Rational tangle surgery and Xer recombination on catenanes

The protein recombinase can change the knot type of circular DNA. The action of a recombinase converting one knot into another knot is normally mathematically modeled by band surgery. Band surgeries on a 2-bridge knot N((4mn-1)/(2m)) yielding a (2,2k)-torus link are characterized. We apply this and other rational tangle surgery results to analyze Xer recombination on DNA catenanes using the tangle model for protein-bound DNA.Comment: 20 pages, 23 figure

Magnetization curve of the kagome-strip-lattice antiferromagnet

We study the magnetization curve of the Heisenberg model on the quasi-one-dimensional kagome-strip lattice that shares the same lattice structure in the inner part with the two-dimensional kagome lattice. Our numerical calculations based on the density matrix renormalization group method reveal that the system shows several magnetization plateaus between zero magnetization and the saturated one; we find the presence of the magnetic plateaus with the n=7 height of the saturation for n =1,2,3,4,5 and 6 in the S =1/2 case, whereas we detect only the magnetic plateaus of n =1,3,5 and 6 in the S =1 case. In the cases of n =2,4 and 6 for the S=1/2 system, the Oshikawa-Yamanaka-Affleck condition suggests the occurrence of the translational symmetry breaking (TSB). We numerically confirm this non-trivial TSB in our results of local magnetizations. We have also found that the macroscopic jump appears near the saturation field irrespective of the spin amplitude as well as the two-dimensional kagome model.Comment: 6pages, 3figures, accepted for publication in Journal of Low Temperature Physic

Characterization of Knots and Links Arising From Site-specific Recombination on Twist Knots

We develop a model characterizing all possible knots and links arising from recombination starting with a twist knot substrate, extending previous work of Buck and Flapan. We show that all knot or link products fall into three well-understood families of knots and links, and prove that given a positive integer $n$, the number of product knots and links with minimal crossing number equal to $n$ grows proportionally to $n^5$. In the (common) case of twist knot substrates whose products have minimal crossing number one more than the substrate, we prove that the types of products are tightly prescribed. Finally, we give two simple examples to illustrate how this model can help determine previously uncharacterized experimental data.Comment: 32 pages, 7 tables, 27 figures, revised: figures re-arranged, and minor corrections. To appear in Journal of Physics

Ferrimagnetism of the Heisenberg Models on the Quasi-One-Dimensional Kagome Strip Lattices

We study the ground-state properties of the S=1/2 Heisenberg models on the quasi-onedimensional kagome strip lattices by the exact diagonalization and density matrix renormalization group methods. The models with two different strip widths share the same lattice structure in their inner part with the spatially anisotropic two-dimensional kagome lattice. When there is no magnetic frustration, the well-known Lieb-Mattis ferrimagnetic state is realized in both models. When the strength of magnetic frustration is increased, on the other hand, the Lieb-Mattis-type ferrimagnetism is collapsed. We find that there exists a non-Lieb-Mattis ferrimagnetic state between the Lieb-Mattis ferrimagnetic state and the nonmagnetic ground state. The local magnetization clearly shows an incommensurate modulation with long-distance periodicity in the non-Lieb-Mattis ferrimagnetic state. The intermediate non-Lieb-Mattis ferrimagnetic state occurs irrespective of strip width, which suggests that the intermediate phase of the two-dimensional kagome lattice is also the non-Lieb-Mattis-type ferrimagnetism.Comment: 9pages, 11figures, accepted for publication in J. Phys. Soc. Jp

Study of Liquefaction Damages of Quay-Walls and Breakwaters During Kobe Earthquake

During Kobe Earthquake, very extensive damages of harbor facilities such as quay-wall and breakwater occurred in Kobe Port and also along the coastal areas between Kobe and Osaka cities. Major causes of the damages were the liquefaction of sands underlying and behind the concrete caisson and also strong earthquake shaking force on the caisson. The degree of damage varied considerably depending on location and also on the size of structure. In order to understand the mechanism of damage as well as the factors that controlled the degree of damage, it was necessary to examine and analyze the case records of damages of these structures. This paper describes the result of such study on liquefaction damage of quay-walls and breakwaters. Through the study, it was found that the movement of sand at shallow depth below the caisson base is mainly responsible for a large settlement of caisson, but the mode of deformation is different between quay wall and breakwater. Also an effective stress liquefaction analysis was performed on the damaged quay-walls and breakwaters in order to check the applicability of effective stress liquefaction analysis on damage assessment. It was found that the effective stress analysis may be used to establish the overall trend of damage variation with the intensity of seismic motion, but problems exist in setting the dynamic parameters for the analysis, such as damping parameters, in order to obtain a reliable result

Frustration-Induced Ferrimagnetism in Heisenberg Spin Chains

We study ground-state properties of the Heisenberg frustrated spin chain with interactions up to fourth nearest neighbors by the exact-diagonalization method and the density matrix renormalization group method. We find that ferrimagnetism is realized not only in the case of S=1/2 but also S=1 despite that there is only a single spin site in each unit cell determined from the shape of the Hamiltonian. Our numerical results suggest that a "multi-sublattice structure" is not required for the occurrence of ferrimagnetism in quantum spin systems with isotropic interactions.Comment: 6 pages, 3 figures, accepted for publication in Journal of the Physical Society of Japa

Synchronization of uncoupled oscillators by common gamma impulses: from phase locking to noise-induced synchronization

Nonlinear oscillators can mutually synchronize when they are driven by common external impulses. Two important scenarios are (i) synchronization resulting from phase locking of each oscillator to regular periodic impulses and (ii) noise-induced synchronization caused by Poisson random impulses, but their difference has not been fully quantified. Here we analyze a pair of uncoupled oscillators subject to common random impulses with gamma-distributed intervals, which can be smoothly interpolated between regular periodic and random Poisson impulses. Their dynamics are charac- terized by phase distributions, frequency detuning, Lyapunov exponents, and information-theoretic measures, which clearly reveal the differences between the two synchronization scenarios.Comment: 18 page