Tag Archives: unzip operation

Fold rewrite, dynamic DNA material and visual DSD

As it happened with chemlambda programs, I decided it is shorter to take a look myself at possible physical realizations of chemlambda than to wait for others, uninterested or very interested really, people.

Let me recall a banner I used two years ago

KeepCalmStudio.com-Shortest-Explanation-Of-Chemlambda-[Knitting-Crown]-Keep-Calm-And-Use-Rna-For-Interaction-Nets

It turns out that I know exactly how to do this. I contacted Andrew Phillips, in charge with Microsoft’ Visual DSD  with the message:

Dear Andrew,

I am interested in using Visual DSD to implement several graph-rewriting formalisms with strand graphs: Lafont Interaction Combinators, knots, spin braids and links rewrite systems, my chemlambda and emergent algebra formalisms.

AFAIK this has not been tried. Is this true? I suggest this in my project chemlambda but I don’t have the chemical expertise.

About me: geometer working with graph rewrite systems, homepage: http://imar.ro/~mbuliga/index.html or
https://mbuliga.github.io/

Some links (thank you for a short reception of the message reply):

Chemlambda:
– github project: https://github.com/chorasimilarity/chemlambda-gui/blob/gh-pages/dynamic/README.md
– page with more links: http://imar.ro/~mbuliga/chemlambda-v2.html
– arXiv version of my Molecular computers article https://arxiv.org/abs/1811.04960

Emergent algebras:
– em-convex https://arxiv.org/abs/1807.02058

 

I still wait for an answer, even if Microsoft’ Washington Microsoft Azure and Google Europe immediately loaded the pages I suggested in the mail.

Previously, I was noticed by somebody [if you want to be acknowledged then send me a message and I’ll update this] about Hamada and Luo Dynamic DNA material with emergent locomotion behavior powered by artificial metabolism  and I sent them the following message

Dear Professors Hamada and Luo,

I was notified about your excellent article Dynamic DNA material with emergent locomotion behavior powered by artificial metabolism, by colleagues familiar with my artificial chemistry chemlambda.

This message is to make you aware of it. I am a mathematician working with artificial chemistries and I look for ways to implement them in real chemistry. The shortest description of chemlambda is: an artificial chemistry where the chemical reactions are alike a Turing complete family of graph rewrites.

If such a way is possible then molecular computers would be not far away.

Here is a list of references about chemlambda:

– GitHub repository with the scripts https://github.com/chorasimilarity/chemlambda-gui/blob/gh-pages/dynamic/README.md
– page which collects most of the resources http://imar.ro/~mbuliga/chemlambda-v2.html

Thank you for letting me know if this has any relation to your interests. For my part I would be very thrilled if so.

Best regards,
Marius Buliga

Again, seems that these biology/chemistry people have problems with replies to mathematicians, but all ths makes me more happy because soon I’ll probably release instructions about how everybody could make molecular computers along the lines of Molecular computers.

I’ll let you know if there are future “inspiration” work. Unrelated to chemlambda, there are several academic works which shamelessly borrow from my open work without acknowledgements, I’ll let you know about these and I’ll react in more formal ways. I hope though this will not be the case with chemlambda, however, this happened before twice at least.  (I say nothing about enzymes/catalysts, category theory and cryptocurrencies… for the moment.)

Finally, here is a realization of the lambda calculus beta rewrite via a FOLD rewrite

arrowlink-2

which shares a relation with the ZIP rewrite from Zipper Logic. It seems I was close to reality,  now though I got it exactly 🙂 .

Let’s talk soon!

 

 

 

The graphic beta move, with details

This is part of the Tutorial:Graphic lambda calculus.

Here it is explained the most important move in graphic lambda calculus: the graphic beta move.

A move is a transformation of a graph into another. It is not a function from GRAPH to GRAPH though, as we shall see.

The graphic beta move takes its name from the beta reduction in lambda calculus.

Consider the set GRAPH with the equality of oriented,  locally planar graphs (with leaves not numbered), denoted by \equiv.

A graphic beta move is a local move which consists in replacing a pattern (sub-graph)  by another pattern. More precisely, we can apply the graphic beta move to any graph which contains a certain pattern (sub-graph) and we obtain a new graph, which is identical with the initial one, with the exception of the pattern, now replaced by the other pattern.

Here is the precise definition of the graphic beta move. See the explanations after the figure.

beta_move_1

The labels “1, 2, 3, 4” are used only as guides for gluing correctly the new pattern, after removing the old one. Imagine that we have a graph which contains as a sub-graph the one from the left hand side (LHS) of the previous figure. Then, by a graphic beta move, we may replace the pair of nodes from the LHS figure with two arrows, as indicated by the labelling “1,2,3,4”. The rest of the graph is unchanged.

We may represent the graphic beta move like this:

beta_move_6

Up to the particular embedding in the plane of the graph from the right hand side (RHS), the move is the same. The crossing of the “1,3” arrow with the “4,2” arrow is an artefact of the embedding, there is no node there. Crossings of arrows have no meaning, remember that we work with graphs which are locally planar, not globally planar.

The graphic beta move goes into both directions. Referring to the first two pictures,  we may pick a pair of arrows and label them with “1,2,3,4”, such that, according to the orientation of the arrows,  “1” points to “3” and “4” points to “2”, without any node or label between “1” and “3” and between “4” and “2” respectively. Then, by a graphic beta move, we may replace the portions of the two arrows which are between “1” and “3”, respectively between “4” and “2”, by the pattern from the LHS of the figure.

Here is an example.

beta_move_2

The red drawings have no meaning in the formalism, I have put them only to make a more clear drawing of the move. Remark that we may read the move from left to right, as well as from right to left. The dashed closed curve serves to mark the pattern.

The graphic beta move may be applied to a single arrow, or to a loop, there is nothing which might stop this. For example, here are three applications of the graphic beta move:

beta_move_3

In particular we have a justification of considering loops and wires as members of GRAPH.

A point important to stress is that the graphic beta move is not dependent of the particular embedding into the plane of the graphs (which we use when we draw the graphs). This will be important further, when we discuss about the crossing macros, see the post “Graphic beta rule as braiding“.

Also, different labelling (of the same graphs) leads to different outcomes of the graphic beta move. This is explained in the next figure:

beta_move_4

Here “A, B, C, D” denote four graphs in GRAPH. Two possible graphic beta moves are depicted. Let’s read them from right to left.

At the right we have a graph with two arrows, connecting “A” with “B” and “D” with “C”. We may apply the graphic beta move to this graph in two ways, depending on the labelling of the arrows. If we mark the arrow from “A” to “B” with “1,3” and the arrow from “D” to “C” with “4,2” then we get the first graphic beta move. However, we may choose to mark the arrow from “A” to “B” with “4,2” and the arrow from “D” to “C” with “1,3”, applying then the graphic beta move. The outcome is different.

A particular case of the previous figure is yet another justification for having loops as elements in GRAPH.

beta_move_5

These two applications of the graphic beta move may be represented alternatively like this:

beta_move_8

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A move which resembles very much with the graphic beta move is the unzip operation from  the  knotted trivalent graphs formalism, see for example the paper  The algebra of knotted trivalent graphs and Turaev’s shadow world by D.P. Thurston, section 3. (this was mentioned also in the post “Graphic beta rule as braiding“).

In order to see this, let’s draw again the graphic beta move, this time without labelling the arrows:

beta_move_9

The unzip operation acts only from left to right in the following figure. Remarkably, it acts on trivalent graphs (but not oriented).

beta_move_10

UNZIP is not a move in graphic lambda calculus.

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