How are quarks arranged within different subatomic particles?
Not sure if this answers your question, but:
An up Quark has a positive charge, and a down Quark has a negative charge. For reasons of mathematical convenience, these charges are measured in thirds, mainly because nucleons are thought to be groups of three quarks. Therefore, the strength of these charges is given as +2/3 for the up Quark, and -1/3 for the down.
So proton has two up quarks, and one down (+4/3 and -1/3), giving it a positive charge of 1 (+3/3).
A neutron has one up, and two down (+2/3 and -2/3), giving it a total charge of zero.
And electron is a "lepton" which is almost like a Quark, except that it can move on its own. It has a charge of -1.
As for the configuration of the quarks within the protons and neutrons, I do not think that has ever been determined. However, my information is not the most up-to-date, so perhaps someone else has heard of more recent discoveries as to their exact arrangements.
'Arranged' really doesn't have a great meaning on that scale, I imagine something simlair to the liquid-drop model for a nucleus is used. They are 'arranged' so that they have an integer charge and are 'colourless'. There are 5 types of quarks that have been observed and another quark which there is strong evidence for.
If 'UP and 'DOWN' quarks make up the atoms what do the 'TOP', 'BOTTOM', 'STRANGE' and 'CHARMED' quarks do or are they just theoretical?
As of 1995, there is experimental verification of all six "flavors" that a quark comes in. The final ("top") quark was detected that year. The main reason it took so long is that it has a large effective mass of 181(+-)12 GeV, which is at the high end of energies that have been obtained in accelerators (and so it couldn't be created until then).
As for the quark model of composite particles (most familiarly due to their high stability: the neutron and proton...but there are many others), it is a difficult thing to picture and, in fact, all the details aren't clear yet. The simplest hand-waving explanation I can give is that the quarks form a bound state, analogous to the bound state of an electron and a nucleus to form atoms. Just as in that case, the bound state is not like a planet going around the Sun, but rather a *quantum mechanical* bound state, which is fuzzier. In this way, you can have 2 or 3 (and recently observed, 5) quarks in a quantum mechanical bound state, making up the myriad of compositie particles we see in accelerators. There are certain rules for what kind of composite particles you can form, which come from the "standard model of particle physics".
There are subtleties that exist here that don't exist for the analogy of the electron bound to a nucleus. This is due to the fact that the strong interaction (mediated by "gluons") is the governing interaction among quarks, while in the analogy, the eletron and nucleus are goverened by the electromagnetic interaction (mediated by photons). *The strong interaction is very different from the electromagnetic*. For one thing, the gluons interact with each other (photons don't do this, with a technical exception that's unimportant), and so in a compositie particle like a proton, the quarks are bound together by virtual gluon exchange, but there is also a haze of gluon goo they sit in (instantons). It's a very interesting picture, but is difficult to relay in "first principles" language.
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