TY  - JOUR
A1  - Goldobin, Denis S.
A1  - Zaikin, Alexey
T1  - Towards quantitative prediction of proteasomal digestion patterns of proteins
N2  - 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.
Y1  - 2009
UR  - http://iopscience.iop.org/1742-5468/
U6  - https://doi.org/10.1088/1742-5468/2009/01/P01009
SN  - 1742-5468
ER  - 
TY  - JOUR
A1  - Goldobin, Denis S.
A1  - Shklyaeva, Elizaveta V.
T1  - Diffusion of a passive scalar by convective flows under parametric disorder
N2  - We study transport of a weakly diffusive pollutant (a passive scalar) through thermoconvective flow in a fluid- saturated horizontal porous layer heated from below under frozen parametric disorder. In the presence of disorder (random frozen inhomogeneities of the heating or of macroscopic properties of the porous matrix), spatially localized flow patterns appear below the convective instability threshold of the system without disorder. Thermoconvective. ows crucially affect the transport of a pollutant along the layer, especially when its molecular diffusion is weak. The effective (or eddy) diffusivity also allows us to observe the transition from a set of localized currents to an almost everywhere intense 'global' flow. We present results of numerical calculation of the effective diffusivity and discuss them in the context of localization of fluid currents and the transition to a 'global' flow. Our numerical findings are in good agreement with the analytical theory that we develop for the limit of a small molecular diffusivity and sparse domains of localized currents. Though the results are obtained for a specific physical system, they are relevant for a broad variety of fluid dynamical systems.
Y1  - 2009
UR  - http://iopscience.iop.org/1742-5468/
U6  - https://doi.org/10.1088/1742-5468/2009/01/P01024
SN  - 1742-5468
ER  -