Why did the Doctor think he was going to die in "The Time of the Doctor" even though he saw Capaldi in "The Day of the Doctor"?

TL; DR: Yes, it's possible that during Time of the Doctor, the Eleventh Doctor has forgotten his future self's involvement in the saving of Gallifrey.

To add to the answer by Hypnosifl and to answer the specific part of your question "Could he have just forgotten?", remember that the War Doctor and the Tenth Doctor (and by extension, the Ninth) don't retain the memories because of the muddled time streams, but the Eleventh does, because it's his present. Capaldi's appearance, though, would be from his future, and so it's entirely likely that he doesn't remember it for the same reason.

Maybe it's that Time Lords can't generally retain memories of interactions with their future selves. This is a consequence of the Blinovitch Limitation Effect shown with the Brigadier in Mawdryn Undead -- the younger version can't remember the interaction with the older. It also explains why the Fifth Doctor doesn't recall being pulled into the Death Zone in The Five Doctors despite having been there three times previously. (I say "generally" because it seems like the Second Doctor remembers the events of The Three Doctors during his conversation with the Brigadier in The Five Doctors. However, since the Time Lords deliberately brought the three incarnations together, they may have had some way to circumvent the effect.)

Granted, the events of Time Crash seem to contradict that since it implies that the Fifth Doctor would remember watching the Tenth fix the TARDIS, but that could be explained by the memories of the younger simply being suppressed until he "catches up" with the future events. So he does remember, he just doesn't remember that he remembers until he's on the other side of the conversation; that is, when he's Ten.

This also accounts for Eleven's line in Day of the Doctor, "This is where I come in." That implies that he remembers meeting his future self when he was Ten, in spite of explicitly saying that Ten won't remember. The memories are still there, just inaccessible until the most forward point in the timeline. At the point where the time streams cross, Eleven suddenly has access to the memory his past self made, leading him to remark, essentially, "Oh, right! This happened. I'd forgotten."

grammaticality - Seem small clause

It is said that the omission of "to be" is allowed only when the adjective (phrases), noun (phrases), or prepositional phrase comes after the to be like this:

a He seemed (to be) angry about the decision.

b This seemed (to be) of great importance.

c She seemed (to be) a great player.

But I found some strange things about it. For example, this.

d He seemed excited by the news.

Well, excited by the news is definitely not an adjective phrase. Were the to be inserted in it, it would describe the action like this: the news excited him. So "excited" would be a past participle used as a verb after an auxiliary verb, not an adjective.

Like in a passive voice where the participles after the "to be" are considered verbal, or stative, participle phrase when not considered a pure adjective.

e He was bored by the music. <- bored by the music is not an adjective phrase but a stative, or verbal, participle phrase.

https://en.wikipedia.org/wiki/English_passive_voice#Stative_and_adjectival_uses

So why is it possible to say sentence d when "excited by the news" is a stative phrase not an adjective phrase? Wouldn't it be equivalent to deleting to be with present participle like this : He seemed doing the job.

Edit: What I referred to as stative past participle is known as dynamic passive by many. I think Wikipedia had some problem.
http://www.grammarphobia.com/blog/2008/11/stative-seeking.html

offensive language - What term describes enjambment alluding to a taboo word?

First of all, 'enjambment' is a technical word used when describing poetry.

In poetry, enjambment or enjambement is the breaking of a syntactic unit (a phrase, clause, or sentence) by the end of a line or between two verses.

http://en.wikipedia.org/wiki/Enjambment

An example of a Mind Rhyme is given in Wikipedia:

http://en.wikipedia.org/wiki/Mind_Rhyme

One very hot day in the summer last year

A young man was seen swimming round Brighton Pier;

He dived underneath it and swam to a rock

And amused all the ladies by shaking his

Fist at a copper who stood on the shore,
The very same copper who copped him before.
For the policeman to order him out was a farce,
For the cheeky young man simply showed him his

Graceful manoeuvres and wonderful pace...[3]

The missing word in the first verse is of course - cock - and in the second verse - arse.

The missing word, which is a rude word is not spoken out loud. So it is a way of saying something rude without saying something rude.

Subverted Rhyme

http://tvtropes.org/pmwiki/pmwiki.php/Main/SubvertedRhymeEveryOccasion

Para: We are villains who like to rhyme...
Dox: In fact, we do it all the time.
Para: You may think it's rather crass...
Dox: But you can stick your cards right up your nose.
Para: ...You were supposed to say "ass," brother. I thought we rehearsed this.

Again, the rude word is 'ass' or 'arse'.

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trope [trəʊp]
n
1. (Literature / Rhetoric) Rhetoric a word or expression used in a figurative sense
2. (Music, other) an interpolation of words or music into the plainsong settings of the Roman Catholic liturgy

To answer the question

Is "Miss Susie" a mind rhyme?

Yes and No

I am not particularly familiar with Miss Susie. I think part of a idea is that people are already thinking of different versions when they hear the first version.

Is there a literary or poetic term for this usage of enjambment?

If I was a Moderator I might consider doing something with this question. Because it is not really a question at all, but more of an excuse for the person asking the question to show off their knowledge.

Enjambment is a literary or poetic term. What more do you want?

A mind rhyme based on enjambment.

It is a mistake to imagine there is a corresponding single word to describe everything that exists in the known universe.

biochemistry - How crowded is the bacterial cell?

Composition of E. coli (dry weight): 55% protein, 20% RNA, 10% lipid, 15% other

Protein concentration is about 100 mg/ml or 3 mM. From the size of an E. coli cell, 1 nM is about 1 molecule/cell. This is ~1000 molecules/cell for HeLa cells.

Diffusion coefficient for an "average" protein: D ~ 5-15 microns^2/s, or ~10 ms to traverse an E. coli. For reference, a small metabolite in water diffuses about 30-100x faster.

Reference: Cell 141:1262, Key Numbers in Biology

biochemistry - Basic Amino Acid Residue Binding Mechanism to DNA

This question has no particular answer. There are several families of DNA binding proteins, some of them bind specifically (e.g. restriction enzymes like EcoRI which binds to and cuts GAATTC or transcription factors like lac repressor which binds a particular point of the e coli genome about 25 base pairs long) and some of them bind semi-specifically (e.g. zinc fingers which bind GC rich regions), others non specifically (e.g. the sliding DNA clamp).

For all of these proteins, they will have a tendency to have positively charged amino acids facing the DNA because the DNA's phosphate backbone is negatively charged. There are lots of protein motifs (like the helix turn helix motif) that fits into the major or minor groove of the DNA. The lysine and argenine are important because they are the positively charged amino acids. Histidine is also positively charged, but it is not as long and flexible, and doesn't seem to fit as often or as well.

http://en.wikipedia.org/wiki/DNA-binding_protein

cell biology - RNA or ribosome, which one moves during translation?

The ribosome moves relative to the mRNA by, in effect, pulling itself along it. If both the ribosome and the mRNA are freely floating and not attached to anything else (as in jp89's answer), the relative amount of movement should depend on their relative masses.

(Actually, it also depends on how much drag each of them experiences with respect to the surrounding liquid medium, but since I have no idea how much that is, and since it's probably highly conformation-dependent anyway, I'm going to just ignore that and just assume that the drag is also more or less proportional to mass, at least to first order.)

As it happens, a quick Google search and some back of the envelope calculation suggests that the mass of a ribosome and the average mass of an mRNA are both around a megadalton. Of course, the length (and thus the mass) of an mRNA varies quite a lot, so it would seem likely that sometimes it's the ribosome that moves mostly, sometimes it's the mRNA, and sometimes it's both.

Also, as shigeta and others have pointed out, there can be more than one ribosome attached to the same mRNA strand. That's going to make the mRNA move more (and, correspondingly, the ribosomes move less), since there are more ribosomes pulling it along.
Then there's also the protein being transcribed, which is attached to the ribosome but also being moved with respect to it. And I really have no idea how negligible the interactions with the tRNAs and so on are. It's a mess, but my guess would be that, usually, it's mostly the mRNA that moves, but that the ribosomes aren't completely stationary either (unless they're attached to something, of course).

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Ps. Here's an exercise for you, which you may try out if you happen to have a friend who works at a public swimming pool. Otherwise consider it a gedankenexperiment. You know those floating ropes that separate the lanes in the pool? Try getting your friend to let you into the pool when it's not in use and to release one of the ropes from the walls. Then get in, grab the rope with your arms and legs and try pulling yourself along it. While doing so, try to decide whether it's you or the rope who moves more. (Also, to more closely approximate the Reynolds numbers involved inside a cell, imagine doing this in treacle instead of water.)

genetics - Could Junk DNA be used as a Turing Machine by nature?

By programmable, I suppose you mean that it contains information or can be altered in response to some input or stimulus. The answer is "no" for both. Well, sort of.

Does noncoding DNA contain information? By definition, no. There are probably many regions of the genome that appear to have no information, only later to be found to contain introns, regulatory elements such as enhancers, boundary element, MAR/SARs, targeting sites, etc. Even functional tests (such as removing the region) may not reveal anything because the effects could be minor, or only evident under special conditions. But arguably, if you remove a region and it has an effect on the organism, then it's not really a noncoding DNA, it's just you didn't see the coding before hand.

As for the latter, can it altered, the answer is again "no," or at least "apparently not." Intergenic regions (those stretches of DNA that do not contain obvious or characterized transcribed regions or their control elements) are very stable between organisms and even between species. They seem to have a mutation rate expected for having no information, and thus free to mutate slowly without being swept away. There is no evidence (as far as I know) of any region of the genome being purposefully altered, with the exception of a handful of specific genes whose regulation is controlled by DNA nicking or some such.

Perhaps I am missing your question, being a biologist and not really knowing what a "Turing Machine" is. If I misunderstood, please clarify.