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The water which is used to cool a nuclear plant is usually taken from a river or a lake.
Specific water.
The electrons by which the nucleus is surrounded have a very low mass.
Specific electrons.

Crystals that are formed from ionic compounds generally have high melting points.
Is this a defining relative clause? If so, this part may imply that there should be crystals that are formed from other compounds.

Moreover, the part does not have "the".
∅ noun that ---
can work like a defining relative clause? What is that part? Unfortunately, I'm not an expert of minerals.

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SupercatThe water which is used to cool a nuclear plant is usually taken from a river or a lake.

Specific water.

Yes, It is the cooling water or the coolant.

SupercatThe electrons by which surrounding the nucleus is surrounded have a very low mass.

Specific electrons.

That is not good phrasing. If the context is a description of an atom, then the clause is a relative clause.

All electrons have exactly the same mass. Their mass is much lower than the protons or neutrons which form the nucleus. Generally electrons are found in "orbital shells" around a nucleus, but there are also free electrons not associated with a particular nucleus. Electrons have three fundamental properties: charge, mass, and spin. By definition, the electric charge on an electron is −1. The mass of an electron has been measured and found to be 9.109389 × 10 −31 kilograms.

SupercatCrystals that are formed from ionic compounds generally have high melting points.
SupercatIs this a defining relative clause?

Yes. Commas would be incorrect.

Supercat∅ noun

Is equivalent to "All crystals." It is not talking about specific crystals in the context.

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Thank you. Which does the sentence mean?

1. Crystals that are formed from ionic compounds generally have high melting points.

(On the other hand, there are crystals that are not formed from ionic compounds.) Why does not the part have "the"?

2. (All) Crystals are formed from ionic compounds, and they have high melting points.

SupercatCrystals that are formed from ionic compounds generally have high melting points.

Take ordinary table salt is an example. It is a crystal of an ionic compound. It has a high melting point (just over 800 degrees centigrade.) High melting points are characteristic of crystals that are formed from ionic compounds.

Covalent compounds are another type of compound. Water is an example. Ice is a crystal formed from water, a covalent compound. It melts at a relatively low temperature, zero degrees centigrade.

Understood. Thank you. Without "the", is that way also possible? Sometimes I see similar cases such as, Men and women who attend to patients in a hospital are called nurses.

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The definite article is optional if the plural form of the noun is used with a defining clause.

(The) Men and women who attend to patients in a hospital are called nurses.

(The) Viruses that can jump between animal species are called Zoonotic.
(The) Crystals formed from ionic compounds have high melting points.
(The) People who are descendants of the Mongols typically have very little Neanderthal sequences in their genome.

Oh wonderful! Thank you.