@article{ZaikinKurths2006,
  author    = {Zaikin, Alexey and Kurths, J{\"u}rgen},
  title     = {Optimal length transportation hypothesis to model proteasome product size distribution},
  series = {Journal of biological physics : emphasizing physical principles in biological research ; an international journal for the formulation and application of mathematical models in the biological sciences},
  volume    = {32},
  journal   = {Journal of biological physics : emphasizing physical principles in biological research ; an international journal for the formulation and application of mathematical models in the biological sciences},
  number    = {3-4},
  publisher = {Springer},
  address   = {Dordrecht},
  issn      = {0092-0606},
  doi       = {10.1007/s10867-006-9014-z},
  pages     = {231 -- 243},
  year      = {2006},
  abstract  = {This paper discusses translocation features of the 20S proteasome in order to explain typical proteasome length distributions. We assume that the protein transport depends significantly on the fragment length with some optimal length which is transported most efficiently. By means of a simple one-channel model, we show that this hypothesis can explain both the one- and the three-peak length distributions found in experiments. A possible mechanism of such translocation is provided by so-called fluctuation-driven transport.},
  language  = {en}
}
@misc{KoseskaZaikinKurthsetal.2009,
  author    = {Koseska, Aneta and Zaikin, Alexey and Kurths, J{\"u}rgen and Garc{\´i}a-Ojalvo, Jordi},
  title     = {Timing cellular decision making under noise via cell-cell communication},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45260},
  year      = {2009},
  abstract  = {Many cellular processes require decision making mechanisms, which must act reliably even in the unavoidable presence of substantial amounts of noise. However, the multistable genetic switches that underlie most decision-making processes are dominated by fluctuations that can induce random jumps between alternative cellular states. Here we show, via theoretical modeling of a population of noise-driven bistable genetic switches, that reliable timing of decision-making processes can be accomplished for large enough population sizes, as long as cells are globally coupled by chemical means. In the light of these results, we conjecture that cell proliferation, in the presence of cell-cell communication, could provide a mechanism for reliable decision making in the presence of noise, by triggering cellular transitions only when the whole cell population reaches a certain size. In other words , the summation performed by the cell population would average out the noise and reduce its detrimental impact.},
  language  = {en}
}
@article{GoldobinZaikin2009,
  author    = {Goldobin, Denis S. and Zaikin, Alexey},
  title     = {Towards quantitative prediction of proteasomal digestion patterns of proteins},
  issn      = {1742-5468},
  doi       = {10.1088/1742-5468/2009/01/P01009},
  year      = {2009},
  abstract  = {We discuss the problem of proteasomal degradation of proteins. Though proteasomes are important for all aspects of cellular metabolism, some details of the physical mechanism of the process remain unknown. We introduce a stochastic model of the proteasomal degradation of proteins, which accounts for the protein translocation and the topology of the positioning of cleavage centers of a proteasome from first principles. For this model we develop a mathematical description based on a master equation and techniques for reconstruction of the cleavage specificity inherent to proteins and the proteasomal translocation rates, which are a property of the proteasome species, from mass spectroscopy data on digestion patterns. With these properties determined, one can quantitatively predict digestion patterns for new experimental set-ups. Additionally we design an experimental set-up for a synthetic polypeptide with a periodic sequence of amino acids, which enables especially reliable determination of translocation rates.},
  language  = {en}
}