As we have already seen an atom is indivisible and indestructible, it cannot be seen, burnt or divided into parts. The description of these qualities might create some difficulty in our minds, because modern science has shown that atom is not indivisible, it can be split.[24] Accordingly, an atom of a chemical element is rather a complicated system of smaller units such as protons, neutrons, electrons, etc. which are now called sub-atomic particles. The number of such sub-atomic particles has now crossed the figure of 250. Moreover, it has been established beyond doubt that atoms of various chemical elements are very much similar to our solar system, with a number of negatively charged particles (electrons) rotating round the central nucleus in the form of standing waves, which in itself is composed of a number of positively charged particles (protons) and electrically neutral particles (neutrons). Protons and neutrons are much heavier than electrons; the nucleus made up of the former two contains 99.97% of the total atomic mass.[25]
The number of protons, neutrons, and electrons is different in different elements but the atom on the whole is electrically neutral because the total charge of all the negatively charged particles equals the total positive charge. The simplest and lightest atom is the hydrogen. It is composed of single proton as the nucleus and a single electron orbiting round it. Its diameter is 10-8 centimeter and mass 1.64x10-23 grammes. The distance between the nucleus and the rotating electron is such that the atomic diameter is 100,000 times greater than the diameter of the nucleus. The uranium atom is the heaviest natural element, in which there are as many as 92 protons and 146 neutrons in the nucleus and 92 electrons rotating round it in different orbits.[26]
Later on theoretical physicists branched into two schools. One of these branches continued their search for the elementary building blocks, since it was not satisfied that sub-atomic particles such as protons, neutrons, etc. were indivisible: while the other one abandoned this search. Although no one has found the particles that compose the protons, theoretically it has been established that protons are composed of quarks. The hunt for quarks is going on. Whether they actually exist or not, a new area of research: 'what quarks are made up of ' has emerged.
Regarding the problem whether an atom is divisible or not, a satisfactory solution can be found in the Anuyogadvara, a Jain canonical text. The text postulates two types of atoms, viz; transcendental atom (sūkṣma paramāṇu) and empirical atom (vyavahāra paramāṇu).[27]
Description of the atom as indivisible, indestructible etc. refers to the transcendental atom. Empirical or practical atom consists of infinite number of the transcendental atoms.[28] The noticeable thing here is that, in spite of being a composite body, empirical atom is too subtle to be cognized when it is single. It can only be cognized through effects of collective action of a group of them. Its interactions and mutations are very subtle and so it is known as an atom. We can compare a sub-atomic particle or an atom of modern physics with this empirical atom.
The transcendental atom, as defined previously, is a truly indivisible fundamental unit of matter. It is not composed of any particles. Hence, it is indivisible and dimensionless. Like a true geometrical point, it has no length, no breadth, and no thickness; its center is identical with its end. Thus, it has no extension and occupies only a single space-point. It has no shape and mass. However, it is not an abstract entity deprived of qualities of colour, smell etc. unlike the atom of Democritus. In spite of it, a transcendental atom is not perceivable by sense-organs and can only be cognized by inference through effects of collective actions or by direct experience of a transcendental knowledge.[29] This contradictory feature of being an object of sensuous qualities on the one hand and yet not being an object of sensuous cognition on the other, is easily resolved by the explanation of quantum phenomena and the principle of uncertainty. Quantum physicists do not concern themselves with the properties of an individual electron because it is impossible to ascertain them. On the other hand, electron's behavior can be accurately defined when dealt with collectively in great numbers (Schroedinger's wave equation). The individual electron is indeterminate and the indeterminacy is not a sign of immature science but an ultimate barrier of nature.
An atom in its free state is as real as an atom of material cluster and the qualities of colour, etc. are as real in a free atom as they are in an attached one. A free atom when captured by an aggregate loses its free state and is converted to a component of the aggregate. Similarly, its qualities also undergo changes of intensity. Thus, the same atom that is possessed of one unit of blackness can become infinitely black. The Bh.S refers to a number of such atoms.[30]
Two or more atoms mutually combine to produce composite bodies and this process composes the entire physical world. The clusters composed of atoms have shape and extension. On the contrary, atoms are devoid of shape and have no extensions. It is quite natural to ask here how can a mass less and shapeless atom produce an aggregate, which has mass and shape as well? In this case, of course, the principle 'ax nihilo nihil fit' fails to operate. But the question seems quite superficial as we go into the depth of the problem. Mass and shape are the results of the combination of two different qualities of atoms i.e. dryness and viscosity in a determined proportion. The more is the proportion of dryness the more is the lightness. The more is the proportion of viscosity the more is the heaviness. Likewise, the other properties such as shape, length etc. are the consequences of the combination of two different qualitative atoms. Thus, the atoms have mass and shape potentially, which appear in the relation of other different atoms. In modern science, the sub-atomic particles are presumed to be spherical in shape.[31] Their diameters, though very small are measurable and therefore their extension in space covers innumerable space-points. According to the Jains, the sub-atomic particles of science, viz; protons, electrons, etc. are not atoms in its true sense. They are divisible because they are composed of innumerable transcendental atoms.
As discussed above, theoretical considerations in modern physics have already established that protons and for that matter all particles are made up of quarks and the question 'what are the quarks made up of?' looms large before the physicists. In conclusion it can be stated that the sub-atomic particles are not the ultimate constituents of matter but are only a gross form of it.