Category Archives: Reaction Systems

My talk at the 2nd Workshop on Reaction Systems

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Following the 1st School on Reaction Systems in Torun, Poland, there was the 2nd Workshop on Reaction Systems, also held in Torun.

The workshop programme is listed here:

http://wors2019.mat.umk.pl//workshop/

I gave a talk on “Bringing Asynchrony to Reaction Systems”. This talk was work in (pre-)progress. Mostly developed during the Reaction Systems week in Torun.

The abstract of my talk is below:

Reaction systems have a number of underlining principles that govern them in their operation. They are: (i) maximum concurrency, (ii) complete renewal of state (no permanency), (iii) both promotion and inhibition, (iv) 0/1 (binary) resource availability, (v) no contention between resources. Most of these principles could be seen as constraints in a traditional asynchronous behaviour setting. However, under a certain viewpoint these principles do not contradict to principles underpinning asynchronous circuits if the latter were considered at an appropriate level of abstraction. Asynchrony typically allows enabled actions to execute in either order, retains the state of enabled actions while other actions are executed, involves fine grained causality between elementary events and permits arbitration for shared resources. This talk will discuss some of these potential controversies and attempt to show ways of resolving them and thereby bringing asynchrony into the realm of reaction systems. Besides that, we will also look at how the paradigm of reaction systems can be exploited in designing concurrent electronic systems.

The slides of my talk are here

 

My lecture on Asynchronous Computation at the 1st School on Reaction Systems

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The 1st School on Reaction Systems has taken place in historical Toruń, Poland.

Organised by Dr Lukasz Mikulski and Prof Grzegorz Rozenberg at the Nicolaus Copernicus University.

I managed to attend a number of lectures and gave my own lecture on Asynchronous Computation (from the perspective of electronic designer).

Here are the slides:

https://www.staff.ncl.ac.uk/alex.yakovlev/home.formal/talks/Torun-Yakovlev-lecture-final.pdf

Ideas picked up at the 1st School on Reaction Systems in Torun, Poland

Grzegorz Rozenberg’s lecture on Modularity and looking inside the reaction system states.

  • Some subsets of reactants will be physical – they form modules.
  • Stability implies lattice: a state transition is locally stable if the subsets (modules) in the states are isomorphic. These subset structures form partial order, so we have an isomorphism between partial orders. So, structurally, nothing really changes during those transitions – nothing new!
  • Biologists call this “adulthood”. It would be nice to have completion detection for that class of equivalence!

Paolo Milazzo’s talk (via Skype) on Genetic Regulatory Networks.

  • Some methods exist in gene regulation for saving energy – say by using lactose (as some sort of inhibitor)
  • He talked about sync/async Boolean networks of regulatory gene networks.

Paolo Bottoni on Networks of Reaction Systems.

  • Basic model – Environment influences the reaction systems
  • Here we consider reaction systems influences the environment

Robert Brijder on Chemical Reaction Networks.

Hans-Joerg Kreowski on Reaction Systems on Graphs.

  • Interesting graph transformations as reaction systems.
  • Examples involved some graph growth (e.g. fractal such as Serpinski graphs)

Grzegorz Rozenberg on Zoom Structures.

  • Interesting way of formalizing the process of knowledge management and acquistioon.
  • Could be used by people from say drug discovery and other data analytics

Alberto Leporati on membrane Computing and P-systems.

  • Result of action in a membrane is produced to the outside world only whne computation halts.
  • Question: what if the system is so distributed that we have no ability to guarantee the whole system halts? Can we have partial halts?
  • Catalysts can limit parallelism – sounds a bit like some sort of energy or power tokens

Maciej Koutny on Petri nets and Reaction Systems

  • We need not only prevent consumption (use of read arcs) but also prevent (inhibit!) production – something like “joint OR causality” or opportunistic merge can help.