12,244 research outputs found
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 -anaolg of the sixth Painlev\'e equation
A -difference analog of the sixth Painlev\'e equation is presented. It
arises as the condition for preserving the connection matrix of linear
-difference equations, in close analogy with the monodromy preserving
deformation of linear differential equations. The continuous limit and special
solutions in terms of -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 there are and actions on the space of solutions of
the first nontrivial equation in the 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
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