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Approximate Scaling Properties of RNA Free Energy Landscapes

Author

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  • Subbiah Baskaran
  • Peter F. Stadler
  • Peter Schuster

Abstract

RNA free energy landscapes are analyzed by means of "time-series" that are obtained from random walks restricted to excursion sets. The power spectra, the scaling of the jump size distribution, and the scaling of the curve length measured with different yard stick lengths are used to describe the structure of these "time-series". Although they are stationary by construction, we find that their local behavior is consistent with both AR(1) and self-affine processes. Random walks confined to excursion sets (i.e., with the restriction that the fitness value exceeds a certain threshold at each step) exhibit essentially the same statistics are free random walks. We find that an AR(1) time series is in general approximately self-affine on time scales up to approximately the correlation length. We present an empirical relation between the correlation parameter rho of the AR(1) model and the exponents characterizing self-affinity.

Suggested Citation

  • Subbiah Baskaran & Peter F. Stadler & Peter Schuster, 1995. "Approximate Scaling Properties of RNA Free Energy Landscapes," Working Papers 95-10-083, Santa Fe Institute.
    • Handle: RePEc:wop:safiwp:95-10-083
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    References listed on IDEAS

    as
    1. Peter F. Stadler & Robert Happel, 1995. "Random Field Models for Fitness Landscapes," Working Papers 95-07-069, Santa Fe Institute.
    2. Robert Happel & Peter F. Stadler, 1995. "Canonical Approximation of Fitness Landscapes," Working Papers 95-07-068, Santa Fe Institute.
    3. Christian Reidys & Peter F. Stadler & Peter Schuster, 1995. "Generic Properties of Combinatory Maps: Neutral Networks of RNA Secondary Structures," Working Papers 95-07-058, Santa Fe Institute.
    4. Wim Hordijk, 1995. "A Measure of Landscapes," Working Papers 95-05-049, Santa Fe Institute.
    5. Martijn Huynen & Peter Stadler & Walter Fontana, 1995. "Evolutionary Dynamics of RNA and the Neutral Theory," Working Papers 95-01-006, Santa Fe Institute.
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