Replica-Exchange Method in van der Waals Radius Space: Overcoming Steric Restrictions for Biomolecules

We present a new type of the Hamiltonian replica-exchange method, in which not temperatures but the van der Waals radius parameter is exchanged. By decreasing the van der Waals radii that control spatial sizes of atoms, this Hamiltonian replica-exchange method overcomes the steric restrictions and energy barriers. Furthermore, the simulation based on this method escapes from the local-minimum free-energy states and realizes effective sampling in the conformational space. We applied this method to an alanine dipeptide in aqueous solution and showed the effectiveness of the method by comparing the results with those obtained from the conventional canonical method.Comment: 14 pages, (Revtex4), 11 figure

A qq-anaolg of the sixth Painlev\'e equation

A $q$-difference analog of the sixth Painlev\'e equation is presented. It arises as the condition for preserving the connection matrix of linear $q$-difference equations, in close analogy with the monodromy preserving deformation of linear differential equations. The continuous limit and special solutions in terms of $q$-hypergeometric functions are also discussed.Comment: 8 pages, LaTeX file (Two misprints corrected

B, Bs -> K form factors: an update of light-cone sum rule results

We present an improved QCD light-cone sum rule (LCSR) calculation of the B -> K and Bs -> K form factors, by including SU(3)-symmetry breaking corrections. We use recently updated K-meson distribution amplitudes which incorporate the complete SU(3)-breaking structure. By applying the method of the direct integration in the complex plane, which is presented in a detail, the analytical extraction of the imaginary parts of LCSR hard-scattering amplitudes becomes unnecessary and therefore the complexity of the calculation is greatly reduced. The values obtained for the relevant B_{(s)} -> K form factors are as follows: f^+_{BK}(0)= 0.36^{+0.05}_{-0.04}, f^+_{B_sK}(0)= 0.30^{+0.04}_{-0.03} and f^T_{BK}(0)= 0.38\pm 0.05, f^T_{B_sK}(0)= 0.30\pm 0.05. By comparing with the B -> pi form factors extracted recently by the same method, we find the following SU(3) violation among the B -> light form factors: f^+_{BK}(0)/f^+_{B\pi}(0) = 1.38^{+0.11}_{-0.10}, f^+_{B_sK}(0)/f^+_{B\pi}(0) = 1.15^{+0.17}_{-0.09}, f^T_{BK}(0)/f^T_{B\pi}(0) = 1.49^{+0.18}_{-0.06} and f^T_{B_sK}(0)/f^T_{B\pi}(0) = 1.17^{+0.15}_{-0.11}.Comment: 14 pages, 9 figures, some figures and discussions added; version to appear in PR

B\"acklund Transformations of MKdV and Painlev\'e Equations

For $N\ge 3$ there are $S_N$ and $D_N$ actions on the space of solutions of the first nontrivial equation in the $SL(N) MKdV hierarchy, generalizing the two$Z_2$ actions on the space of solutions of the standard MKdV equation. These actions survive scaling reduction, and give rise to transformation groups for certain (systems of) ODEs, including the second, fourth and fifth Painlev\'e equations.Comment: 8 pages, plain te

Observation of the Ettingshausen effect in quantum Hall systems

Evidence of the Ettingshausen effect in the breakdown regime of the integer quantum Hall effect has been observed in a GaAs/AlGaAs two-dimensional electron system. Resistance of micro Hall bars attached to both edges of a current channel shows remarkable asymmetric behaviors which indicate an electron temperature difference between the edges. The sign of the difference depends on the direction of the electric current and the polarity of the magnetic field. The results are consistent with the recent theory of Akera.Comment: 4 pages, 6 figures, submitted to Phys. Rev.

Stochastic Model and Equivalent Ferromagnetic Spin Chain with Alternation

We investigate a non-equilibrium reaction-diffusion model and equivalent ferromagnetic spin 1/2 XY spin chain with alternating coupling constant. The exact energy spectrum and the n-point hole correlations are considered with the help of the Jordan-Wigner fermionization and the inter-particle distribution function method. Although the Hamiltonian has no explicit translational symmetry, the translational invariance is recovered after long time due to the diffusion. We see the scaling relations for the concentration and the two-point function in finite size analysis.Comment: 7 pages, LaTeX file, to appear in J. Phys. A: Math. and Ge

Effective Sampling in the Configurational Space by the Multicanonical-Multioverlap Algorithm

We propose a new generalized-ensemble algorithm, which we refer to as the multicanonical-multioverlap algorithm. By utilizing a non-Boltzmann weight factor, this method realizes a random walk in the multi-dimensional, energy-overlap space and explores widely in the configurational space including specific configurations, where the overlap of a configuration with respect to a reference state is a measure for structural similarity. We apply the multicanonical-multioverlap molecular dynamics method to a penta peptide, Met-enkephalin, in vacuum as a test system. We also apply the multicanonical and multioverlap molecular dynamics methods to this system for the purpose of comparisons. We see that the multicanonical-multioverlap molecular dynamics method realizes effective sampling in the configurational space including specific configurations more than the other two methods. From the results of the multicanonical-multioverlap molecular dynamics simulation, furthermore, we obtain a new local-minimum state of the Met-enkephalin system.Comment: 15 pages, (Revtex4), 9 figure

Fabrication of FeSi and Fe3Si compounds by electron beam induced mixing of [Fe/Si]2 and [Fe3/Si]2 multilayers grown by focused electron beam induced deposition

Fe-Si binary compounds have been fabricated by focused electron beam induced deposition by the alternating use of iron pentacarbonyl, Fe(CO)5, and neopentasilane, Si5H12 as precursor gases. The fabrication procedure consisted in preparing multilayer structures which were treated by low-energy electron irradiation and annealing to induce atomic species intermixing. In this way we are able to fabricate FeSi and Fe3Si binary compounds from [Fe=Si]2 and [Fe3=Si]2 multilayers, as shown by transmission electron microscopy investigations. This fabrication procedure is useful to obtain nanostructured binary alloys from precursors which compete for adsorption sites during growth and, therefore, cannot be used simultaneously