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Thomas Fink's Homepage 63,800 visitors last year Online since Apr 1996 Last modified 3 Nov 2008 Home  I am a physicist at the Curie Institute/CNRS and the London Institute for Mathematical Sciences; I also periodically visit Cambridge.I use statistical mechanics to study complex systems in physics and interdisciplinary fields, including systems biology.My research interests are discrete dynamics, complex networks and fundamental laws of biology.I have also written two popular books:The Man's Book, a comprehensive almanac for men; andThe 85 Ways to Tie a Tie, a treatise on ties and tie knots. The Man's Book 2009  The third edition of The Man's Book will be published in the United States by Little, Brown in April 2009.Completely updated and retypeset, this is the first time that the definitive almanac for men will be available in the U.S.New features include:12 more sections,25 more figures andnumerically organized sections and subsections. Directed Networks Clustering signatures classify directed networksWe use a clustering signature, based on a recently introduced generalization of the clustering coefficient to directed networks,to analyze 16 directed real-world networks of five different types:social networks, genetic transcription networks, word adjacency networks, food webs and electric circuits. We show that these five classes of networks are cleanly separated in the space of clustering signatures due to the statistical properties of their local neighbourhoods, demonstrating the usefulness of clustering signatures as a classifier of directed networks. Non-coding DNA  How much non-coding DNA do eukaryotes require?In most eukaryotes, a large proportion of the genome does not code for proteins.The non-coding part is observed to vary greatly in size even between closely related species.We report evidence that eukaryotes require a certain minimum amount of non-coding DNA (ncDNA), and that thisminimum increases quadratically with the amount of coding DNA.Based on a simple model of the growth of regulatory networks, we derive a theoreticalprediction of the required quantity of ncDNA and find it to be in excellent agreement with observation. Mathematics of Conkers  Conkers is a popular game played with the nuts of the common horse-chestnut tree (conkers), in which pairs of players take turns swiping each other's conker with their own until one conker is broken.Each conker is assigned a score as follows.All new conkers start with a score of 1.Each time a conker beats another conker, it adds to its score the score of the defeated.In Single elimination competition,we study a simple model of competition in which each player has a fixed strength.Randomly selected pairs of players compete and the stronger one wins.We show that the best indicator of future success is not the number of wins but a player's wealth:the accumulated wealth of all defeated players.We calculate statistics of a conker with a given score and offer advice on strategy. Fundamental Laws of Biology  In the summer of 2007 I joined the DARPA Fundamental Laws of Biology (FunBio) program.Organised by the Defense Sciences Office, it is a team of biologists, mathematicians, and physicists working together to 'Bring new mathematical perspectives to biology. Use the stimulus of those challenges to create new mathematics that will reveal unanticipated structures in large complex systems. Explain biological organization at multiple scales. Discover the fundamental laws of biology that span all biological scales.' The Man's Book 2008  The Man's Bookis the authoritative handbook of men's customs, habits and pursuits - a vade mecum for modern-day manliness.At a time when the sexes are muddled and masculinity is marginalized, The Man's Book unabashedly celebrates being male. Chaps, cads, blokes and bounders, rejoice: The Man's Book will bring you back to wear you belong.The 2008 edition of The Man's Book, published on 19 September, 2007, has been expanded, revised and updated.A free sample chapter can be downloaded. Dynamics of Network Motifs Complex dynamical networks are found in biology,technology and sociology.Recently it was observed that some local network structures,or network motifs, are much more frequently observed in complex networksthan would be expected by chance.Although this biased distribution of motifs appears to apply to a broad range of networks,it remains unclear why some motifs are ubiquitous and others are not.In a recent paper,we study the dynamics of network motifs by treating them as small Booleannetworks and comprehensively evaluating all possible binary (Boolean) update rules.We introduce a formalism for classifying dynamical behaviour andshow that some network motifs are fundamentally moreversatile—capable of executing a variety of tasks—than others.Because it is more likely to be capable of an arbitrary task,a versatile motif would ostensibly occur more frequently in real networks, all else being equal.While versatility roughly increases with motif complexity,we find evidence of a critical complexity, after which increasingthe number of bonds confers no advantage. Can Biology Lead to New Theorems?  R. A. Fisher 7x7 Latin square, from Caius College Hall, CambridgeMore often than not, collaboration between biologists and mathematical scientists is a one-sided affair.Mathematicians and physicists are under pressure to make real biological contributions,irrespective of whether the mathematics is of interest or importance.From their point of view, such interdisciplinary collaborations are of limited real interest.This picture is starting to change.In '...Biology Is Mathematics' Next Physics, Only Better',Joel Cohen argues that in the 21st century, biology, like physics in the century before it, will drive mathematics in new directions.Bernd Sturmfels offers more explicit evidence in his paper 'Can Biology Lead to New Theorems?'.He outlines four theorems which are direct outgrowths of biological research. These prognostications suggest an exciting future for quantitative biology.While much of systems biology is applied (it has immediate practical applications), it is now clear that it also comprises basic science.New mathematical understanding, and new mathematics, are needed to make sense of phenomena ranging from the complex dynamics in regulatory networks to the faint deviation from randomness in genetic expression curves. Here is an example from my work where studying microarray expression led to a theorem in number theory (Microarray expression series, Properties of up-down numbers).Let CN(s)be the number of permutations of length N+1 with a given up-down signature s. Then, for p prime, Cp(s) = -1,0,1 (mod p)  Thomas Fink Contact About Me About My Page CV FAQ Pics Academic Page physics, academia, esoterica Home Publications Papers Books Patent Thesis Research Interests Collaborators Talks, Trips & Lectures In the News Miscellaneous Ephemera Links Physics Journals Physics Roots .plan Highlights What's New 10/08 Research interests updated 10/08 Use QuarkXPress to write talks 09/08 New LIMS office opened 09/08 Human Frontier grant (ii) sub. 07/08 Moved to new Curie building 05/08 FunBio Phase III approved 04/08 Moved from pine to Gmail 03/08 Erdös number down to 3 Some Recent and Popular Papers 08 Random cellular automata, EPL 08 Classifying directed networks, PRE 08 Temp. in complex networks, sub. 08 Single elimination competition, EPL 08 Expression networks, J. Phys. A 08 Segmentation clock genes, PLoS 1 07 Classifying weighted networks, PRE 07 Non-random data series, sub. 07 How much non-coding DNA?, JTB 07 1-D random landscapes, EPL 06 Dynamics of network motifs, sub. 06 Up-down numbers, Disc. Math. 06 Pattern in microarrays, Bioinfo. 03 Stochastic annealing, PRL 02 Genome shotgun sequencing, PRL 01 What can a protein remember?, PRL 00 Knots, walks & topology , Physica A 99 Designing tie knots, Nature 98 Proteins & optimisation, Ph.D. Thesis 93 Beach cusps, Science Some Upcoming Visits / Meetings / Talks 09/03/09 John Harer visits me 04/03/09 DARPA FunBio prog. meeting 19/10/08 Ahnert, Boston Univ. 12/10/08 Math/Biology, Duke University Some Recent Visits / Meetings / Talks 07/10/08 Robin Ball Warwick Univ. 17/09/08 Olivier Pourquie visits me 20/08/08 DARPA FunBio prog. meeting 12/08/08 Math/Biology, Duke University 18/07/08 TCM, Cambridge University 14/07/08 John Harer visits me 07/07/08 Benfey lab visits me 0?/06/08 TCM, Cambridge University 27/04/08 Olivier Pourquie, Stowers Inst. 18/03/08 TCM, Cambridge University 25/02/08 TCM, Cambridge University 14/01/08 Pourquie lab: Network inference 09/01/08 DARPA FunBio prog. meeting Some recent collaborators Sebastian Ahnert, Cambridge Francis Brown, IHES Guido Caldarelli, La Sapienza Jonathan Coe, Curie (postdoc) John Harer, Duke Olivier Pourquie, Stowers Andrei Zinovyev, Curie Some Links of Note Erik Demaine Free will theorem 23 mathematical challenges Typographic Style for the Web My Favorite Integer Sequences Pocket Protectors Scale-Free Networks David MacKay FAQ about Calendars Bernd Sturmfels Popular Page chaps, cads, blokes and bounders Home Books The Man's Book 80,000 sold (Free chapter) 85 Ways to Tie a Tie 210,000 sold Miscellaneous 50 Essential Books Encyclopedia of Tie Knots Wit and Wisdom Mathematics of conkers Literary James Bond Highlights What's New 04/09 The Man's Book 2009 published 02/08 New 3-column webpage format 01/08 Mathematics of conkers sub. 12/07 Herrenhandbuch published 11/07 Little, Brown to pub. US Man's Book 09/07 The Man's Book 2008 published The Man's Book About and reviews Amazon: UK, Austria, Canada, France, Germany, Japan The 85 Ways to Tie a Tie About and reviews Amazon: UK, US, Germany Encyclopedia of Tie Knots Paper: Designing tie knots Paper: Knots, walks & topology Wikipedia article Some Links of Note Maa Designs (book illustration) ReTRo HouSeWiFe Modern Drunkard Magazine RateBeer Wild wood survival Chemex coffee maker Dandyism.net Chocolate Revolution The Athanasius Kircher Society A Suitable Wardrobe Spud Gun Technology Center The Chap Magazine |
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