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, $R_G$, follows the Flory scaling law, namely, $R_G =5.5 N^{1/3}$ \AA where N is the number of nucleotides. The shape of RNA molecules is characterized by the asphericity $\Delta$ and the shape $S$ parameters that are computed using the eigenvalues of the moment of inertia tensor. From the distribution of $\Delta$, we find that a large fraction of folded RNA structures are aspherical and the distribution of $S$ values shows that RNA molecules are prolate ($S>0$). The flexibility of folded structures is characterized by the persistence length $l_p$. By fitting the distance distribution function $P(r)$ to the worm-like chain model we extracted the persistence length $l_p$. We find that $l_p\approx 1.5 N^{0.33}$ \AA. The dependence of $l_p$ on $N$ 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 $R_G$, $\Delta$, $S$, and $l_p$. 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