Cluster Heat Bath Algorithm in Monte Carlo Simulations of Ising Models

We have proposed a cluster heat bath method in Monte Carlo simulations of Ising models in which one of the possible spin configurations of a cluster is selected in accordance with its Boltzmann weight. We have argued that the method improves slow relaxation in complex systems and demonstrated it in an axial next-nearest-neighbor Ising(ANNNI) model in two-dimensions.Comment: 10 pages, REVTeX, 2 figures, to appear in Phys.Rev.Let

Quantum fluctuation induced ordered phase in the Blume-Capel model

We consider the Blume-Capel model with the quantum tunneling between the excited states. We find a magnetically ordered phase transition induced by quantum fluctuation in a model. The model has no phase transition in the corresponding classical case. Usually, quantum fluctuation breaks ordered phase as in the case of the transverse field Ising model. However, in present case, an ordered phase is induced by quantum fluctuation. Moreover, we find a phase transition between a quantum paramagnetic phase and a classical diamagnetic phase at zero temperature. We study the properties of the phase transition by using a mean field approximation (MFA), and then, by a quantum Monte Carlo method to confirm the result of the MFA.Comment: 7 pages, 6 figures, corrected some typo

Practical Application of Near-Infrared Spectroscopy for Determining Rice Amylose Content at Grain Elevator

The major chemical constituent contents of rice are moisture, protein and starch (amylose and amylopectin). Those constituent contents associate with eating quality of rice. Near-infrared (NIR) spectroscopy is one of the non-destructive methods for determining grain chemical contents. At grain elevator, moisture and protein contents can be measured with high accuracy using an NIR spectrometer by the effort of our research activities in Japan. However, the accuracy to determine amylose content is not sufficient. Thus, the objective of this study was to develop non-destructive method to determine rice amylose content for practical use at grain elevator. Milled rice amylose content measurement was performed using an auto-analyzer for reference (chemical) analysis. Spectra data of milled rice were obtained using an NIR spectrometer with a wavelength range of 850 to 1048 nm. Calibration model to determine amylose content was developed using non-waxy Japonica-type rice samples. Partial least squares (PLS) regression analysis was used to develop calibration model. The accuracy of the model was validated and the validation statistics were shown: coefficient of determination (r2) was 0.72, bias was -0.04%, standard error of prediction (SEP) was 0.92%, and ratio of SEP to standard deviation of reference data (RPD) was 1.90. Production year of the validation set (2017) was different from that of the calibration set (2008 to 2016). This means the same condition as practical use of this method at grain elevator. The result obtained in this study indicated that this calibration model enables non-destructive determination of rice amylose content at grain elevator. &nbsp

Ordered phase and phase transitions in the three-dimensional generalized six-state clock model

We study the three-dimensional generalized six-state clock model at values of the energy parameters, at which the system is considered to have the same behavior as the stacked triangular antiferromagnetic Ising model and the three-state antiferromagnetic Potts model. First, we investigate ordered phases by using the Monte Carlo twist method (MCTM). We confirmed the existence of an incompletely ordered phase (IOP1) at intermediate temperature, besides the completely ordered phase (COP) at low-temperature. In this intermediate phase, two neighboring states of the six-state model mix, while one of them is selected in the low temperature phase. We examine the fluctuation the mixing rate of the two states in IOP1 and clarify that the mixing rate is very stable around 1:1. The high temperature phase transition is investigated by using non-equilibrium relaxation method (NERM). We estimate the critical exponents beta=0.34(1) and nu=0.66(4). These values are consistent with the 3D-XY universality class. The low temperature phase transition is found to be of first-order by using MCTM and the finite-size-scaling analysis

A Theory of Ferroelectric Phase Transition in SrTiO3_3 induced by Isotope Replacement

A theory to describe the dielectric anomalies and the ferroelectric phase transition induced by oxygen isotope replacement in SrTiO$_3$ is developed. The proposed model gives consistent explanation between apparently contradictory experimental results on macroscopic dielectric measurements versus microscopic lattice dynamical measurements by neutron scattering studies. The essential feature is described by a 3-state quantum order-disorder system characterizing the degenerated excited states in addition to the ground state of TiO$_6$ cluster. The effect of isotope replacement is taken into account through the tunneling frequency between the excited states. The dielectric properties are analyzed by the mean field approximation (MFA), which gives qualitative agreements with experimental results throughout full range of the isotope concentration.The phase diagram in the temperature-tunneling frequencycoordinate is studied by a QMC method to confirm the qualitative validity of the MFA analysis.Comment: 26 pages, 8 figure

Average Structures of a Single Knotted Ring Polymer

Two types of average structures of a single knotted ring polymer are studied by Brownian dynamics simulations. For a ring polymer with N segments, its structure is represented by a 3N -dimensional conformation vector consisting of the Cartesian coordinates of the segment positions relative to the center of mass of the ring polymer. The average structure is given by the average conformation vector, which is self-consistently defined as the average of the conformation vectors obtained from a simulation each of which is rotated to minimize its distance from the average conformation vector. From each conformation vector sampled in a simulation, 2N conformation vectors are generated by changing the numbering of the segments. Among the 2N conformation vectors, the one closest to the average conformation vector is used for one type of the average structure. The other type of the averages structure uses all the conformation vectors generated from those sampled in a simulation. In thecase of the former average structure, the knotted part of the average structure is delocalized for small N and becomes localized as N is increased. In the case of the latter average structure, the average structure changes from a double loop structure for small N to a single loop structure for large N, which indicates the localization-delocalization transition of the knotted part.Comment: 15 pages, 19 figures, uses jpsj2.cl

Common and Distant Structural Characteristics of Feruloyl Esterase Families from Aspergillus oryzae

Background: Feruloyl esterases (FAEs) are important biomass degrading accessory enzymes due to their capability of cleaving the ester links between hemicellulose and pectin to aromatic compounds of lignin, thus enhancing the accessibility of plant tissues to cellulolytic and hemicellulolytic enzymes. FAEs have gained increased attention in the area of biocatalytic transformations for the synthesis of value added compounds with medicinal and nutritional applications. Following the increasing attention on these enzymes, a novel descriptor based classification system has been proposed for FAEs resulting into 12 distinct families and pharmacophore models for three FAE sub-families have been developed. Methodology/Principal Findings: The feruloylome of Aspergillus oryzae contains 13 predicted FAEs belonging to six sub-families based on our recently developed descriptor-based classification system. The three-dimensional structures of the 13 FAEs were modeled for structural analysis of the feruloylome. The three genes coding for three enzymes, viz., A.O.2, A.O.8 and A.O.10 from the feruloylome of A. oryzae, representing sub-families with unknown functional features, were heterologously expressed in Pichia pastoris, characterized for substrate specificity and structural characterization through CD spectroscopy. Common feature-based pharamacophore models were developed according to substrate specificity characteristics of the three enzymes. The active site residues were identified for the three expressed FAEs by determining the titration curves of amino acid residues as a function of the pH by applying molecular simulations. Conclusions/Significance: Our findings on the structure-function relationships and substrate specificity of the FAEs of A. oryzae will be instrumental for further understanding of the FAE families in the novel classification system. The developed pharmacophore models could be applied for virtual screening of compound databases for short listing the putative substrates prior to docking studies or for post-processing docking results to remove false positives. Our study exemplifies how computational predictions can complement to the information obtained through experimental methods. © 2012 Udatha et al.published_or_final_versio

Measurement of Neutrino Oscillation with KamLAND: Evidence of Spectral Distortion

We present results of a study of neutrino oscillation based on a 766 ton-year exposure of KamLAND to reactor anti-neutrinos. We observe 258 \nuebar\ candidate events with energies above 3.4 MeV compared to 365.2 events expected in the absence of neutrino oscillation. Accounting for 17.8 expected background events, the statistical significance for reactor \nuebar disappearance is 99.998%. The observed energy spectrum disagrees with the expected spectral shape in the absence of neutrino oscillation at 99.6% significance and prefers the distortion expected from \nuebar oscillation effects. A two-neutrino oscillation analysis of the KamLAND data gives \DeltaMSq = 7.9$^{+0.6}_{-0.5}\times10^{-5}$ eV$^2$. A global analysis of data from KamLAND and solar neutrino experiments yields \DeltaMSq = 7.9$^{+0.6}_{-0.5}\times10^{-5}$ eV$^2$ and \ThetaParam = 0.40$^{+0.10}_{-0.07}$, the most precise determination to date.Comment: 5 pages, 4 figures; submitted to Phys.Rev.Letter

First Results from KamLAND: Evidence for Reactor Anti-Neutrino Disappearance

KamLAND has been used to measure the flux of $\bar{\nu}_e$'s from distant nuclear reactors. In an exposure of 162 ton$\cdot$yr (145.1 days) the ratio of the number of observed inverse $\beta$-decay events to the expected number of events without disappearance is $0.611\pm 0.085 {\rm (stat)} \pm 0.041 {\rm (syst)}$ for $\bar{\nu}_e$ energies $>$ 3.4 MeV. The deficit of events is inconsistent with the expected rate for standard $\bar{\nu}_e$ propagation at the 99.95% confidence level. In the context of two-flavor neutrino oscillations with CPT invariance, these results exclude all oscillation solutions but the `Large Mixing Angle' solution to the solar neutrino problem using reactor $\bar{\nu}_e$ sources.Comment: 6 pages, 6 figure