An Overview of Atoms
There have been many models for the atom, but even now, this is subject to revision. We do have some basic ideas though.
Atoms make up all the matter that we see and can't see, but it does not stop there.
The earliest references that have been found concerning the concept of the atom dates back to ancient India in the 6th century BCE. The Nyaya and Vaisheshika schools of thought in India developed elaborate ideas and theories of how atoms combined into more complex objects, first in pairs, then in trios of pairs. The references to atoms in the West emerged a century later in Greece from Leucippus whose student, Democritus, systematized his views. In approximately 450 BCE, Democritus defined the atom for the western world. He thought that it was a basic piece of matter that could not be further subdivided. That view remained unchanged and unchallenged for the next two millennia. His view of the atom was derived from observation of sparks generated when amber was rubbed with wool. The spark was viewed as a kind of fluid flowing between the two. Democritus philosophized about this and the nature of dividing matter to its ultimate unit. With the advent of the atomic age, we have learned differently from experiment and theory progressing in lock step with each other.
There have been many ideas of the atom from the original concept to our current understanding. Today we know that atoms have many properties and are made up of smaller "sub-atomic" parts. We know from radiological experiments that atoms are mostly empty space. The structure of atoms defines the 92 natural elements, the several man-made elements and their isotopes by their internal construction. Electrons, a sub atomic particle, exist in states defined as an electron cloud of probabilities and they also exist in discrete manifestation according to the photo-electric effect. Two or more electrons cannot exist in the same energy state in an atom according to the Pauli Exclusion Principle. In the case of the simple hydrogen atom, electrons can manifest in a sphere of probabilities about the nucleus. In more complex atoms, electrons manifest in regions about the nucleus due to mutual repulsion. Protons can emit positrons in certain circumstances and become neutrons. Atoms can be fused or made to fission to release energy in something called transmutation, producing other elements within the range defined by the Periodic Table of elements. Atoms of each element have a specific mass and number that defines their particular chemical, electrical, magnetic and metallic properties. Sub-atomic particles also have a mass and they possess a specific charge. Atoms are defined under a different law of physics that the classic or relativistic one. Atoms exist in the quantum world. On this, the entire cosmos is built.
Parts of an atom
The simplest complete atom is made of a proton and an electron. The electron exists in a state of probability around the proton/nucleus in the condition of several energy levels. This is the simple hydrogen atom, the most abundant form in the cosmos. Most hydrogen exists either as dust or as ionized plasma within stars or in the interstellar medium. The cosmos comprises about 97 percent hydrogen. Some hydrogen exists that has one or two neutrons in the nucleus (center) of the atom. These isotopes are call deuterium and tritium where one has two particles in the nucleus and the other three respectively, the other particles are neutrons. The proton is defined as positively charged, the electron negatively charged and the neutron is neutral; without charge.
The so called physical structures of the atom comprise on average only about one millionth of the total volume. The rest is "empty space" that exists within the relationship of the nucleus and the electron probability shell. The empty space component of the atom is highly variable. The volume of space varies according to the energy state of the electron and the complexity of the atom. The empty space was found during experiments that bombarded a thin foil of gold with highly energized and high speed protons (ionized hydrogen). It was observed that almost all of the protons went straight through as if nothing was in the way. A tiny few were deflected and even less were bounced back. After calculating the probabilities, it was found that the gold atom at least was mostly empty space as described above. Further experiments found similar results for other elements with minor differences depending on the element in question. Some were found to be denser and others less so.
The Elements and Isotopes
There are 92 naturally occurring elements found in this world and by extension, off world. We have examples of off world elements from the moon and meteorites and have found that the elements are identical to ones on Earth. The elements are characterized by the number of protons in their nucleus. The natural elements are those that range from hydrogen through to uranium. Some elements have one isotope and others like tin as many as ten. Two elements, technetium (43) and promethium (61) have no stable or long lived isotopes. There are far more natural isotopes by number, each group belonging to a particular element then there are elements. On the other hand, isotopes are relatively rare compared to natural occurring non isotope elements. Hydrogen exists in three states as mentioned above. All elements and isotopes are classified according to the number of nucleons (protons and neutrons) in the nucleus.
Electron states and quanta
Electrons are particles that exist in a state of probability according to quantum theory. One cannot simultaneously measure position and momentum. Our methods of observing the sub-atomic world are very limited; basically using other sub-atomic particles and electromagnetic radiation. It is akin to observing a moving baseball in the dark that we have no idea of speed, position and direction by throwing other balls around and observing the effects on the thrown balls that we know by way of the speed thrown and the direction of the throw. For this kind of observation; and we need a lot of them to draw a statistical picture of the sub-atomic realm. We have come a long way in understanding the electron. In 1905 Einstein wrote his piece on the photo-electric effect that explained why only certain wavelengths of light would dislodge electrons from atoms. This became the foundation of the quantum theory. He actually coined the term quanta to describe these phenomena. Now we know that electrons exist in “layered” shells, that these shells are sometimes in the form of lobes surrounding the nucleus and that they respond to element characteristic wavelengths. Each element has its characteristic signature by way of absorption and emission wavelengths. The simple hydrogen atom has no less than 21 electron energy states, two in visible light and the rest in the invisible part of the spectrum. Absorption and emission has been classified along the permutations and combinations of wavelengths that can be absorbed and emitted. These are known as the Lyman, Balmer, Paschen, Brackett, Pfund and Humphreys series. The seventh level results in ionization. There are 21 specific wavelengths for hydrogen electrons. The 22nd level results in ionization where the electron is severed completely from the proton. Every other element from Helium on, has multiple electron shells and even more levels of quanta exchange. Characteristic signatures of each element can be seen in Fraunhoffer emission and absorption spectra. This is what the electron can tell us halfway across the observable universe.
Wolfgang Pauli tells us that no more than two electrons can occupy the same energy level in an atom, and if they do, they must have opposite spin. Now spin is not like we visualize in our marco world of experience. Spin in the subatomic realm is something entirely different and is difficult to explain in layman’s terms. To explain this type of spin, one must invoke rather arcane mathematical concepts verging on concepts like topology and multiple dimensions. The Calcium atom has 20 protons and 20 electrons in its neutral state. Thus it must have ten energy levels at all times. Metals however, are a different story. When an aggregate of atoms of the same metal bond together, each atom releases one electron. All the atoms become positive ions and share electrons to balance. This means that electrons are free roaming in the entire context of the metal lump. The energy levels permitted are equivalent to the number of atoms in the lump. Energy by way of electricity and heat can travel very rapidly through metal. This same fact is what gives solid metal its tensile strength.
When two protons fuse in the core of the sun, one of them emits a positron and becomes a neutron in the process. This first step is crucial in the process of hydrogen fusion toward the step of helium production. The first step produces an isotope called deuterium. This released positron merges with one of the two electrons in a matter - antimatter collision which produces gamma rays. This process is what creates the energy in nuclear fusion within a star. Extreme pressure and temperatures are needed to duplicate this process. In the next step, another hydrogen or deuterium nucleus fuses with it and the result is helium. Humanity is edging toward that goal with sophisticated colliders and prototype fusion reactors. We are using deuterium and tritium in our experimental reactions.
Fusion, fission and the transmutation of elements
All elements are created in stellar interiors either by direct fusion, or as a result of a super-nova explosion. Anything up to and including iron (56) is created by fusion. Iron represents an energy divide and represents that boundary where energy is not derived by fusion or fission. Iron (56) is at the bottom of the nuclear energy well. All nuclear processes, whether in stars or in nuclear reactors on Earth result in the transmutation of one element into others. This was the dream of alchemists for centuries and we can now do it routinely. We have even made artificial elements beyond uranium. We can make specific isotopes such as cobalt (60), Caesium (137) and Iridium (192) for various applications in the medical and construction industries. Lead can be transmuted into gold, but it is a costly process and is not nearly as cost effective as making cobalt (60) or iridium (192) or plutonium (239).
Mass and number
Atomic number is strictly defined by the number of protons in the nucleus. The number of neutrons can vary in a specific element due to the existence of isotopes that have the same properties as the defined element, but a slightly greater or lesser mass. The mass of the atom is defined by what is called a mole of atoms; a quantity that is defined as enough atoms to make a gram of a particular element. The less atoms it takes to make up a gram of the element, the greater the mass of each atom and the less it takes to fill that quantity, the less the mass of the individual atom. It stands to reason then that the higher the mass of an atom, the more difficult it is to move it.
Electrical, magnetic, chemical and metallic properties
Pure elements differ by way of chemical, electrical, magnetic and metallic properties. Some elements are highly reactive, like oxygen and readily combine with other atoms, even oxygen. Others like helium and neon are not chemically reactive at all. Each element can be identified for its reactive qualities. Some elements like gold, copper and aluminum can conduct electrical impulses readily. Others, like carbon cannot. Elements can be identified by their magnetic properties with iron, nickel and cobalt responding by being attracted to a magnetic field. Others like copper, aluminum, hydrogen and oxygen are repelled by a magnetic field. In each case, the electrons strongly influence the magnetic properties of atoms and the elements. It is considered that elements like copper and iron are metallic and elements like carbon and silicon are not, favoring a crystalline arrangement of atoms. Under favorable conditions, metallic elements can also crystallize, but they retain characteristics like being ductile as opposed to brittle, reactive to magnetism instead of inert. All of this has to do with how atoms react singularly to influences or in combination such as in a lump of metal.
Charge and quark theory
Protons, neutrons and electrons according to current thinking, are comprised of quarks which come in six flavors like up, down, charm, strange, top and bottom that combine to make hadrons and leptons. The strange, charm, top and bottom are very unstable. The up and down varieties are abundant and can be distinguished by electrical and color charge, spin and mass. The charge part is the important consideration for the construction of protons, electrons and neutrons. The up quark is considered to have a positive 2/3 charge and the down quark a negative 1/3 charge. By combining quarks in groups, we can determine the quark structure of protons, electrons and neutrons. Antiparticles have their own types of particles and anti-quarks. By definition, a neutron would have two down quarks and one up quark in its structure, giving and overall charge of zero. A Proton would have two up quarks and a down quark to give a net plus one charge. An electron would be comprised of three down quarks with a net charge of negative one. Experiments thus far have not demonstrated definite proof of their existence, but this is explained by confinement 
The quantum world of uncertainty and probability
Warner Heisenberg developed the uncertainty theory based on quantum observation of momentum versus position. We know from him, that we can determine position of a sub-atomic particle and not its momentum and vice versa; not both. Under special circumstances, we can determine both through quantum entanglement experiments. Without invoking entanglement, the uncertainty principle holds. We have built our view of the atomic, sub-atomic and now quarks basically on probability and statistics.
Foundation of the cosmos
The entire cosmos is built on atoms and combinations of atoms. The quantum world of atoms, sub-atomic particles and quarks are what everything is ultimately composed of. Looking at the foregoing facts we see a fractal dimensional structure to everything that there is. This is true of atoms and the large structures that are made up of them. A fractal dimension is defined as a partial dimension and this is due to that fact that there is a lot of space between the “solid bits”. Thus a three dimensional structure is actually closer to two dimensions but more than two. In atoms, the three dimensional structure is vanishingly close to two dimensions. What we have is a profound mystery mediated by charge and spin right down to the quarks.
1. Gangopadhyaya (1981).
2. Teresi (2003:213–214).