Reading a lot after asking my question, I understood that it is too broad. So, I asked only the second part of my question.
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1If the 1st law of Thermodynamics is correct, it the universe has to have it 0. Is this sentence saying that the universe has to have zero total energy? If so, then please see the answers to this question: https://physics.stackexchange.com/questions/2838/is-the-total-energy-of-the-universe-zero Basically the total energy is not a well-defined thing in cosmological spacetimes. – Feb 25 '19 at 17:54
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1More generally, I'm not clear on what your question is. It seems that you're asking about the mechanisms by which structure formed, and you want to analyze that in terms of energy, but it's not clear to me what you mean by points 1 and 2, or why you think positive or negative energy is relevant. Basically gravitational interactions cause matter to collapse into structures, and at the smaller scales this is well described by Newtonian gravity. At larger scales, you need general relativity. – Feb 25 '19 at 17:56
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Basically, because gravity is wholly attractive so it continues to act on cosmological distances. They only came as a surprise because large scale surveys of the universe have only been recently available. – Mozibur Ullah Mar 02 '19 at 16:37
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To Mozibur Ullah: Yes, you are right. But it is only the superficial mechanism that brings clusters together. This mechanism does not explain why the structure is hierarchical. Nor, from my viewpoint, the Einstein field equations can be used to explain the hierarchical structure (HS). Looking deeper, every entity at some level of HS has its new emergent properties that did not come from the lower level properties. At least, it is at the microscopic levels of the universe structures. – Emil Mar 03 '19 at 14:07