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# Category Archives: Reading clubs

## 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.

## Summing up 10 classic papers on Computation

For about 3 years we have every 3rd week read a classic paper in physics, statistics, probability theory, information theory, game theory and computation. So far we have gone through about 40-50 papers and the papers have generally been superb.

Søren Riis (Queen Mary, London) and Jotun Hein gave a talk to summarize 10 of the papers that fall within computation/complexity theory. The papers are Babbage, Turing, McCullough/Pitt, von Neumann, Cook, Karp, Smale, Shor, Impagliazzo, Papadimitriou.

The slides of his presentation are available here

## Summary: McCullough and Pitts (1943) A Logical Calculus of the Ideas Immanent in Nervous Activity

This a most peculiar paper that must be the initial Neural Networks paper and thus is extremely famous.

The paper is not easy to read due to a lot of terms taking from a 1938 textbook by Rudolf Carnap and I (Jotun) could well have missed some finer points, but I think I got the the basic ideas: We have discrete time, only boolean values, and the fundamental unit is the neuron and has input from many neuron and all that matters is how many 0s and 1s it receives (not their order). From this networks evaluating most logical expression can be designed. One can add extra “carrier neurons” that copies the content of a neuron and effectively allows a neuron to receive input from another neuron several time steps back. Cycles needs special treatment.

There is no Hebbian (1949) learning in this paper, so the parameters of each neuron is preset.

The paper is motivated by the brain but the M-P states that model should not be interpreted to literally as representing how the brain works. Nevertheless they end the paper with a series of very specific hopes for this model lile (131):

“To psychology, however defined, the net would contribute all that could be achieved in that field – even if the fields were pushed to ultimate psychic units or ‘psychons,’ for a psychon can be no less than the activity of a single neuron. Since that activity is inherently propositional, all psychic events have an intentional, or semiotic character. The ‘all-or-none’ character of these activities, and the conformity of their relations to those of the logic of propositions, insure that the relations of those of the logic of propositions insure thtat the relations of psychins are those of the the two-valued logic of propositions. Thus in psychology, introspective, behavioristic and physiological, the fundamental relations are those of two-value logic”

Thus M-P is quite confident that their model represent some sort physical reality of the brain. They also mention tinitus, paraesthesias, hallucinations, delusions and disorientations (p131) so they are keen to move on the applicability of their network theory.

I find it fascinating to read the papers from 30s, 40s and 50s by von Neumann, Wiener, MP and their wild ambition and optimism stemming from the belief that a biological machine, such as the brain, is just the right kind of wired system that can be exactly modelled. It has proven a lot harder and it is still an open question what a biological machine is and how detailed physics needs to be retained to for instance modeling the neurone. Ganti (1971) used the term Soft Machine that is a nice metaphor, but seems to have contributed little.

## 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.

## ROGER PENROSE: THE ROAD to REALITY

We (not royal we here) intend to read this over the next 2 years in installments of 20ish pages every 2nd week. I think it will do wonders for our understanding of physics and if not, we will write an angry letter to Sir Roger Penrose and The Times.

Since one of us have standard working hours we will do it before work – probably like 6.30AM to 8.00 AM – per Skype. A good start of the day and your breakfast will taste better. If somebody want to join, please contact me. We will start in January.