Brainwave entrainment is also known as brainwave synchronization.  According to Wikipedia  brainwave entrainment is “any practice that aims to cause brainwave frequencies to fall into step with a periodic stimulus having a frequency corresponding to the intended brain-state (for example, to induce sleep), usually attempted with the use of specialized software.”

So using the example track above, the right ear is sent a 20Hz beat, compared to a 10Hz beat in the left ear.  As the right ear receives the higher frequency of beat, this works to increase the speed of the ‘left' brain hemisphere, which can be helpful for people with conditions like ADD, who are often found to have an abundance of slow wave activity in the left brain.
This is something which will come to you with practice. For instance you may feel an energy around and inside you like you have shifted dimensions but are still there. Instead of thinking this is God, the Zone or whatever, think of this as your soul, you essence, your expanded pure light being. In this way you will begin to train yourself to find your identity in your expanded being and your internal identity. This is what we want - to let go of the idea that we are a limited ego.
"The brain is set up in such a way as to have spiritual experiences and religious experiences," said Andrew Newberg, a Philadelphia scientist who authored the book "Why God Won't Go Away." "Unless there is a fundamental change in the brain, religion and spirituality will be here for a very long time. The brain is predisposed to having those experiences and that is why so many people believe in God."
The Transparent Corp forum – This forum is an invaluable resource for any brainwave entrainment user or enthusiast.  Most of the feedback is obviously focused on the Transparent Corp software, but with over 20,000+ posts now you can find answers to the whole array of brainwave entrainment questions on there.  (UPDATE: Sadly, the Transparent Corp forum has now been taken offline)
4. Theta State: (4 — 8Hz) We're able to begin meditation. This is the point where the verbal/thinking mind transitions to the meditative/visual mind. We begin to move from the planning mind to a deeper state of awareness (often felt as drowsy), with stronger intuition, more capacity for wholeness and complicated problem solving. The Theta state is associated with visualization.
Your brainwave activity during sleep is largely distinct from your brain activity when you’re awake. (REM sleep is one exception to this—during REM, your brain is active in ways very much like when you’re awake.) During non-REM sleep, the slower, lower frequency theta and delta waves dominate, compared to the alpha and beta waves that are prominent when you’re alert and active.

Binaural beats were first discovered in 1839. The effects of using audio instead of light for brainwave entrainment were noted in 1959. Oster’s research paper in 1973 brought attention to the use of binaural beats in a medical setting and this inspired a range of studies in the 1980s indicating very positive findings. The effects of brainwave entrainment using binaural beats has become of a hot topic of research ever since but despite their reported successes, they have never quite shook off the sometimes negative connotations of being an “alternative medicine”.

With these studies in mind, EquiSync's revolutionary, multi-layered, multi-tiered approach was born. Designed to synchronize and harmonize your brainwaves while allowing you access to the deepest, most pleasurable, most beneficial states of meditation — much faster than the traditional route, EquiSync® has made mastering meditation easier than ever!
Meditation Begins • Mind Chatter Slows Down • Great For Learning & Studying • Creative Ideas Flow • Reverse Brain’s Aging • Habits, Fears, Phobias Melt Away • Calm & Peaceful • First Layer Of Subconscious Mind • Gateway To Deeper Mental States • Advanced Focus • Relaxation Begins • Serotonin • Endorphins • Good For Anxiety, Depression, Stress, Panic • Mind Power • Happiness • Confidence
Listening to binaural beats is not something to be feared, however. In most situations, listening is safe and very enjoyable. Choosing a track from various websites online, as well as some videos on YouTube.com, can assist you in relaxing and can bring about a more restful sleep. Choosing a Beta entrainment can help with alertness and focus, while listening to an Alpha wave track can help you to relax and learn new information. Theta tracks can help to change some negative emotions, or to help you drift off to a sounder sleep. Delta waves will help to accelerate healing. To use them, you must use headphones or earphones, because each ear will hear a different frequency. You should make the commitment and listen daily; consistency is key in order to achieve maximum benefits. However, please don't listen to binaural beats twenty four hours a day; once daily for a short period of time is perfectly fine. You should also make yourself comfortable; either lying down or sitting in a comfortable chair will help you to relax. You can do them right before sleep, or right upon awakening. Listening during meditation or visualization exercises will help to improve and deepen your practice. If you feel a little blue or you need a break from the daily routine, you can pop a CD in and unplug completely. When you return to whatever you were doing, you will find that you are more refreshed and ready to take on whatever is before you.
This blog was created from an interview with Joseph Kao, creator of iAwake’s Journey to the Center of the Self, and iAwake’s CEO John Dupuy, by Heidi Mitchell, who has been working with John for 11 years as assistant and editor. John introduced her to Integral theory and practice and brainwave entrainment enhanced meditation in 2007. Heidi is also a freelance editor of nonfiction books, blogs, and web sites. She can be reached at www.heidimitchelleditor.com.
“In order to get into a flow state, you have to calm a part of the brain, the posterior cingulate cortex, which is the source of what brain scientists call the default state, which is the non-focused state,” says Harris. “At any rate, it turns out that Holosync [binaural beats], when you listen to it, [calms that part of the brain] and so does traditional meditation. It’s just Holosync does it faster and more easily and more effortlessly. It turns down the posterior cingulate cortex and it enhances the other part of the brain that, when it’s enhanced, you can easily go into a flow state.”

Despite the lack of solid evidence of the effectiveness of binaural beats in producing brainwave changes, and that those changes can be effective in altering our conscious states, there do exist hours of recorded binaural beat videos available on YouTube. Some of these are just straight beats designed to ease the listener into various states by gradually varying the frequencies of the beats. A nice example of this can be found in a 90-minute video by Jody Hatton. Others embed the beats into a musical score, which some people find easier to listen to. Spotify has a whole playlist devoted to binaural beats. You can try these and many others to see if this is something that may be helpful to you. The soothing nature of the sounds may be what really helps, but that’s fine if you just want to relax and drift off to sleep. You can also find quite a few apps that generate binaural beats at your phone’s app store. If you want to relax and sleep just be sure to set the frequency in the theta range (4 – 7 Hz). Patients have reported to me that they felt energized or even anxious after listening to a few minutes of the beats, but this was usually because they were set to a high frequency like beta (13 – 16 Hz). Be sure to try listening to the beats for a short time and if they have a negative effect, just stop listening. If you find them helpful, that’s great, and you have a new technique that can be used to promote relaxation, something most of us can use. 
The activity of neurons generate electric currents; and the synchronous action of neural ensembles in the cerebral cortex, comprising large numbers of neurons, produce macroscopic oscillations. These phenomena can be monitored and graphically documented by an electroencephalogram (EEG). The electroencephalographic representations of those oscillations are typically denoted by the term 'brainwaves' in common parlance.[4][5]

Effects on cortisol: The hormone cortisol is commonly associated with stress, and when levels are higher than usual, it can have a negative impact on the body. High levels of cortisol can lead to a range of conditions, including Cushing syndrome, menstrual cycle and female libido changes, anxiety, and depression. Dr. Giampapa noted a reduction of cortisol of up to 70-80 percent in several study participants.
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