ATOMIC THEORY: The Structure and Formation of Atoms





The Greek philosopher Democritus, in the 5th century B.C., developed the first theory of the atom. He believed atoms were tiny and indestructible, the smallest constituents that made up the four Greek elements of earth, water, fire, and air. In fact, the word atom comes from the Greek word for “indivisible.” For 2300 years, Democritus’ concept
remained a cornerstone in our thinking about how the universe is put together. When scientists of the 19th century  began to delve deeper, it began to lay the groundwork for answering one of cosmology’s central questions: How did the elements in our universe form and evolve?

The first inkling that atoms might have structure came in the 1860s, when the Russian scientist Dmitri Mendeleev developed the periodic table. By then, of course, scientists knew that there were many more elements than the Greeks’ four. What Mendeleev realized was that when the elements were arranged according to their atomic weight, he could group different elements into families with similar characteristics……

Born in Siberia, the last of at least 14 children, Dmitri Mendeleev (1834-1907) revolutionized our understanding of the properties of atoms and created a table that probably adorns every chemistry classroom in the world. After his father went blind and could no longer support the family, Mendeleev’s mother started a glass factory to help make ends meet. But just as Mendeleev was finishing high school, his father died and the glass factory burned down. With most of her other children now out on their own, his mother took her son to St. Petersburg, working tirelessly and successfully to get him into college.

In the late 1860s, Mendeleev began working on his great achievement: the periodic table of the elements. By arranging all of the 63 elements then known by their atomic weights, he managed to organize them into groups possessing similar properties. Sodium and potassium, for instance, share similar properties, as do carbon, silicon, and titanium, but the attributes of each family are very different from each another. Where a gap existed in the table, he predicted a new element would one day be found and deduced its properties. And he was right. Three of those elements were found during his lifetime—gallium, scandium, and germanium. They provided the strongest support for his periodic table, a cornerstone both in chemistry and in our understanding of how the universe is put together. But neither he nor his contemporaries made the conceptual leap to realizing that an atom’s weight and properties were a measure of its internal structure. As had happened so many times before, the ingrained beliefs of the time (in this case, that the atom is indivisible) made such thoughts inconceivable.

This view would change rapidly as the 19th century wound down, setting the stage for our understanding how the various elements evolved in our universe. The first step in this process came with the opening up of the atom, which proceeded on two separate experimental trails. In the first trail, British physicist Joseph John Thomson discovered the negatively charged electron in 1897. More importantly, he showed that it had a tiny mass, just 1/1837 the mass of the lightest element, hydrogen. This proved that particles smaller than atoms existed, that atoms had some structure

The other trail began with the discovery of X-rays by the German physicist Wilhelm Roentgen in 1895 (for which he won the first Nobel Prize in physics in 1901). Inspired by Roentgen’s work, the Frenchman Henri Becquerel discovered radioactivity,  the physical transformation of one element into another,  a few months later while trying to detect X-rays emanating from uranium. And shortly after that, Marie Curie (who coined the term radioactivity) measured the strength of uranium’s radioactivity, and with her husband Pierre discovered two new radioactive elements, polonium and radium.

The energy released through radioactivity took three forms: one having a positive electrical charge, the second having a negative charge, and the third having no charge. The British physicist Ernest Rutherford called these alpha, beta, and gamma rays, respectively. The alpha rays turned out to be particles, the nuclei of helium atoms. Likewise the beta rays were particles, simple electrons. The gamma rays were found to be the highest energy form of light, more energetic even than X-rays.

Working with his colleague Frederick Soddy, Rutherford discovered that radioactive elements, like uranium, physically changed as they emitted their radiation. The alpha particles signaled the decay of the element into a lighter element, and through a series of steps the atoms eventually ended up as lead. In a way, the alchemists had been right that one element could be transformed into another. (Unfortunately, none of these steps produced the gold so dear to alchemists!)

The Curies

Born in Poland during a time of Russian domination, Marie Sklodowska (1867-1934) had no real opportunity for an education after high school. She saved her hard-earned money to help pay for her older sister’s medical studies in Paris, then followed her to France in 1891, studying at the Sorbonne. In 1894, she met the French chemist Pierre Curie (1859-1906), and they were married a year later. Although Pierre had already made a name for himself, their collaboration proved far more fruitful than his solo career.

They spent much of their careers studying radioactivity (a term coined by Marie), examining the particles and energy produced as radioactive atoms decayed, and in the process learned about the building blocks of matter. They established that the heavy element thorium was radioactive and discovered two new elements: polonium and radium. They refined techniques for extracting radium from ores.

Marie won Nobel Prizes in both physics and chemistry for their work. (Pierre failed to share in the second simply because he was dead.) Yet despite living in near poverty, they spent most of their money on further research. They were idealistic enough to refuse to patent any of their potentially lucrative discoveries. Pierre was killed when he was run down by a horse-drawn carriage. Marie died of leukemia, almost certainly the result of a lifetime of exposure to high levels of radiation. Ironically, one of the enduring applications of their work has been in the treatment of cancer with radiation.

Ernest Rutherford

Born and raised in New Zealand, Ernest Rutherford (1871-1937) came to study at Cambridge University in England in 1895. Like the Curies, he wanted to learn how matter was put together. And as much as anyone, he succeeded. He showed that radioactivity was caused by the breakdown of one atom into another. He named the three forms of radiation produced by radioactivity alpha, beta, and gamma rays, and went on to prove that the alpha rays were actually the nuclei of helium atoms.

Perhaps his biggest contribution to science was his idea of the structure of the atom. By bombarding gold foil with alpha particles in 1909, he found that most of the particles passed through unaffected but a few bounced nearly straight back. From this, he deduced that atoms consist mostly of empty space with a heavy, positively charged nucleus at the center and a swarm of negatively charged electrons surrounding it. His idea, still accepted today, overthrew the notion of Democritus that the atom was without structure. After devising methods to locate submarines in World War I, he made his last great discovery. He used alpha particles to literally transform nitrogen atoms into oxygen, the first man-made transformation of one element into another, and opened the door to the idea that elements could change.

One of the key moments in scientists’ quest to comprehend the structure of matter came when they realized that not all elements are stable. The nuclei of many heavy elements—uranium, radium, and plutonium, to name a few—are unstable, spontaneously decaying into other nuclei and releasing energy in the process. This radioactivity can occur in any of three ways: alpha decay, beta decay, and gamma decay. In the first, an alpha particle (the nucleus of a helium atom, which consists of two protons and two neutrons) comes shooting out of the nucleus at high speed. In the second, an energetic beta particle (an electron or its antiparticle, a positron) is emitted. And in the third, which usually follows immediately after an alpha or beta decay, a high-energy gamma-ray photon radiates from the nucleus. The amount of energy released in radioactive decay depends on the difference in mass between the original and final nucleus multiplied by the speed of light squared, as expressed by Einstein’s famous E=mc2 equation.

Big Bang and our Sun

That seems to be just what happened at the beginning of the universe. After all, the Big Bang was unimaginably energetic, so the potential existed to produce a lot of mass. Collisions between highly energetic gamma rays would produce a particle/antiparticle pair—a negative electron and positive positron, or a positive proton and negative anti-proton. Many of these particles would soon collide with their antiparticle, returning radiation back to the expanding universe.

By a second after the Big Bang, the protons, neutrons, and electrons that make up the bulk of what we see in the universe had formed. Then, about three minutes after the Big Bang, when the temperature had dropped to a still-scorching one billion degrees, protons and neutrons started to combine. These reactions formed deuterium (a form of hydrogen with one proton and one neutron in its nucleus) and helium (with two protons and two neutrons). And that was about it. The temperature of the universe was falling so quickly that there wasn’t enough time for the helium to combine into heavier elements.

That would leave us (i.e. human beings) essentially nowhere. The oxygen we breathe, the iron in our blood, the silicon in the rocks we walk on—none of these existed during the first billion years or so of the universe. But hydrogen and helium did and, just as importantly, so did gravity. Gravity pulled together clouds of hydrogen and helium gas to form stars.

Deep in the pressure-cooker cores of stars, hydrogen gets converted into helium. In a slow, complex process, four atoms of hydrogen combine into one atom of helium. The helium has slightly less mass than the four hydrogens, however, and the lost mass gets converted to energy. In the Sun, for example, about 4 million tons of matter get converted into energy every second in a core that reaches a temperature of about 15 million degrees Celsius. Fortunately for us, the Sun has so much mass that it has been shining for 4.5 billion years, and should keep going for another 5 billion more.

But all stars must run out of hydrogen fuel eventually. When they do, their helium cores begin to contract under the weight of the overlying layers and in the process heat up. Finally, the temperature gets so high (about 100 million degrees) that the helium starts to fuse into carbon, once again releasing energy in the process.

For a star like the Sun, this marks the end of the road. It can’t generate high enough temperatures to fuse any heavier elements, and it will slowly fade away after puffing off its outer layers. But stars much bigger than the Sun don’t die so calmly. Because they have more mass, they crush the material in their cores to much higher temperatures. This means they can fuse even heavier elements than helium, eventually creating oxygen, neon, sulfur, silicon, and, lastly, iron

But iron marks a dead end, because energy is required to fuse iron. Without any further source of energy, the star’s core collapses, triggering a mammoth explosion called a supernova. The chaotic conditions during a supernova create still more elements, all of which get spewed into space by the explosion. Eventually, the outrushing debris joins up with other clouds of gas to form new stars that incorporate the heavier elements.

Our Sun was one of those stars, and the planets orbiting the Sun and the life that arose on one of them all owe their existence to those earlier stars. “We are,” as the late astronomer Carl Sagan liked to say, “literally star-stuff.” Star-stuff we may be, but within a span of just 100 years, we have deduced this entire, fastastic story of the stars


The ultimate building blocks of matter? In the 1960s experiments began to show that protons and neutrons display internal structure and thus must be made of still smaller particles. Dubbed “quarks” by the American physicist Murray Gell-Mann after a line from James Joyce’s Finnegan’s Wake, these particles come in six “flavors,” called up, down, strange, charmed, top, and bottom. A proton consists of two up quarks and one down quark, while a neutron is made of two downs and one up. Combinations of quarks yield still more particles, although most are unstable and decay quickly to protons or neutrons. The very early universe was likely a dense soup of quarks and antiquarks.


Every type of particle in the universe has a corresponding anti-particle that has the opposite charge. The anti-particle of the negatively charged electron is the positively charged positron, the anti-particle of the proton and the neutron are the anti-proton and anti-neutron, respectively. The anti-proton has a negative charge, and the anti-neutron is neutral, since the opposite charge of a neutral particle (no charge) is also neutral. Predicted in 1928 by physicist Paul Dirac, anti-particles were first detected in 1932.

The early universe had nearly equal amounts of matter and antimatter, with just a slight excess of matter—about one extra particle for every 100 million photons and particle/anti-particle pairs. Because matter and antimatter annihilate one another in a burst of electromagnetic radiation (energy in the form of particles called photons, visible light is a kind of electromagnetic radiation) the universe we see today is dominated by the extra matter that couldn’t find antimatter with which to annihilate.


Baryons are particles which interact via the strong nuclear force, the force responsible for holding the nucleus together. Protons and neutrons (a.k.a. nucleons), and their constituent parts called quarks, are all baryons.

“Where does matter come from?” by Marcelo Gleiser

It is said, and rightly so, that cosmology is the branch of physics that asks the grandest questions. After all, few questions within science can equal the impact of: “Where does the universe come from?” or “What is the fate of the universe” or “Where does the matter we are made of come from?” But perhaps even more exciting than asking these questions is the fairly recent power that we have of answering them, at least partially, through a rational study of nature.

Most of us learned in high school that matter is made of atoms and that atoms are made of protons, neutrons and electrons. What we don’t usually learn in high school is that to each particle of matter there is another particle, an “anti-particle,” which is essentially the same as the particle but with opposite electric charge

Thus, the negatively charged electron has its “anti-electron,” called a positron, which has positive electric charge; the proton has an anti-proton, and so on. Now comes the interesting part. According to the laws of particle physics, matter and antimatter should be present in the universe in equal amounts. And yet, we have ample observational evidence that, at least in a very large volume that surrounds us and extends far beyond our galaxy, there is much more matter than antimatter.

When particles collide with their anti-particles, the effects are devastating; they both disintegrate into electromagnetic radiation, their energy carried away in neutral particles called photons.  In other words, if there were as much antimatter as matter in the universe, we wouldn’t be here to ask grand questions. The universe is somehow unbalanced, biased toward the existence of matter over antimatter. One of the greatest challenges in modern cosmology is to unveil the roots of this cosmic imperfection.

As with any scientific explanation, we need a few “basic ingredients,” a minimum amount of knowledge from which to build our models. The first ingredient we need is the Big Bang model of cosmology. According to this model, a small fraction of a second after the “beginning,” many kinds of particles and their anti-particles, in equal amounts, roamed about and collided with each other immersed in tremendous heat, as in a cosmic minestrone soup.

In this hot cosmic furnace, many different types of particles were being cooked, not necessarily the familiar quarks (the constituents of protons and neutrons) or electrons. As the universe expanded and cooled, a sort of selection mechanism not only biased the creation of quarks and electrons over other types of particles, but also generated the excess number of particles over anti-particles. Surviving the annihilation with their antimatter cousins, these excess particles organized themselves into more complex structures, until eventually atoms, mostly hydrogen, were formed when the universe was about 300,000 years old. The mystery is to understand what kind of physics could generate this bias.

At first, resolving this question seems impossible. How can we possibly understand the mechanism that selected the existence of matter over antimatter during the earliest stages of evolution of the universe? In 1968, Andrei Sakharov, best known as the father of the Soviet bomb, proposed a recipe to generate more matter than antimatter in an expanding universe. He suggested that three conditions must be satisfied in order to produce the matter excess. First, there must be a way of creating more matter and antimatter particles of the kinds important to us, the kinds that make up the atoms we are made of. Then, there must be a mechanism to bias the creation of more matter than antimatter. And finally, once we have an excess of matter particles over their antimatter partners, we must make sure that this excess is not erased as the universe continues to expand.

The first of these conditions is the creation of both baryons and anti-baryons from collisions involving the other particles present in the primordial soup. Baryons are particles which interact via the strong nuclear force, the force responsible for holding the nucleus together. Protons and neutrons (a.k.a. nucleons), and their constituent parts called quarks, are all baryons. At low energies, the number of baryons participating in collisions between different particles is conserved: that is, just like electric charge, the total number of baryons before an interaction equals the total after. If we are interested in making baryons, as we must in order to create matter in the universe, this conservation law is not very useful. According to Sakharov’s requirement, however, at very high energies the interactions between elementary particles should not conserve the number of baryons. That is, at high energies both baryons and anti-baryons can be created from “other” particles. These high energies are naturally realized in the hot furnace of the early universe.

But this first condition does not differentiate between baryons and anti-baryons. At high temperatures we could still create the same number of each, and that wouldn’t cause a bias toward matter over antimatter. We need a second condition. Once the high energies of the early universe allow for the creation of baryons and anti-baryons, we need a condition that selects, or biases, the creation of baryons over anti-baryons, an arrow pointing in the correct direction (i.e., toward matter).

In 1964, J.H. Christenson and his collaborators found experimental evidence that interactions between certain baryons do indeed exhibit this bias. It is as if Nature has its own biases, in this case toward more baryons. If this is true in laboratory experiments, no doubt this will also be true in the early universe. Making excess matter over antimatter is not as hard as it initially seemed to be. But this is still not the whole story. One more challenge remains, which has to do with the physics of hot systems, also known as thermodynamics.  

One of the properties of very hot systems is that they have no memory of their past. Imagine a coffee spoon which is initially cold. Now immerse one of its ends into a very hot cup of coffee. What happens? Although initially only the end in the coffee will be hot, very quickly the whole spoon will be equally hot. You won’t be able to tell which of the two ends was immersed into the coffee cup; the system (coffee spoon and hot coffee) lost its “memory.” Another term for this loss of memory is thermal equilibrium. If the early universe was in thermal equilibrium, any excess baryons would have been deleted; in equilibrium, the net baryon number is zero. In order to maintain the baryon bias as the universe cools, we need to make sure the universe doesn’t “lose its memory” and delete the new baryons. Therefore, we need a third condition

We need what are called “out of equilibrium” conditions. In order to “freeze” the net number of baryons produced by the first two conditions, the early universe could not have been always in thermal equilibrium.  We are very familiar with systems that are out of thermal equilibrium in our everyday life.  An example is condensation of steam. More specifically, imagine a container filled with hot steam which is immersed into a large bucket with cold water. The steam, being too hot compared with the cold water, is out of thermal equilibrium. In order to attain equilibrium it will go through a phase transition; the steam will cool down and condense, going from a gas phase to a liquid phase. As it does so, we will observe the appearance of droplets of the liquid phase that will grow and coalesce. The phase transition ends when the steam is completely converted into water.

How does this reasoning apply to the early universe? Strange as this may sound,  the universe also went through phase transitions. Particles—and their properties—are also sensitive to temperature. The standard model of particle physics successfully describes how particles interact at energies over a thousand times larger than nuclear energies. According to this model, at very high temperatures all particles but one, the so-called Higgs particle, have no mass, while at lower temperatures they acquire a mass through their interactions with the Higgs particle. We say that matter has two different “phases,” above and below the temperature at which particles like the quarks and the electron acquire a mass.

Thus, as the temperature of the early universe dropped, it went through a phase transition, and particles gained their mass.  Like water droplets in steam, droplets of the low temperature (massive) phase appeared within the high temperature (massless) phase, growing and coalescing, in a typical out-of-equilibrium phase transition. Since only in the high temperature phase are baryons created in excess over anti-baryons (recall that the first two conditions apply only at high temperatures), these excess baryonic particles will penetrate the droplets of the massive phase, like viruses invading cells, becoming the net baryon number in the low temperature phase. As the droplets grow and coalesce, the whole universe is converted into the massive phase, completing the phase transition. According to our current models of “baryogenesis,” the creation of the excess baryons occurred when the universe was about one thousandth of a billionth of a second old. The protons and neutrons we are made of are the fossils of this primordial event.

So is this it? Is our work finished? Far from it. The simplest particle physics models we have do not generate the observed excess of matter over antimatter. Even worse, our true understanding of the complicated dynamics of these phase transitions is at best incomplete, leaving many questions unanswered at the moment. We have the broad outline of an explanation for the generation of matter in the universe, but the details are far from being understood.