“Every universe is full of atoms, and the Lord is not only within the universe but also within the atoms.”
This is from the Srimad-Bhagavatam 8.3.17
[This chapter of the Srimad-Bhagavatam is entitled “Gajendra’s Prayers of Surrender.” In this chapter, the King of the elephants, Gajendra, having been attacked by a crocodile, prayed to the Personality of Godhead for protection.]
Since an animal such as me has surrendered unto You, who are supremely liberated, certainly You will release me from this dangerous position. Indeed, being extremely merciful, You incessantly try to deliver me. By your partial feature as Paramatma, You are situated in the hearts of all embodied beings. You are celebrated as direct transcendental knowledge, and You are unlimited. I offer my respectful obeisances unto You, the Supreme Personality of Godhead.
…Krishna says that the entire material world is maintained by His partial representation as Paramatma. The Lord enters every universe as Garbhodakasayi Vishhnu and then expands Himself as Ksirodakasayi Visnu to enter the hearts of all living entities and even enter the atoms.
Andantara-stha-paramanu-cayantara-stham. Every universe is full of atoms, and the Lord is not only within the universe but also within the atoms. Thus within every atom the Supreme Lord exists in His Vishnu feature as Paramatma, but all the vishnu-tattvas emanate from Krishna.
As confirmed in Bhagavad-gita (10.2), aham adir hi devanam: Krishna is the adi, or beginning, of the devas of this material world — Brahma, Vishnu and Mahesvara. Therefore He is described here as bhagavate brhate. Everyone is bhagavan — everyone possesses opulence — but Krsna is brhan bhagavan, the possessor of unlimited opulence.
Isvarah paramah krsnah. Krishna is the origin of everyone. Aham sarvasya prabhavah. Even Brahma, Vishnu and Mahesvara come from Krishna. Mattah parataram nanyat kiñcid asti dhanañjaya: there is no personality superior to Krishna. Therefore Visvanatha Cakravarti Thakura says that bhagavate brhate means “unto Sri Krishna.”