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

Individual Microscopic Results Of Bottleneck Experiments

This contribution provides microscopic experimental study of pedestrian motion in front of the bottleneck, explains the high variance of individual travel time by the statistical analysis of trajectories. The analysis shows that this heterogeneity increases with increasing occupancy. Some participants were able to reach lower travel time due more efficient path selection and more aggressive behavior within the crowd. Based on this observations, linear model predicting travel time with respect to the aggressiveness of pedestrian is proposed.Comment: Submitted to Traffic and Granullar Flow 2015, Springe

Room-temperature high-speed nuclear-spin quantum memory in diamond

Quantum memories provide intermediate storage of quantum information until it is needed for the next step of a quantum algorithm or a quantum communication process. Relevant figures of merit are therefore the fidelity with which the information can be written and retrieved, the storage time, and also the speed of the read-write process. Here, we present experimental data on a quantum memory consisting of a single $^{13}$C nuclear spin that is strongly coupled to the electron spin of a nitrogen-vacancy (NV) center in diamond. The strong hyperfine interaction of the nearest-neighbor carbon results in transfer times of 300 ns between the register qubit and the memory qubit, with an overall fidelity of 88 % for the write - storage - read cycle. The observed storage times of 3.3 ms appear to be limited by the T$_1$ relaxation of the electron spin. We discuss a possible scheme that may extend the storage time beyond this limit.Comment: 7 pages, 6 figure

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