Ciro Santilli @cirosantilli 40

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OpenWorm Updated 2025-07-16

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openworm.org

Whole organism simulation of C. elegans.

High level simulation only, no way to get from DNA to worm! :-) Includes:

nervous system
muscle system

3D body viewer at: browser.openworm.org/ TODO can you click on a cell to get its name?

Video 1.

OpenWorm Sibernetic demo by Mike Vella (2013)

Source. Sibernetic adds a fluid dynamics solver for brain-in-the-loop simulation of C. elegans.

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s-orbital Updated 2025-07-16

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x86 Paging Tutorial / Basic TLB operation Updated 2025-07-16

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After a translation between linear and physical address happens, it is stored on the TLB. For example, a 4 entry TLB starts in the following state:

  valid  linear  physical
  -----  ------  --------
> 0      00000   00000
  0      00000   00000
  0      00000   00000
  0      00000   00000

The > indicates the current entry to be replaced.

And after a page linear address 00003 is translated to a physical address 00005, the TLB becomes:

  valid  linear  physical
  -----  ------  --------
  1      00003   00005
> 0      00000   00000
  0      00000   00000
  0      00000   00000

and after a second translation of 00007 to 00009 it becomes:

  valid  linear  physical
  -----  ------  --------
  1      00003   00005
  1      00007   00009
> 0      00000   00000
  0      00000   00000

Now if 00003 needs to be translated again, hardware first looks up the TLB and finds out its address with a single RAM access 00003 --> 00005.

Of course, 00000 is not on the TLB since no valid entry contains 00000 as a key.

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CIA 2010 covert communication websites / Non Reuters ranges Updated 2025-07-16

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Electron configuration notation Updated 2025-07-16

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We will sometimes just write them without superscript, as it saves typing and is useless.

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Invalid Bitcoin script Updated 2025-07-16

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They appear to be included, with rationale that you can already include syntactically valid crap in an unprovable way: github.com/bitcoin/bitcoin/issues/320 Better then have syntactically invalid crap that is provable.

The outputs of this transaction seem to be the first syntactically incorrect scripts of the blockchain: blockchain.info/tx/ebc9fa1196a59e192352d76c0f6e73167046b9d37b8302b6bb6968dfd279b767?format=json, found by parsing everything locally. The transaction was made in 2013 for 0.1 BTC, which then became unspendable.

The first invalid script is just e.g. "script":"01", which says will push one byte into the stack, but then ends prematurely.

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x86 Paging Tutorial / Hardware implementation Updated 2025-07-16

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Paging is implemented by the CPU hardware itself.

Paging could be implemented in software, but that would be too slow, because every single RAM memory access uses it!

Operating systems must setup and control paging by communicating to the CPU hardware. This is done mostly via:

the CR3 register, which tells the CPU where the page table is in RAM memory
writing the correct paging data structures to the RAM pointed to the CR3 register.
Using RAM data structures is a common technique when lots of data must be transmitted to the CPU as it would cost too much to have such a large CPU register.
The format of the configuration data structures is fixed by the hardware, but it is up to the OS to set up and manage those data structures on RAM correctly, and to tell the hardware where to find them (via cr3).
Then some heavy caching is done to ensure that the RAM access will be fast, in particular using the TLB.
Another notable example of RAM data structure used by the CPU is the IDT which sets up interrupt handlers.
The OS makes it impossible for programs to change the paging setup directly without going through the OS:
CR3 cannot be modified in ring 3. The OS runs in ring 0. See also:
- stackoverflow.com/questions/5957570/what-is-the-difference-between-the-kernel-space-and-the-user-space/44285809#44285809
- stackoverflow.com/questions/18717016/what-are-ring-0-and-ring-3-in-os
the page table structures are made invisible to the process using paging itself!

Processes can however make requests to the OS that cause the page tables to be modified, notably:

stack size changes
brk and mmap calls, see also: stackoverflow.com/questions/6988487/what-does-brk-system-call-do/31082353#31082353

The kernel then decides if the request will be granted or not in a controlled manner.

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Classification of 3-transitive groups Updated 2025-07-16

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Might be a bit complex: math.stackexchange.com/questions/698327/classification-of-triply-transitive-finite-groups

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Collimated beam Updated 2025-07-16

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Cool data embedded in the Bitcoin blockchain / Rickrolling Updated 2025-07-16

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Rickrolling lyrics were mined several times into the blockchain.

The first currently known instance is as a link right during the prayer wars on block 142573 (2011-08-25) as the miner message:

Militant atheists, bit.ly/naNhG2 -- happy now?"

which redirects to www.youtube.com/watch?v=mGDuExhS6Nw&blockchain

Around block block 246k (e.g. 27b7c526489dac8245747fa1c425a2e3eb07dea57b294eb4ae583fec9b859fcf, 2013-10-17) we note several transactions starting with a XML format <CG SZ="1156"><MG>... the first one being 0b4efe49ea1454020c4d51a163a93f726a20cd75ad50bb9ed0f4623c141a8008 As mentioned not very clearly at www.righto.com/2014/02/ascii-bernanke-wikileaks-photographs.html#ref12 the content of the first <MG><payload></MG> is a Base64 encoded string

Catagory: Poetry
Title: Never Gonna Give You Up
Performer: Rick Astley
Writer: Mike Stock, Matt Aitken, Pete Waterman
Label: RCA Records

followed by lyrics also base64 encoded as part of the XML metadata. Hidden surprises in the Bitcoin blockchain by Ken Shirriff (2014) was not able to identify the exact format either. At twitter.com/EMBII4U/status/1655831533750562816 EMBII mentions that this was part of an upload test.

tx d29c9c0e8e4d2a9790922af73f0b8d51f0bd4bb19940d9cf910ead8fbe85bc9b (2013-11-13) contains a plaintext Rickroll lyric in an output script via OP_RETURN.

tx 15b11e8d4e5b9425f024b381ba0cb7a54a35e52389bb4855f505772ce685b39c (2014-06-24): starting from this transaction, the lyrics were inscribed several times via input scripts. Then again:
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 (2015-09-30)

They were mega obnoxious!!! Who does this kind of crap for more than one year!!!

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E. Coli K-12 MG1655 origin of replication Updated 2025-07-16

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biocyc.org/ECOLI/NEW-IMAGE?type=EXTRAGENIC-SITE&object=G0-10506:

Note that this is not the conventional starting point for gene numbering: Section "E. Coli genome starting point".

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ELF Hello World Tutorial / Dynamic section Updated 2025-07-16

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Contains a lot of different flag masks.

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GitHub Sponsors Updated 2025-07-16

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GitHub users deleted by GitHub Updated 2025-07-16

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stackoverflow.com/questions/50720844/can-github-delete-your-account/66105692#66105692

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Newton supported the corpuscular theory of light Updated 2025-07-16

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Quantum circuit Updated 2025-07-16

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A quantum circuit is a graph of quantum logic gates.

Quantum circuits are the prevailing model of quantum computing as of the 2010's - 2020's

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Sallie (FutureAI) Updated 2025-07-16

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Not having a manipulator claw is a major issue with this one.

But they also have a co-simulation focus, which is a bit of a win.

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Serial wire debug Updated 2025-07-16

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Tachyon Updated 2025-07-16

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Undecidable Diophantine equation example Updated 2025-07-16

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mathoverflow.net/questions/11540/what-are-the-most-attractive-turing-undecidable-problems-in-mathematics/103415#103415 provides a specific single undecidable Diophantine equation.

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