Mi amiga dice que un átomo es difícil de imaginar, igual que la gravedad cuando nadie la explica bien.

Because the verb decir normally takes que directly when introducing a full clause:

• Mi amiga dice que... = My friend says that...

Using de que here would be a common mistake called dequeísmo. With decir, the standard pattern is:

• decir que + clause

Examples:

• Dice que tiene razón.
• Dijeron que iban a venir.

Not:

• Dice de que tiene razón.

Both are possible, but they mean slightly different things.

• un átomo = an atom, any atom, one example of that kind of thing
• el átomo = the atom, often meaning the concept of the atom in general

In this sentence, un átomo sounds natural because the speaker is using an atom as an example of something hard to picture.

Compare:

• Un átomo es difícil de imaginar. = any atom / the idea of an atom is hard to imagine
• El átomo es difícil de imaginar. = the atom as a concept is hard to imagine

The accent mark shows where the stress falls.

• átomo → stress on the first syllable: A-to-mo
• difícil → stress on the second-to-last syllable: di-FÍ-cil

These written accents are required by Spanish spelling rules. They are not optional.

They help you pronounce the words correctly and distinguish them from how they would be stressed without an accent.

This is a very common Spanish pattern:

• adjective + de + infinitive

So:

• difícil de imaginar = hard to imagine
• fácil de entender = easy to understand
• imposible de explicar = impossible to explain

English often uses to + verb, but Spanish frequently uses de + infinitive after adjectives like this.

Normally, no. In standard Spanish, after difícil, you usually need de before the infinitive in this kind of structure:

• Es difícil de imaginar.

Without de, it sounds incomplete or unnatural here.

A different structure is possible, though:

• Es difícil imaginar un átomo.

That version works because imaginar now has its own direct object: un átomo.

So both are correct, but they are built differently:

• Un átomo es difícil de imaginar.
• Es difícil imaginar un átomo.

Igual que means just like or the same as. It is used to compare one thing with another.

Here:

• igual que la gravedad = just like gravity

You may also hear como in comparisons in everyday speech, and in some contexts it can sound similar:

• ..., como la gravedad...

But igual que makes the comparison more explicit: in the same way as.

So in this sentence, igual que is a very natural choice.

Spanish often uses the definite article with abstract nouns or general concepts where English may not.

So:

• la gravedad = gravity
• la música = music
• la historia = history

English often drops the article:

• Gravity is hard to explain.

But Spanish often keeps it:

• La gravedad es difícil de explicar.

That is completely normal.

Because explicar usually needs a direct object: you explain something.

Here, the thing being explained is la gravedad, so Spanish replaces it with the direct object pronoun la:

• nadie la explica bien = nobody explains it well

That la refers back to la gravedad.

If you said only nadie explica bien, it would sound incomplete unless the object were understood very strongly from context.

In Spanish, object pronouns normally go before a conjugated verb.

So:

• la explica
• lo entiende
• me ayuda

That is the standard position with normal finite verbs.

Compare:

• Nadie la explica bien.
• Quiero explicarla bien.

In the second example, the pronoun is attached to the infinitive explicar because pronouns can attach to infinitives and gerunds.

Because object pronouns such as lo, la, los, las cannot be separated and placed after the noun-like way English sometimes works. They either:

1. go before a conjugated verb
   
   • nadie la explica

or

2. attach to an infinitive/gerund/affirmative command
   
   • explicarla
   • explicándola
   • explícala

So la bien is not possible here.

Because dice que normally introduces information presented as a statement, so the indicative is used:

• Mi amiga dice que un átomo es difícil...

Spanish usually uses the subjunctive after expressions of doubt, denial, emotion, influence, and similar triggers. But decir que by itself does not trigger the subjunctive.

Compare:

• Dice que es difícil. → indicative
• No dice que sea difícil. → this can vary by meaning and context, but the structure changes because now there is negation and interpretation involved

In your sentence, es is completely normal.

Here bien means well, and it modifies explica:

• nadie la explica bien = nobody explains it well

So the idea is not just that nobody explains gravity, but that nobody explains it clearly or properly.

Compare:

• explica bien = explains well
• explica mal = explains badly

Yes, literally it is when nobody explains it well, but here cuando is being used more generally, almost like in cases where or when in a broad sense.

So it does not have to refer to one specific moment in time. It can describe a general situation:

• La gravedad es difícil de imaginar cuando nadie la explica bien.

Meaning:

• gravity is hard to imagine in situations where nobody explains it properly

This kind of general cuando is very common in Spanish.

Yes, that is a natural alternative.

Compare:

• Un átomo es difícil de imaginar.
• Es difícil imaginar un átomo.

Both mean basically the same thing, but the focus changes a little:

• Un átomo es difícil de imaginar focuses on the atom
• Es difícil imaginar un átomo focuses on the action of imagining

Spanish often allows both patterns.

In igual que, the word que is part of the comparison structure. Together they mean:

• igual que = just like / the same as

So this que is not the same kind of que as in dice que...

There are two different uses in the sentence:

1. dice que → introduces a clause
2. igual que → forms a comparison

That is why you see que twice, but each one is doing a different job.