective at lessening the overload and out of control thought processes that feed the cascade of other events.

Now, I have over done this topic. I even get to the point of confusing myself as I try to keep my thoughts organized.