I like this question. This is a foundational question that concerns what our physical reality is made up of and what the afterlife dimension is made up of.
To answer the question correctly we would have to discern what our physical dimension is made of and what the spirit realm is made of. The spirit realm is the place that the soul resides in before being born and then returns to after a person’s life is over.
For simplicity sake lets just agree that the material world that we physically experience is made up of particle fields and static fields of force. All of this matter and energy are nothing more than different configurations of physical forms of matter and energy.
The Soul is not made of physical matter or energy and it is not made of an electromagnetic force. So the quick answer is no the soul is not made up of atoms or any particles.
On the other hand souls which are made from spiritual energy are definitely real. An individual soul actually represents a being’s individual consciousness. Thanks to many NDExperiencers we now know for sure that souls exist in the afterlife. These same souls can also be contained within the brains of humans while they are alive. Soul energy or spiritual energy is a different type of energy than the energy that physicists talk about. Spirit energy is indestructible as souls and spirits are indestructible they are eternal things that mainly reside in the afterlife. What is really interesting is the miracle of life which is the process of attaching a soul to a body when a human is born. In this state of being the soul’s power and abilities are diminished greatly while connected to the physical body.
So what is real? There exists a duality in my answer. The physical realm is real as it was created to have the laws of physics with physical properties that can be measured in lab experiments. So physical reality is just another dimension of reality that exists. The spirit realm is also real and is some sort of higher dimension of reality. It just can not be measured or observed using the physical senses or instruments. The spirit realm is even more real than the physical realm. Just ask anyone who has had a Near Death Experience. The physics (how things mechanically work) of the spirit realm is not known by us at this time. I think that in this realm consciousness is what is real and the energy and things that exist there are made of some sort of spiritual substance. My research clearly indicates that God created both the physical and spiritual realms. Someday I would like to better understand the physics of the spirit realm.
So far I know this much. The spirits can use spirit energy to interface and effect the physical realm and this spirit energy can be used to communicate to physical beings as well as occasionally work in the capacity to perform miracles such as healing. There are many documented cases of people being healed of cancer or other real physical health problems by God or spirit beings. So this means that the spirit realm is most likely the ruling force in all Universes and dimensions. This is true because the spirit realm can effect real changes in the physical world but we cannot physically effect changes in the spirit realm. In other words we can not harm or alter anything in the spirit realm by using energy beams or physical forces.
Therefore souls are real they are made up of a spiritual type of energy that can not be destroyed. Souls can exist in the physical realm when they are incarnate in a physical being. Souls are real. What we need to realize is that we have to expand our definition of what is real to include more than that which is physical. The Spirit realm where the soul normally resides in is even more real than our physical Universe.