27,712 research outputs found
Signatures of arithmetic simplicity in metabolic network architecture
Metabolic networks perform some of the most fundamental functions in living
cells, including energy transduction and building block biosynthesis. While
these are the best characterized networks in living systems, understanding
their evolutionary history and complex wiring constitutes one of the most
fascinating open questions in biology, intimately related to the enigma of
life's origin itself. Is the evolution of metabolism subject to general
principles, beyond the unpredictable accumulation of multiple historical
accidents? Here we search for such principles by applying to an artificial
chemical universe some of the methodologies developed for the study of genome
scale models of cellular metabolism. In particular, we use metabolic flux
constraint-based models to exhaustively search for artificial chemistry
pathways that can optimally perform an array of elementary metabolic functions.
Despite the simplicity of the model employed, we find that the ensuing pathways
display a surprisingly rich set of properties, including the existence of
autocatalytic cycles and hierarchical modules, the appearance of universally
preferable metabolites and reactions, and a logarithmic trend of pathway length
as a function of input/output molecule size. Some of these properties can be
derived analytically, borrowing methods previously used in cryptography. In
addition, by mapping biochemical networks onto a simplified carbon atom
reaction backbone, we find that several of the properties predicted by the
artificial chemistry model hold for real metabolic networks. These findings
suggest that optimality principles and arithmetic simplicity might lie beneath
some aspects of biochemical complexity
Knots and Random Walks in Vibrated Granular Chains
We study experimentally statistical properties of the opening times of knots
in vertically vibrated granular chains. Our measurements are in good
qualitative and quantitative agreement with a theoretical model involving three
random walks interacting via hard core exclusion in one spatial dimension. In
particular, the knot survival probability follows a universal scaling function
which is independent of the chain length, with a corresponding diffusive
characteristic time scale. Both the large-exit-time and the small-exit-time
tails of the distribution are suppressed exponentially, and the corresponding
decay coefficients are in excellent agreement with the theoretical values.Comment: 4 pages, 5 figure
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