Protons and neutrons are made of quarks, which are point particles in the same way as electrons.

Atoms have mass and volume; atoms are mostly space, with the majority of their volume occupied by the electron cloud surrounding a tiny nucleus.
Protons and neutrons are made of quarks, which are point particles in the same way as electrons. This intricate and fascinating structure suggests that not 99% of the space is empty, but rather 100% is. With their complex makeup, atoms consist of a tiny, positively charged nucleus surrounded by a cloud of negatively charged electrons. Although the nucleus is typically less than one ten-thousandth the size of the atom, it contains more than 99.9% of its mass. Gases are then defined as phases without any type of arrangement; neither short- nor long-distance. A single atom, of course, has no arrangements of other atoms around it, so it cannot be considered a liquid or a solid.

Atoms consist of a tiny, positively charged nucleus surrounded by a cloud of negatively charged electrons. Although the nucleus is typically less than one ten-thousandth the size of the atom, it contains more than 99.9% of its mass.
The basic structure of an atom includes a tiny, relatively massive nucleus containing at least one proton and usually one or more neutrons. Outside the nucleus are energy levels (shells) containing one or more electrons.
In reality, atoms are not just space. Spread-out electrons fill atoms, a crucial component that prevents atoms from shrinking and plays a significant role in their behavior.
Based on an examination of our DNA, any two human beings are 99.9 percent identical. This means that if we were to compare the DNA of two random individuals, we would find that 99.9% of their genetic code is the same. The genetic differences between different groups of human beings are similarly minute. Still, we only have to look around to see an astonishing variety of individual differences in sizes, shapes, and facial features. This analogy can help us understand the concept of atomic structure, where atoms may seem similar but exhibit a wide range of behaviors and properties.

· Although by volume, an atom is mostly space, dominated by the electron cloud, the dense atomic nucleus, responsible for only 1 part in 10^15 of an atom’s volume, contains ~99.95% of an atom’s mass.
While atoms do not have a solid surface to ‘touch‘ in the traditional sense, they interact in a way that can be described as ‘touching ‘. This interaction, seen in chemical reactions, is not a physical touch but a sharing or transfer of electrons, which is fundamental to atomic behavior. When atoms ‘touch ‘in a chemical reaction, it is not a physical collision but an exchange of electrons, leading to the formation of new substances.

Atoms consist of a tiny, positively charged nucleus surrounded by a cloud of negatively charged electrons. Although the nucleus is typically less than one ten-thousandth the size of the atom, it contains more than 99.9% of its mass.
How do we know they exist? We can witness their effects through chemical reactions. We can calculate their various sizes through mathematical equations combined with indirect observations. Moreover, with new technologies such as the scanning tunneling microscope, atoms can now be seen, a testament to scientific research and technological progress.
The quantum-theoretical answer is that atoms are not 99.99% empty. Despite what many descriptions in popular texts, and even in high school physics or chemistry textbooks, try to convey, they are ultimately misleading metaphors.
Yes, an electron and the nucleus take up a finite, near-point-like amount of space, but only if you measure them. If you leave them alone, the electrons are everywhere around the nucleus. This near-point-like nature of the electron and the nucleus is a fascinating aspect of atomic structure that sparks curiosity.

Claimer before we launch into this: I am only a science fiction author, not an actual physicist. Everything I am about to write is my best understanding of what I have learned. A real expert in the field might read this and cringe at how wrong it is (though I hope otherwise). However, with all that being said, protons and neutrons are composed of quarks, which are point particles analogous to electrons. This complex and intriguing structure indicates that the concept of atoms being 99% space may be misleading; in fact, one could argue that it is close to 100% empty. Atoms consist of a diminutive, positively charged nucleus encircled by a cloud of negatively charged electrons. Despite the nucleus typically occupying less than one ten-thousandth of the volume of an atom, it contains over 99.9% of the atom’s mass.
The fundamental structure of an atom comprises a relatively massive nucleus that contains at least one proton and usually one or more neutrons. Surrounding the nucleus are energy levels or shells that house one or more electrons. In practice, atoms do not merely consist of space. The distributed electrons within atoms are essential for preventing them from collapsing and play a significant role in their overall behavior.

Research shows that any two human beings share 99.9 percent of their DNA, suggesting that if the genetic code of two random individuals is compared, 99.9% will be identical. The genetic variations among different groups of humans are similarly small, yet a multitude of individual differences in size, shape, and facial features is evident. This comparison aids in conceptualizing atomic structure, where atoms may exhibit similarities while also demonstrating a diverse range of behaviors and properties.
Although the volume of an atom is primarily composed of space dominated by the electron cloud, the dense atomic nucleus, which constitutes only 1 part in 10^15 of the atom’s volume, houses approximately 99.95% of its mass. It is important to note that, while atoms lack a solid surface to “touch” in the conventional sense, they do interact in ways that can be characterized as “touching.” This interaction, observable in chemical reactions, is not a tangible collision but rather an exchange or sharing of electrons, which is fundamental to atomic behavior. When atoms “touch” during a chemical reaction, it involves an exchange of electrons that leads to the formation of new substances.
We can ascertain the existence of atoms through their effects in chemical reactions, and by employing mathematical equations combined with indirect observations, we can calculate their sizes. With advancements in technology, such as the scanning tunneling microscope, scientists are now able to visualize atoms directly, marking significant progress in scientific research.

The quantum-theoretical perspective suggests that atoms are not 99.99% empty, despite common portrayals in popular literature and educational materials that may perpetuate this misconception. While an electron and the nucleus may occupy a finite, near-point-like amount of space when measured, their nature is fundamentally different when considered in a state of rest, wherein electrons are distributed around the nucleus. This intriguing aspect of atomic structure invites further exploration and raises questions about its implications.

I wish to clarify that I am a science fiction author and not a physicist. The following ideas reflect my current understanding of atomic structure as derived from my readings. A specialist in the field may find inconsistencies in this explanation; however, I present this information to contribute to the discussion. On with the show.
The model of an atom we learn in school looks like this: a ball made of balls.

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