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  • Partition function  (1)
  • ultrasound absorption  (1)
  • Springer  (2)
  • 1990-1994  (1)
  • 1985-1989  (1)
  • 1975-1979
  • 1970-1974
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  • Springer  (2)
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  • 1990-1994  (1)
  • 1985-1989  (1)
  • 1975-1979
  • 1970-1974
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  • 1
    Electronic Resource
    Electronic Resource
    Springer
    European biophysics journal 22 (1993), S. 13-24 
    ISSN: 1432-1017
    Keywords: Fitness landscapes ; Partition function ; Quasispecies ; RNA secondary structures
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract Statistical properties of RNA folding landscapes obtained by the partition function algorithm (McCaskill 1990) are investigated in detail. The pair correlation of free energies as a function of the Hamming distance is used as a measure for the ruggedness of the landscape. The calculation of the partition function contains information about the entire ensemble of secondary structures as a function of temperature and opens the door to all quantities of thermodynamic interest, in contrast with the conventional minimal free energy approach. A metric distance of structure ensembles is introduced and pair correlations at the level of the structures themselves are computed. Just as with landscapes based on most stable secondary structure prediction, the landscapes defined on the full biophysical GCAU alphabet are much smoother than the landscapes restricted to pure GC sequences and the correlation lengths are almost constant fractions of the chain lengths. Correlation functions for multi-structure landscapes exhibit an increased correlation length, especially near the melting temperature. However, the main effect on evolution is rather an effective increase in sampling for finite populations where each sequence explores multiple structures.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    Springer
    European biophysics journal 16 (1988), S. 219-229 
    ISSN: 1432-1017
    Keywords: Relaxation kinetics ; ultrasound absorption ; temperature jump ; proton transfer ; vitamin B 6
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract UV-visible and 13C NMR measurements described in the literature and our 31P NMR measurements support the following mechanism of proton transfer reactions in aqueous solutions of pyridoxamine phosphate: Only the tautomeric equilibrium between neutral form, A N, and zwitterion, A Z, which is analogous to the tautomeric equilibrium of 3-hydroxypyridine in aqueous solution, is important, and that equilibrium does not change upon the dissociation of the second phosphate proton. With these simplifying assumption, we have simulated the relaxation spectrum of the proton transfer reactions of pyridoxamine phosphate in water using parameters from analogous reactions and compared it with our ultrasound and temperature jump measurements. We have found that the relaxation process measured by the temperature jump experiment is mainly caused by the overall reaction A N=A Z (or A N - =A Z - ) and the ultrasound absorption at the isoelectric point between pK2 and pK3 is mainly caused by the overall reaction $$A^{\text{ + }} + {\text{x}} A_N^ - + \left( {1 - {\text{x}}} \right)A_Z^ - = {\text{y}}A_N + \left( {2 - {\text{y}}} \right)A_Z , 0 \leqq {\text{x}} \leqq {\text{1,}} {\text{0}} \leqq {\text{y}} \leqq 2$$ .
    Type of Medium: Electronic Resource
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