Categories used to describe molecules

Categories used to describe molecules

[Dennis Stevenson]

I would appreciate references to the use of category theory to describe molecular structure and/or changes in molecules.

—
D. E. (Steve) Stevenson
Emeritus Associate Professor,
School of Computing, Clemson University



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Re: Categories used to describe molecules

[David Spivak]

Here is a paper using operads as a language for forming proteins from
simpler proteins:
https://pubs.acs.org/doi/abs/10.1021/acsbiomaterials.5b00251

On Sat, Apr 28, 2018 at 11:54 AM, Dennis Stevenson <fatmarauder@gmail.com>
wrote:

> I would appreciate references to the use of category theory to describe
> molecular structure and/or changes in molecules.
>
> —
> D. E. (Steve) Stevenson
> Emeritus Associate Professor,
> School of Computing, Clemson University
>
>

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Re: Categories used to describe molecules

[John Baez]

Hi -

Dennis Stevenson wrote:

> I would appreciate references to the use of category theory
> to describe molecular structure and/or changes in molecules.

I recommend the papers by Christoph Flamm and collaborators:

https://arxiv.org/search/?searchtype=author&query=%22Flamm%2C+Christoph%22

I heard Flamm and Merkle talk at "Dynamics, Thermodynamics and
Information Processing in Chemical Networks" in Luxembourg last year,
and I wrote:

> Merkle is speaking. This is the first talk I’ve seen where someone
> argues strongly for the usefulness of category theory, then explains
> the definition of pushouts, and then illustrates it with examples from
> organic chemistry! Good thing I’d explained the definition of ‘category’
> earlier in the day! Double-pushout graph rewriting applied to chemistry,
> and implemented in software that creates pictures of molecules using TikZ.

Best,
jb


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