1,134 research outputs found
Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins
Using self-organized polymer models, we predict mechanical unfolding and
refolding pathways of ribo-zymes, and the green fluorescent protein. In
agreement with experiments, there are between six and eight unfolding
transitions in the Tetrahymena ribozyme. Depending on the loading rate, the
number of rips in the force-ramp unfolding of the Azoarcus ribozymes is between
two and four. Force-quench refolding of the P4-P6 subdomain of the Tetrahymena
ribozyme occurs through a compact intermediate. Subsequent formation of
tertiary contacts between helices P5b-P6a and P5a/P5c-P4 leads to the native
state. The force-quench refolding pathways agree with ensemble experiments. In
the dominant unfolding route, the N-terminal a helix of GFP unravels first,
followed by disruption of the N terminus b strand. There is a third
intermediate that involves disruption of three other strands. In accord with
experiments, the force-quench refolding pathway of GFP is hierarchic, with the
rate-limiting step being the closure of the barrel.Comment: 33 pages 7 figure
New Infrared Tools to Measure the Solar Coronal Magnetic Field.
Ph.D. Thesis. University of Hawaiʻi at Mānoa 2017
Extended Quantum XOR Gate in Terms of Two-Spin Interactions
Considerations of feasibility of quantum computing lead to the study of
multispin quantum gates in which the input and output two-state systems (spins)
are not identical. We provide a general discussion of this approach and then
propose an explicit two-spin interaction Hamiltonian which accomplishes the
quantum XOR gate function for a system of three spins: two input and one
output.Comment: 15 pages in plain TeX with 1 Postscript figur
Size, shape, and flexibility of RNA structures
Determination of sizes and flexibilities of RNA molecules is important in
understanding the nature of packing in folded structures and in elucidating
interactions between RNA and DNA or proteins. Using the coordinates of the
structures of RNA in the Protein Data Bank we find that the size of the folded
RNA structures, measured using the radius of gyration, , follows the Flory
scaling law, namely, \AA where N is the number of
nucleotides. The shape of RNA molecules is characterized by the asphericity
and the shape parameters that are computed using the eigenvalues
of the moment of inertia tensor. From the distribution of , we find
that a large fraction of folded RNA structures are aspherical and the
distribution of values shows that RNA molecules are prolate (). The
flexibility of folded structures is characterized by the persistence length
. By fitting the distance distribution function to the worm-like
chain model we extracted the persistence length . We find that \AA. The dependence of on implies the average length of
helices should increases as the size of RNA grows. We also analyze packing in
the structures of ribosomes (30S, 50S, and 70S) in terms of , ,
, and . The 70S and the 50S subunits are more spherical compared to
most RNA molecules. The globularity in 50S is due to the presence of an
unusually large number (compared to 30S subunit) of small helices that are
stitched together by bulges and loops. Comparison of the shapes of the intact
70S ribosome and the constituent particles suggests that folding of the
individual molecules might occur prior to assembly.Comment: 28 pages, 8 figures, J. Chem. Phys. in pres
Length-based cryptanalysis: The case of Thompson's Group
The length-based approach is a heuristic for solving randomly generated
equations in groups which possess a reasonably behaved length function. We
describe several improvements of the previously suggested length-based
algorithms, that make them applicable to Thompson's group with significant
success rates. In particular, this shows that the Shpilrain-Ushakov public key
cryptosystem based on Thompson's group is insecure, and suggests that no
practical public key cryptosystem based on this group can be secure.Comment: Final version, to appear in JM
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