Think of your brain as a series of roads that you travel every day. This is actually what your brain is like on a physical level: a series of ruts—like paths or highways—that your thoughts travel over and over again. Have you ever noticed how you often have the same thought, as though your brain is on repeat? “I’m so stupid” or “Why can’t I get things right?” This is why our internal monologue can be such a nightmare. Your brain gets used to “driving the same route;” the more times it follows a particular path, the more likely it is to go the same way the next time. On a physical level, in the brain, the neural highways get coated with a fatty substance called myelin, re-enforcing them. Familiar thoughts are marked out on your brain and easy to find because you have already traveled them so many times, like a trail through a forest.
The brain loves the familiarity of this established path even if you hate it. We need stability and familiarity, even if it makes us miserable. But these brain patterns aren’t who you are. The conversation in your mind is not your true self. And our thoughts certainly don’t always represent or reflect the story of “new creation” available in God. A friend of mine has a placard on his desk that reads: “Don’t believe everything you think.” That’s it exactly! We must learn to doubt and supplant what we think is true if it doesn’t align with God’s greater truth. We have to disassociate from the negative thoughts and emotions—whether they’re about God or about ourselves—with which we have over-identified. We have to cease believing that they’re true.
In silence, then, there’s the possibility of a new road being built in our minds. Silence becomes a gateway by which the Spirit of God is able to over-write our normal thinking, freed from the self-deception of our own thoughts. In silence and solitude, in prayer and in Scripture, a new highway appears, and an entry ramp with it. We become free to make a choice to enter this new highway rather than just getting back onto the worn-out old one. To believe the new story of our adoption in God, for example—even if for just a moment. And the more you make this choice and travel this new highway, the bigger it becomes. Indeed, the more the new highway is used, the more it becomes a freeway that’s readily found and traveled.
In silence, we can receive a new God-image, to steadily supplant all the false views of God we have built up over the years. Such views are almost always initially based on our parents and how disciplined or permissive they were, how distant or how loving, or on trauma that we endured growing up. But such impressions are never adequate to fill out a transformative image of God.
What tired story about yourself—perhaps paved by some failure or mistake, or by some way that you were abused or betrayed—needs to be intersected by the new story of “new creation” in Jesus? What tired stories about God (that He's distant or uncaring or angry) need to be supplanted by a transforming image of God? Every one of us need to fall into the story of adoption that Jesus tells, seeing who God is in a way that re-wires us. And we need silence to open our minds to these realities.
As a way of engaging silence, consider this practice: In silence, practice breathing deeply, to calm your body. Then simply say, "I receive your nearness, God," and remain in the silence. Every few moments, repeat this prayer. Such practices train our souls to become open, and it's in openness before God that we are transformed. See how long you can stay in the tension of this prayer, and of silence itself.
 Merriam-Websiter: Myelin: a soft white material that forms a thick layer around the axons of some neurons and is composed chiefly of lipids (such as cerebroside and cholesterol), water, and smaller amounts of protein
Thus the Scripture speaks of “the renewal of the mind” and the “casting down of every obstacle that keeps people from knowing God,” including “rebellious thoughts. See Romans 12:2 and 2 Corinthians 10:5.