People who meditate grow bigger brains than those who don't. Researchers at Harvard, Yale, and the Massachusetts Institute of Technology have found the first evidence that meditation can alter the physical structure of our brains. Brain scans they conducted reveal that experienced meditators boasted increased thickness in parts of the brain that deal with attention and processing sensory input.

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There has been considerable interest in the potential of auditory beat stimulation to affect cognition and mood states.  Chaieb, Wilpert, Reber, & Fell (2015) reviewed the literature on the effects of auditory beat stimulation on memory, creativity, attention, anxiety, mood, and vigilance. They found some support for it being able to affect these modalities but there were contradictory findings. So the area clearly requires significantly more research before firm conclusions can be drawn. 

it says the following: “Running a delta sleep session throughout the night is not recommended as it can interrupt the normal sleep cycle”. I’ve been looping pure delta isochronic tones for about 5 days now, and have had quality sleep. Should I continue looping delta or should I let the videos play out without looping them? Will it will harm my health to do loop delta while I sleep?

Critics, like Owen Flanagan, PhD, believe that Hanson, and those like him, are overextending the results of current scientific studies.[citation needed] In his book Bodhisattva’s Brain: Buddhism Naturalized, Flanagan presents a more conservative viewpoint of current scientific research and cautions readers against the seemingly exciting results of recent studies.[20] Flanagan does not believe current science supports the idea that positive emotion can be strengthened in the same way that stroke victims can recover use of limbs with use.[20] Flanagan does acknowledge that meditation may be beneficial in some way, but the mechanism of how meditation affects the brain is still clouded.[20] Similarly, Awasthi argues that Meditation is non-specific to the research studies showing clinical efficacy in some cases, though mechanisms remain unclear.[21] Flanagan and Hanson use many of the same scientific studies to attempt to support their differing viewpoint, but both authors identify the need and importance of future studies investigating meditation.
How does brainwave entrainment work? Consistent, precisely engineered audio frequencies in the form of binaural beats cause the brain’s frequencies to match the stimulus. Your brain perceives two beats with slightly different frequencies (which are inaudible to the ear) through your headphones. It takes the difference between the two, and matches its own frequency to it. This is called the “frequency following” response.
If you name your emotions, you can tame them, according to new research that suggests why meditation works. Brain scans show that putting negative emotions into words calms the brain's emotion center. That could explain meditationÕs purported emotional benefits, because people who meditate often label their negative emotions in an effort to let them go.
Recent research at the University of Lisbon finally uncovered the reason for the 350 year-old mystery, finding that the resonance of sound is the mechanism for entrainment of swinging pendulums and ticking clocks, and it seems likely that the energy transferred by sound is also responsible for other observations of entrainment, including brainwave entrainment.
Isochronic tones are basically just a single tone with the volume being turned on and off at regular intervals. When you apply the same effects to music or a noise, it’s usually referred to as amplitude entrainment effects (in Mind Workstation anyway). When you apply the on/off effect to music or noise it’s usually done by targeting a specific frequency range in the sound and only turning that part on/off, leaving the rest of the music/noise untouched. What that does is allow parts of the music/noise to play without being distorted/interrupted, making it sound more pleasant to listen to. It produces a kind of fluttering sound as I like to call it and you can adjust the level of intensity.
"When these people talk of religious experience, they are talking of a meditative experience," said John Haught, a professor of theology at Georgetown University. "But religion is more than that. It involves commitments and suffering and struggle ­ it's not all meditative bliss. It also involves moments when you feel abandoned by God." "Religion is visiting widows and orphans," he said. "It is symbolism and myth and story and much richer things. They have isolated one small aspect of religious experience and they are identifying that with the whole of religion."
In 1956, the famous neuroscientist W. Gray Walter published the results of studying thousands of test subjects using photic stimulation, showing their change in mental and emotional states. He also learned that photic stimulation not only altered brainwaves, but that these changes were occurring in areas of the brain outside of vision. In Walter’s words:
Deeper Meditation • Near The Stage Of Sleep • Vivid, Dreamlike Imagery • Creative Visualization • Feel More Open & Connected • Advanced Problem Solving • Super Creativity • Insight • Intuition • Inspiration • Deeper Subconscious To Super-Conscious Mind • Trance-like • GABA • Immune System • Serotonin • Endorphins • Acetylcholine • Lower Cortisol • Deeply Relaxed • Sleep Better • Emotional Intelligence
Entrainment is a term originally derived from complex systems theory, and denotes the way that two or more independent, autonomous oscillators with differing rhythms or frequencies, when situated in a context and at a proximity where they can interact for long enough, influence each other mutually, to a degree dependent on coupling force, such that they adjust until both oscillate with the same frequency. Examples include the mechanical entrainment or cyclic synchronization of two electric clothes dryers placed in close proximity, and the biological entrainment evident in the synchronized illumination of fireflies.[13]
You can experiment with the length of time you listen to the binaural beats to find out what works for you. For example, if you’re experiencing high levels of anxiety or stress, you may want to listen to the audio for a full hour or longer. Remember, you must use headphones for binaural beats to work. You may also want to listen with your eyes closed.
Theta waves have a frequency between 4 and 7.5 hertz, making them slower than more wakeful alpha but faster than the dreamless slumber of delta. Theta brainwaves are the frequencies of nighttime dreams and REM sleep when the brain goes through bursts of activity and eye movement. People also experience theta waves in a state of light sleep, deep relaxation, during meditation and prayer, and when daydreaming. Theta waves produce an experience of inward wakefulness where we become disengaged from the outside world while engaging in inner activity. At the lower frequencies of theta, sleeping states are experienced, and at the higher range of frequency, awake relaxed states are experienced. 
(Shannahoff-Khalsa, 1991; Webb & Dube, 1981). These naturally occurring shifts may underlie the anecdotal reports of fluctuations in the effectiveness of binaural beats. External factors are also thought to play roles in mediating the effects of binaural beats (Owens & Atwater, 1995). The perception of a binaural beat is, for example, said to be heightened by the addition of white noise to the carrier signal (Oster, 1973), so white noise is often used as background. "Music, relaxation exercises, guided imagery, and verbal suggestion have all been used to enhance the state-changing effects of the binaural beat" (Owens & Atwater, 1995). Other practices such as humming, toning, breathing exercises, autogenic training, and/or biofeedback can also be used to interrupt the homeostasis of resistant subjects (Tart, 1975).
But the question is: Does it have a special effect on the brain? A lot of people think so. The basic claim being made for binaural beats is "resonant entrainment". Entrainment, in physics, is when two systems which oscillate at different frequencies independently are brought together, they synchronize with one another, at whatever the combined system's resonant frequency is. Examples of entrainment occur in animals in nature; for example the chirping of crickets or the croaking of frogs. Synchronization of menstrual cycles in women is another example. Even people coming together and dancing with one another is a type of entrainment. The basic claim for binaural beats is that the perceived low-frequency beat will entrain your brain wave pattern, thus forcing your brain into some desired state.