Here's my explanation of the history of the universe in light of the chronology given in the 1st day of creation.
(1) In the beginning, God created the universe.
The universe itself emerged from nothing 13.799 ± 0.021 billion years ago. Before that emergence, there was no time, no space, no energy, and no matter. Right there in that first instant, space-time began. At the incredible temperatures and energies of that first instant, nothing was stable. But as the universe expanded, it cooled, and gradually the basic pieces of normal matter were formed from that incredible energy.
Quarks were the first particles to form. Today, quarks only exist in tightly bound groups, but back then, space was so small and quarks were squeezed so close together that they were not bound to other specific quarks. The colors of these quarks just represent a property that attracts them to one another. There are two kinds (or flavors) of quarks in normal matter:
1. The up quark
2. The down quark.
As space-time got bigger, quarks lost their freedom and found themselves locked into groups of three inside a proton or a neutron. A proton is formed from two up quarks and one down quark while its slightly heavier cousin, the neutron, is composed of two down quarks and one up quark. Just about every proton and every neutron in existence today was formed at the time of inflation and was crammed into that primordial ball.
At the time when these small nuclei began to form, the protons and neutrons were very hot and moving very quickly, and could easily combine. However as the universe rapidly expanded, the density and temperature dropped. This was so rapid that only simple nuclei had time to form. Most of the matter formed was hydrogen-1 (simple hydrogen nuclei with one proton and no neutrons). A small and significant amount of helium nuclei formed and trace amounts of the heavier nuclei lithium, beryllium and boron were also created. It was so hot that these nuclei remained positively charged ions for about 400,000 years; only then was it cool enough for the nuclei to capture electrons and form neutral atoms. These are the simplest elements formed in the time soon after the Big Bang. There are more than 90 naturally occurring elements on Earth, but elements with larger, more complex nuclei did not form in this primordial process. So, you may ask, where did the elements that exist today come from? The answer is that they have been created in stars.
By observing a huge number of stars, astronomers developed a picture of the life of a star. In the early universe, there were no stars. The first generation of stars began to form about one billion years after the Big Bang. Clouds of the original gas mixture formed, and the force of gravity in such large gas clouds was enough to draw gas towards regions of greater density.
The gas heated up as it fell inwards and the result was a large, dense ball of hot gas called a protostar. If the mass of the protostar is high enough, the temperature and pressure at its center are extremely high (many thousands of degrees). Under these conditions, gas does not resemble any state found on Earth. It is known as plasma, which is the 4th state of matter. At these temperatures, hydrogen nuclei begin to fuse to form helium nuclei. Note that atoms are generally in the form of ions, stripped of their electrons. It is these nuclei that fuse together, not neutral atoms.
In a nuclear reaction, you end up with different elements which were not present at the start of the reaction. However, the total mass number and the total charge number are conserved (they stay the same). Sometimes, unusual particles like positrons (positively charged electrons), will be formed to balance the charge number. The most basic reaction occurring in all stars is the proton–proton chain (P–P chain).
The first step is two hydrogen-1 atoms fusing together to form a hydrogen-2 (or deuterium) nucleus:
hydrogen-1 + hydrogen-1 → hydrogen-2
The total mass number on the left is 2, and this is conserved on the right. The hydrogen atoms on the left have a total charge of +2, while the hydrogen atom on the right has a total charge of +1, thus another particle is needed to balance the equation. It must have a charge of +1, but no mass number. A positron is needed to complete the equation:
hydrogen-1 + hydrogen-1 → hydrogen-2 + positron
On the left, the isotopes of hydrogen had no neutrons, but on the right a neutron has been created. One of the original protons formed a neutron by emitting the positron. This removes a positive charge from the newly formed atom. The positron will combine with an electron and form energy. This leads to more steps in the proton–proton chain. As you can see, there's a gradual buildup of material from this simple proton–proton chain reactions:
1. This fusion reaction produces helium-3
hydrogen-2 + hydrogen-1 → helium-3
2. The fusion of two helium-3 nuclei produces helium-4 and regenerates two hydrogen-1 atoms
helium-3 + helium-3 → helium-4 + 2(hydrogen-1)
Stars (like our Sun) produce enormous amounts of energy. How is such a huge amount of energy produced? Nuclear reactions are able to release far more energy than chemical reactions because some of the mass is converted into energy. The energy released is given by the equation e = mc^2, where m is mass lost in kilograms and c is the speed of light, 299,792,458 m/s.
A prediction from Einstein's equation can be made, where a slight loss of mass causes a huge release of energy (I have made a table of the masses of some isotopes below). Einstein's equation is used to calculate the energy released when a given mass is lost in a nuclear reaction. Einstein explained that mass is simply one form of energy. Energy can be converted from one form to another, including the form called mass.
For example, burning 4 grams of hydrogen in oxygen, releases approximately 242 kilojoules of energy. However, nuclear fusion of the same 4 grams of hydrogen releases more than 10 million times as much energy! What happens to the energy released when these reactions occur in stars? Initially it is in the form of gamma rays, which are more energetic and powerful than x-rays. If the Sun emitted mainly gamma rays, life on Earth would not survive. As the gamma rays radiate out from the hottest regions in the center of the star, they are absorbed and re-emitted many times. By the time this energy reaches the surface, it is emitted by stars such as the Sun as mainly visible light, with some UV rays and infrared radiation. The exact color of the light emitted by a star depends on its surface temperature.
For each helim-4 nucleus created by fusion, the calculated mass loss represents large amounts of energy released. To do this in reverse and split the helium nucleus into separate protons and neutrons would require energy. This energy requirement has the effect of binding larger nuclei together, so that the electrical repulsion between the protons does not cause the nucleus to fly apart. The binding energy per nucleon (proton or neutron) is defined as the energy required to separate a nucleus into individual protons and neutrons divided by the total number of nucleons. Iron has the greatest binding energy per nucleon. Formation of elements up to iron by fusion releases energy. Formation of elements heavier than iron requires energy.
Knowing that energy is required to produce heavy elements by fusion, you might wonder how heavier elements form. The high temperatures in a large star provide the necessary energy. Elements heavier than iron also form when free neutrons are absorbed. Elements up to bismuth can form this way. Large amounts of energy are unleashed in a supernova explosion, and the atoms already formed inside a large star are slammed into each other and bombarded with a stream of neutrons. These atoms fuse, creating most of the elements in the periodic table. Elements heavier than iron are much less abundant in the universe than the lighter elements. This is predicted by our knowledge of the life cycles of stars. If you think about it, the larger atoms in your body are dust from ancient stars!
Eventually the hydrogen in the core of a star is all converted to helium. The core then becomes unstable and contracts and the outer shell of hydrogen expands and cools. It begins to glow red rather than yellow or blue. The star becomes a red giant. As the core contracts, fusion reactions convert helium to carbon, producing a further burst of energy. The fusion reactions are:
helium-4 + helium-4 → beryllium-8 + energy
helium-4 + beryllium-8 → carbon-12 + energy
Or you can get carbon-12 via a triple alpha reaction:
3(helium-4) → carbon-12 + energy
As time passes, some of the carbon formed mixes with the outer layers. The next step depends on the mass of the star. For smaller stars up to about 1.4 times the mass of the Sun, fusion stops. The core collapses again. Shock waves cause the outer layers to be expelled. This expanding shell of gas glows brightly and is called a planetary nebula. It is mostly hydrogen, with some helium and carbon. The hot core, called a white dwarf, glows for some time. Eventually it cools and becomes a black dwarf. Larger stars explode in a final burst of energy called a supernova. The remnant core collapses on itself with such force that the electrons are forced into the nuclei of atoms. They combine with protons to form neutrons and the core becomes a tiny dense ball of neutrons called a neutron star. Some of these neutron stars spin rapidly and emit a powerful beam of radiation that can be detected as rapid pulses of energy. This is called a pulsar. For stars that are more than five times the mass of the Sun, the nuclear fusion process does not stop when carbon forms. The huge pressures and temperatures mean elements up to iron can form. Shells, like the layers of an onion, form around the core. In each shell a different element is present, fusing to form a heavier element at the junction between shells. Unused hydrogen forms the outermost layer. During a supernova explosion, these elements (many common in planets and living organisms) are thrown out into space. At the moment of explosion, the core contracts to a singularity. This is a small, dense object with such strong gravitational pull that not even light can escape from its surface, thus we have a black hole.
Finally in relation to v. 1, the word "universe" is accurately translated from the Hebrew phrase haššāmayim weʾēṯ hāʾāres. It's a merism for the expression of "totality". Its use in the bible appears to be restricted to the totality of the present world order and is equivalent to the "all things" in Isaiah 44:24. Particularly important to notice is that its use elsewhere in scripture suggests that the phrase includes the sun and the moon as well as the stars (Joel 3:15–16).
(2) When the earth was as yet unformed and desolate, with the surface of the ocean depths shrouded in darkness, and while the Spirit of God was hovering over the surface of the waters,
At the start of this verse, we see the Earth 4.5662 ± 0.0001 billion years ago, as a chaotic amorphous mass of cooling gases, not yet in its present spherical shape. When Earth formed soon after, the initial conditions on its surface is darkness where the waters initially covered the entire surface of the planet. As King David himself summarized:
You covered the primeval ocean like a garment; the water stood above the mountains.
Here's a 2009 paper for evidence that the Earth first had a ~1 km deep global ocean: The Earth-Moon system during the Late Heavy Bombardment period
No continents rose above the water, and the whole of Earth's watery surface remained in darkness. No light from the Sun reached through due to the thick atmosphere in this early stage, as God confirms to Job:
when I made clouds to be its clothes and thick darkness its swaddling blanket
All planets start with opaque atmospheres. Thick layers of hydrogen, helium, methane, and ammonia surround them (for example, giant cold planets such as Jupiter and Saturn perpetually retain their primordial opaque atmospheres). This gas cloud, combined with a dense shroud of interplanetary dust and debris, guarantees that no sunlight (or starlight) can reach the surface of a primordial planet such as early Earth.
The last phrase of v. 2 says that the "Spirit of God was hovering over the surface of the waters." The Hebrew word for "hovering" is meraḥep̱eṯ, and it appears only one other time in Deuteronomy 32:11 (as yeraḥēp̱). This has led some linguists to infer that the Spirit's "hovering" over the waters refers to life's origination in Earth's ocean, even before light for photosynthesis shone through.
This interpretation goes back to the early Church Fathers where we read of Ephrem the Syrian (4th century) writing: "The Holy Spirit warmed the waters with a kind of vital warmth, even bringing them to a boil through intense heat in order to make them fertile. The action of a hen is similar. It sits on its eggs, making them fertile through the warmth of incubation."
Earth's geology testifies that marine life did indeed arise before all other life-forms. The oldest fossils found to date show us unicellular, marine-like organisms in clearly identified marine sediments.
(3) God said, "Let there be light!" So there was light.
The Hebrew verb used for "Let there be" is hāyāh, and this word choice makes sense. Remembering Earth's initial conditions and that the frame of reference is Earth's surface, we can comprehend what happened:
1. Light penetrated Earth's thick atmosphere for the first time.
2. Earth's atmosphere changed from opaque to translucent.
The change in Earth's atmosphere is unique for our solar system dynamics. In planetary formation, the greater a planet's surface gravity and the greater a planet's distance from its star, the heavier and thicker its atmosphere. Theoretically, Earth should have an atmosphere heavier and thicker than that of Venus, but in fact it has a far lighter and much thinner atmosphere. The solution lies with Earth's moon. The moon is younger than Earth. According to the Apollo lunar rock samples, it is only 4.51 billion years old, compared to Earth's 4.5662 ± 0.0001 billion years. The same lunar rocks gathered by Apollo astronauts tell us that the moon's crust is chemically distinct from Earth's. Its distinct chemical makeup and its younger age establish that the moon and Earth did not form together. The latest study of this was published earlier this year: Early formation of the Moon 4.51 billion years ago
Astronomers have measured the moon's slow and steady spiraling away from the Earth, which in turn slows Earth's rotation. Therefore, these calculations show that the moon was in contact with the Earth ~4.51 billion years ago, thus implying some kind of collision at that time. Indeed, a collision scenario fits all the observed Earth-moon parameters and dynamics: a body at least the size of Mars (nine times the mass of the moon and 1/9 the mass of Earth), made a head-on hit and was absorbed into Earth’s core. Such a collision would have blasted almost all of Earth’s original atmosphere into outer space. The cloud of debris arising from the collision would orbit Earth and eventually coalesce to form our moon. In summary, this collision appears to have been perfectly timed and designed to transform Earth from an "unformed and desolate" place into a site where life could survive and thrive.
(4) God saw that the light was beautiful. He separated the light from the darkness,
(5) calling the light "day," and the darkness "night." The twilight and the dawn were day one.
With sunlight now penetrating Earth's atmosphere, an observer on the planet's surface could detect for the first time the cycle of day and night. Though the Earth had been rotating since its beginning, only now does "day" and "night" become discernible. When all of Earth's surface was permanently dark, no easy means existed for marking time. Now a fixed period of light would follow a fixed period of darkness.