Information Processing in Chemical Networks

There’s a workshop this summer:

• Dynamics, Thermodynamics and Information Processing in Chemical Networks, 13-16 June 2017, Complex Systems and Statistical Mechanics Group, University of Luxembourg. Organized by Massimiliano Esposito and Matteo Polettini.

They write, “The idea of the workshop is to bring in contact a small number of high-profile research groups working at the frontier between physics and biochemistry, with particular emphasis on the role of Chemical Networks.”

Some invited speakers include Vassily Hatzimanikatis, John Baez, Christoff Flamm, Hong Qian, Joshua D. Rabinowitz, Luca Cardelli, Erik Winfree, David Soloveichik, Stefan Schuster, David Fell and Arren Bar-Even. There will also be a session of shorter seminars by researchers from the local institutions such as Luxembourg Center for System Biomedicine. I believe attendance is by invitation only, so I’ll endeavor to make some of the ideas presented available here at this blog.

Some of the people involved

I’m looking forward to this, in part because there will be a mix of speakers I’ve met, speakers I know but haven’t met, and speakers I don’t know yet. I feel like reminiscing a bit, and I hope you’ll forgive me these reminiscences, since if you try the links you’ll get an introduction to the interface between computation and chemical reaction networks.

In part 25 of the network theory series here, I imagined an arbitrary chemical reaction network and said:

We could try to use these reactions to build a ‘chemical computer’. But how powerful can such a computer be? I don’t know the answer.

Luca Cardelli answered my question in part 26. This was just my first introduction to the wonderful world of chemical computing. Erik Winfree has a DNA and Natural Algorithms Group at Caltech, practically next door to Riverside, and the people there do a lot of great work on this subject. David Soloveichik, now at U. T. Austin, is an alumnus of this group.

In 2014 I met all three of these folks, and many other cool people working on these theme, at a workshop I tried to summarize here:

Programming with chemical reaction networks, Azimuth, 23 March 2014.

The computational power of chemical reaction networks, 10 June 2014.

Chemical reaction network talks, 26 June 2014.

I met Matteo Polettini about a year later, at a really big workshop on chemical reaction networks run by Elisenda Feliu and Carsten Wiuf:

Trends in reaction network theory (part 1), Azimuth, 27 January 2015.

Trends in reaction network theory (part 2), Azimuth, 1 July 2015.

Polettini has his own blog, very much worth visiting. For example, you can see his view of the same workshop here:

• Matteo Polettini, Mathematical trends in reaction network theory: part 1 and part 2, Out of Equilibrium, 1 July 2015.

Finally, I met Massimiliano Esposito and Christoph Flamm recently at the Santa Fe Institute, at a workshop summarized here:

Information processing and biology, Azimuth, 7 November 2016.

So, I’ve gradually become educated in this area, and I hope that by June I’ll be ready to say something interesting about the semantics of chemical reaction networks. Blake Pollard and I are writing a paper about this now.

2 Responses to Information Processing in Chemical Networks

  1. Gary Lewis says:

    Not sure what you mean by the semantics of chemical reaction networks. To me it conjures up an image of category theory applied to metabolic pathways, which are conveniently near universal for all species. This would pick up on the work of Harold Morowitz that goes back decades, and the very recent publication of a book by Smith and Morowitz (The Origin and Nature of Life on Earth). Am I anywhere near to what you meant? … Regards, Gary

    • John Baez says:

      I wish my work were closer to the biological ideas you’re talking about! It may take a while to get there. There are many kinds of ‘meaning’ for a chemical reaction network, and each gives a semantics that one can try to formalize. I’m just getting started on this. Here you can see a talk I gave on functorial semantics applied to chemical reaction networks (or actually Petri nets, which are another way of drawing the exact same information):

      • John Baez, Compositionality in network theory.

      You can see the slides here, with links to papers, and a video here:

You can use Markdown or HTML in your comments. You can also use LaTeX, like this: $latex E = m c^2 $. The word 'latex' comes right after the first dollar sign, with a space after it.

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s