We understand from Vedic scripture that God (Visnu) lives within the atom too.

Krsna as His expansion Visnu/Narayana (Visnu-tattva) accompany the individual jiva-soul (marginal living entity) in the material world and also lives within every atom in the temporary decaying material creation that is 1/4 of the Spiritual Sky.

The other 3/4 of the Spiritual Sky is the perpetual "active" realm of the Vaikuntha planets and Goloka-Vrindavana where Visnu and Krsna have their eternal pastimes.

Life is EVERYWHERE which in Sanskrit is called "Sarva-gata." 

ln the mundane material creation, both "active" (in a material bodily vessel) and "inactive" (dormant in the atom or in the impersonal Brahmajyoti or Brahman) the jiva-souls are found.

Tamal Krsna - "Srila Prabhupada, someone asked a question the other day about the atom which I couldn’t give the answer to. His question is that if we say that within the atom the living entity, the jiva-soul, is present, and life symptoms means six symptoms of birth, growth...."

Srila Prabhupada - "That’s all right. Their life symptoms has not yet developed but they are there."

Jayadvaita - "Potential."

Srila Prabhupada - "Yes."

Tamal Krsna - "His question was sort of a dual question. At what time, or what? Just like at the time of disintegration of this body, does the living entity (jiva-soul) leave this material body when it disintegrates? So does the atomic body also disintegrate when the living entity (jiva-soul) leaves it and moves to a higher body?"

Srila Prabhupada - "Atomic body? Atomic body means material body. Unless you are free from this material body, the atomic body will go on with you. That means unless you are mukta, the atomic body will go on. Mind, intelligence, ego — they are also atomic, finer (subtle) atomic body."

Tamal Krsna - "But within each atom the living entity (jiva-soul) is present?"

Srila Prabhupada - "Yes, God (Visnu) is present also; therefore living entity (jiva-soul) is present."

Tamal Krsna - "So the living entity (jiva-soul) is present within the atom just as I am present within this material body. When I leave this body, my body breaks apart?"

Srila Prabhupada - "Yes, you leave this body, then enter another body."

Tamal Krsna - "Right."

Srila Prabhupada - "By nature’s law."

Tamal Krsna - "And when I leave this body, the body breaks apart?"

Srila Prabhupada - "Eh?"

Tamal Krsna - "When I leave this body, the body is....."

Srila Prabhupada - "The body is already atomic combination."

Tamal Krsna - "Yes."

Srila Prabhupada - "So it remains atomic combination. You leave the body."

Tamal Krsna - "Yes, it remains."

Srila Prabhupada - "You leave the house. That does not mean the house is finished."

Tamal Krsna - "Right, I can understand that."

Hamsaduta - "He’s asking that if the jiva-soul leaves the atomic particle, then does the particle break apart, isn’t it?"

Srila Prabhupada - "No, no. You have not left atomic particle."

Tamal Krsna - "No, but you were saying that within the atom there’s also a living entity (jiva-soul). So when that living entity leaves the atomic particle does the particle break apart? Or doesn’t it? I mean what?"

Srila Prabhupada - "Just try to understand. From the sastra, you understand that andantara-stham God lives within the atom."

Tamal Krsna - "Yes."

Srila Prabhupada - "And when God (Visnu) is there, the living entity (jiva-soul) is also there. This much you try to understand. Because God (Visnu) and living entity (jiva-soul), they remain together, as two friends. God (Visnu) is trying to save this fallen friend. That is the information from Upanisad. So when God (Visnu) is there, the living entity (jiva-soul) is also there." (Morning Walk, April 4, 1975, Mayapur)