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Here we collect our writing on various topics from our day-to-day work and our reading clubs.

Graph Grammar Library

Summary of the paper “The Graph Grammar Library – a generic framework for chemical graph rewrite systems” by Flamm et al.

The paper explains how a C++ package works, which implements graph grammar rewriting rules for chemical reaction networks. There are some other chem(o)informatics stuff in the package as well.
The main story of the paper is that Yadav et al. requested a package like GGL, which is now available.
Most of it seems quite logical/intuitive based on the what it tries to do.
The software translates to/from SMILES at the beginning and end, but everything is done using graphs.
For more information and guides on how to use the software, see: http://www.tbi.univie.ac.at/software/GGL/

Mathematical Chemistry and ChemoInformatics part II

Jotun Hein and William Kurdahl will review two books: Leach and Gillet (2010) Introduction to Chemoinformatics and chapters from Faulon Handbook of Chemoinformatics Algorithms (2007). Additionally briefly summarize key papers on Graph Grammars, Reaction prediction and related topics. The talk ends with an attempt to identify projects in chemoinformatics that would be worth it to work on.

The slides can be found here: http://tinyurl.com/j28y67s

Thursday December 8th 10AM to noon LG Department of Statistics

EVOLUTION of PROTEIN STRUCTURE

Michael Golden has worked on an angle (psi,phi) diffusion model of protein evolution and it has turned out well. The first paper was submitted yesterday and a talk is given on Thursday December 1st 3.30Pm in The Department of Statistics.

Preliminary slides can be found here: http://tinyurl.com/PhiPsiEvolution

 

Theory, Modelling and Simulation in Origins of Life Studies

“Theory, Modelling and Simulation in Origins of Life Studies”
By Peter V. Coveney, Jacob B. Swadling, Jonathan A. D. Wattisb and H. Christopher Greenwell

Gives a brief summary of the history of the fields and the major hypothesis out there and some of the current work being done. The most famous experiment being the Urey-Miller experiment, which is still relevant. Possibilities for life arising consist of the pre-biotic soup, black smokers, alkaline vents and “outer space origin”.
The article describes the RNA world and homochiralization, as well as gives a brief comparison between the modelling methods of Quantum Mechanics (typically density functional theory) and classical Molecular dynamics.
Two quotes from the review:
“In particular, whilst symmetry-breaking is exhibited by the hexamer model, it is not possible within the tetramer model. This serves as a warning to theoreticians who wish to deduce the properties of a complex model simply by analysing a significantly reduced version.”
“The intrinsic value of modelling cannot be overstated”

Overall, the article contains a lot of references to further reading but also emphasises some chemical research whose relation to OoL is unclear to this reader.
The paper comes with a slideshow presentation covering the same material using different graphics etc.

Mathematical Chemistry and ChemoInformatics

William Larsen and Jotun Hein gave a book review talk on Monday 7th November 2-4PM in IT Teaching Room, Department of Statistics.

The book is called “Mathematical Chemistry and ChemoInformatics”
The book covers the combinatorics of molecules (especially Polya-Counting), their embedding in 3D Euclidian Space, Chirality, Stereoisomers and a series of application using the program MOLGEN. We are motived to study this book since William is working on models of origin life involving small molecules, but it is obvious that the field could be a rich source of statistical problems to work on.
The slides can be found here:http://preview.tinyurl.com/MoleculeCombinatorics

For the unqualitative verdict: It received 7/10 stars

Grades of previously read books can be found among the slides above.