Pulling hairpinned polynucleotide chains: Does base-pair stacking interaction matter?

Force-induced structural transitions both in relatively random and in designed single-stranded DNA (ssDNA) chains are studied theoretically. At high salt conditions, ssDNA forms compacted hairpin patterns stabilized by base-pairing and base-pair stacking interactions, and a threshold external force is needed to pull the hairpinned structure into a random coiled one. The base-pair stacking interaction in the ssDNA chain makes this hairpin-coil conversion a discontinuous (first-order) phase transition process characterized by a force plateau in the force-extension curve, while lowering this potential below some critical level turns this transition into continuous (second-order) type, no matter how strong the base-pairing interaction is. The phase diagram (including hairpin-I, -II, and random coil) is discussed as a function of stacking potential and external force. These results are in quantitative agreement with recent experimental observations of different ssDNA sequences, and they reveal the necessity to consider the base-pair stacking interactions in order to understand the structural formation of RNA, a polymer designed by nature itself. The theoretical method used may be extended to study the long-range interaction along double-stranded DNA caused by the topological constraint of fixed linking number.Comment: 8 pages using Revte

Physical implementation of holonomic quantum computation in decoherence-free subspaces with trapped ions

We propose a feasible scheme to achieve holonomic quantum computation in a decoherence-free subspace (DFS) with trapped ions. By the application of appropriate bichromatic laser fields on the designated ions, we are able to construct two noncommutable single-qubit gates and one controlled-phase gate using the holonomic scenario in the encoded DFS.Comment: 4 pages, 3 figures. To appear in Phys. Rev. A 74 (2006

Modelling Time-varying Dark Energy with Constraints from Latest Observations

We introduce a set of two-parameter models for the dark energy equation of state (EOS) $w(z)$ to investigate time-varying dark energy. The models are classified into two types according to their boundary behaviors at the redshift $z=(0,\infty)$ and their local extremum properties. A joint analysis based on four observations (SNe + BAO + CMB + $H_0$) is carried out to constrain all the models. It is shown that all models get almost the same $\chi^2_{min}\simeq 469$ and the cosmological parameters $(\Omega_M, h, \Omega_bh^2)$ with the best-fit results $(0.28, 0.70, 2.24)$, although the constraint results on two parameters $(w_0, w_1)$ and the allowed regions for the EOS $w(z)$ are sensitive to different models and a given extra model parameter. For three of Type I models which have similar functional behaviors with the so-called CPL model, the constrained two parameters $w_0$ and $w_1$ have negative correlation and are compatible with the ones in CPL model, and the allowed regions of $w(z)$ get a narrow node at $z\sim 0.2$. The best-fit results from the most stringent constraints in Model Ia give $(w_0,w_1) = (-0.96^{+0.26}_{-0.21}, -0.12^{+0.61}_{-0.89})$ which may compare with the best-fit results $(w_0,w_1) = (-0.97^{+0.22}_{-0.18}, -0.15^{+0.85}_{-1.33})$ in the CPL model. For four of Type II models which have logarithmic function forms and an extremum point, the allowed regions of $w(z)$ are found to be sensitive to different models and a given extra parameter. It is interesting to obtain two models in which two parameters $w_0$ and $w_1$ are strongly correlative and appropriately reduced to one parameter by a linear relation $w_1 \propto (1+w_0)$.Comment: 30 pages, 7 figure