Atom and Atma.

English is based on Saxon, German and Latin, where Latin goes back to Ancient Greece, and German goes back to Sanskrit. So short answer is that the word comes from German Scientists who were the earlier pioneers of the field of Atomic Science. In German the word is called "Atam", but the sound of letter "a", in some languages is built into the constant and in some it is not not. Example, Rama in Sanskrit and Ram in Hindi.

Now the detailed explanation. Let's define what life is or what consciousness behind life is. In one of the Upanishads, life or conciousness behind life is called, something that: (1) has motion, (2) replicates, divides or reproduces, (3) ingests food or energy, and (4) excretes or gives out lower form of food or energy. By this definition we can also call atomic particles having life! But you do not have to go that far. We know that Amoeba has life. And our bodies have millions cells of Amoeba and they die every time and are reborn. Does that mean you have died? You will say no, I am the same Mr. X or Ms. Y. But the truth is that all cells of your body get replaced every 10 years. So are you the body? The answer here can not be "yes" as then your body gets changed every 10 years with all new cells and you have a different body.

So regressing like this, the great Hindu Philosophers came up with the Philosophy of Brahman or Vedanta saying that the whole Universe, what was there, what is now and what would be there, sentient and in-sentient, animate and unanimate, what we can see, no matter how far, at microscopic and macroscopic levels, and what we can not see included, is all Brahman or Supersoul, and like Amoeba Cell Bodies in our bodies, and we will never die as we are that Brahman! But our identification of ourselves with body, mind, ego and intellect fools us to believe this physical world to be true and our senses absolutely fine, but science has already shown that we do not see and hear everything! And science has shown there are 16 dimensions. So how can we all be sure of our religions and say, "Yes my way is the right-way, otherwise Amigos, take the High-way."

This philosophy was also complemented with Hindu Philosophy that everything is made of the same unit and they called it "Atman"/"Atma" or Soul. So you see how scientific it is. In fact the Laws of Conservation of Mass, and Laws of Conservation of Energy, which both laws were later combined by Einstein famous formula of E=MC^2, was first stated by Hindus in their Scriptures, which says Soul or Atma never dies, and it recycles or re-incarnates. So at atomic level we can not argue this.

Now in 1989 there was some article about experiments being done by Japanese Scientists in one the Time or Newsweek magazine, which said they were trying to capture some rare atomic particles, called some Fermi Particles, who were travelling for eons, millions of years in the space, and they were seeking out their "identical twin particle" from whom they had separated millions of years and miles before! So if these particles can have memory, one can still say that the memory is nothing but something made of atomic particles, whether it is an abstract energy or matter, does not matter, as we know they are nothing but same, we can expect Reincarnation at Human Mind Level and Lives!

Updating the posting, when I found this news:
IBM Engineers Store Information in Single Atom