Three-dimensional Ising model in the fixed-magnetization ensemble: a Monte Carlo study

We study the three-dimensional Ising model at the critical point in the fixed-magnetization ensemble, by means of the recently developed geometric cluster Monte Carlo algorithm. We define a magnetic-field-like quantity in terms of microscopic spin-up and spin-down probabilities in a given configuration of neighbors. In the thermodynamic limit, the relation between this field and the magnetization reduces to the canonical relation M(h). However, for finite systems, the relation is different. We establish a close connection between this relation and the probability distribution of the magnetization of a finite-size system in the canonical ensemble.Comment: 8 pages, 2 Postscript figures, uses RevTe

RNA structure prediction from evolutionary patterns of nucleotide composition

Structural elements in RNA molecules have a distinct nucleotide composition, which changes gradually over evolutionary time. We discovered certain features of these compositional patterns that are shared between all RNA families. Based on this information, we developed a structure prediction method that evaluates candidate structures for a set of homologous RNAs on their ability to reproduce the patterns exhibited by biological structures. The method is named SPuNC for ‘Structure Prediction using Nucleotide Composition’. In a performance test on a diverse set of RNA families we demonstrate that the SPuNC algorithm succeeds in selecting the most realistic structures in an ensemble. The average accuracy of top-scoring structures is significantly higher than the average accuracy of all ensemble members (improvements of more than 20% observed). In addition, a consensus structure that includes the most reliable base pairs gleaned from a set of top-scoring structures is generally more accurate than a consensus derived from the full structural ensemble. Our method achieves better accuracy than existing methods on several RNA families, including novel riboswitches and ribozymes. The results clearly show that nucleotide composition can be used to reveal the quality of RNA structures and thus the presented technique should be added to the set of prediction tools

Graphical representations and cluster algorithms for critical points with fields

A two-replica graphical representation and associated cluster algorithm is described that is applicable to ferromagnetic Ising systems with arbitrary fields. Critical points are associated with the percolation threshold of the graphical representation. Results from numerical simulations of the Ising model in a staggered field are presented. The dynamic exponent for the algorithm is measured to be less than 0.5.Comment: Revtex, 12 pages with 2 figure

Generalized Geometric Cluster Algorithm for Fluid Simulation

We present a detailed description of the generalized geometric cluster algorithm for the efficient simulation of continuum fluids. The connection with well-known cluster algorithms for lattice spin models is discussed, and an explicit full cluster decomposition is derived for a particle configuration in a fluid. We investigate a number of basic properties of the geometric cluster algorithm, including the dependence of the cluster-size distribution on density and temperature. Practical aspects of its implementation and possible extensions are discussed. The capabilities and efficiency of our approach are illustrated by means of two example studies.Comment: Accepted for publication in Phys. Rev. E. Follow-up to cond-mat/041274

Numerical Solution of Hard-Core Mixtures

We study the equilibrium phase diagram of binary mixtures of hard spheres as well as of parallel hard cubes. A superior cluster algorithm allows us to establish and to access the demixed phase for both systems and to investigate the subtle interplay between short-range depletion and long-range demixing.Comment: 4 pages, 2 figure

Physical tests for Random Numbers in Simulations

We propose three physical tests to measure correlations in random numbers used in Monte Carlo simulations. The first test uses autocorrelation times of certain physical quantities when the Ising model is simulated with the Wolff algorithm. The second test is based on random walks, and the third on blocks of n successive numbers. We apply the tests to show that recent errors in high precision simulations using generalized feedback shift register algorithms are due to short range correlations in random number sequences. We also determine the length of these correlations.Comment: 16 pages, Post Script file, HU-TFT-94-

Investigations of primary and secondary particulate matter of different wood combustion appliances with a high-resolution time-of-flight aerosol mass spectrometer

A series of photo-oxidation smog chamber experiments were performed to investigate the primary emissions and secondary aerosol formation from two different log wood burners and a residential pellet burner under different burning conditions: starting and flaming phase. Emissions were sampled from the chimney and injected into the smog chamber leading to primary organic aerosol (POA) concentrations comparable to ambient levels. The composition of the aerosol was measured by an Aerodyne high resolution time-of-flight aerosol mass spectrometer (HR-TOF-AMS) and black carbon (BC) instrumentation. The primary emissions were then exposed to xenon light to initiate photo-chemistry and subsequent secondary organic aerosol (SOA) production. After correcting for wall losses, the average increase in organic matter (OM) concentrations by SOA formation for the starting and flaming phase experiments with the two log wood burners was found to be a factor of 4.1±1.4 after five hours of aging. No SOA formation was observed for the stable burning phase of the pellet burner. The startup emissions of the pellet burner showed an increase in OM concentration by a factor of 3.3. Including the measured SOA formation potential, average emission factors of BC+POA+SOA, calculated from CO<sub>2</sub> emission, were found to be in the range of 0.04 to 3.9 g/kg wood for the stable burning pellet burner and an old log wood burner during startup respectively. SOA contributed significantly to the ion C<sub>2</sub>H<sub>4</sub>O<sub>2</sub><sup>+</sup> at mass to charge ratio <i>m/z</i> 60, a commonly used marker for primary emissions of wood burning. This contribution at <i>m/z</i> 60 can overcompensate for the degradation of levoglucosan leading to an overestimation of the contribution of wood burning or biomass burning to the total OM. The primary organic emissions from the three different burners showed a wide range in O:C atomic ratio (0.19−0.60) for the starting and flaming conditions, which also increased during aging. Primary wood burning emissions have a rather low relative contribution at <i>m/z</i> 43 (<i>f</i> 43) to the total organic mass spectrum. The non-oxidized fragment C<sub>3</sub>H<sub>7</sub><sup>+</sup> has a considerable contribution at <i>m/z</i> 43 for the fresh OA with an increasing contribution of the oxygenated ion C<sub>2</sub>H<sub>3</sub>O<sup>+</sup> during aging. After five hours of aging, the OA has a rather low C<sub>2</sub>H<sub>3</sub>O<sup>+</sup> signal for a given CO<sub>2</sub><sup>+</sup> fraction, possibly indicating a higher ratio of acid to non-acid oxygenated compounds in wood burning OA compared to other oxygenated organic aerosol (OOA)

Monte Carlo Renormalization of the 3-D Ising model: Analyticity and Convergence

We review the assumptions on which the Monte Carlo renormalization technique is based, in particular the analyticity of the block spin transformations. On this basis, we select an optimized Kadanoff blocking rule in combination with the simulation of a d=3 Ising model with reduced corrections to scaling. This is achieved by including interactions with second and third neighbors. As a consequence of the improved analyticity properties, this Monte Carlo renormalization method yields a fast convergence and a high accuracy. The results for the critical exponents are y_H=2.481(1) and y_T=1.585(3).Comment: RevTeX, 4 PostScript file

A thermodynamically self-consistent theory for the Blume-Capel model

We use a self-consistent Ornstein-Zernike approximation to study the Blume-Capel ferromagnet on three-dimensional lattices. The correlation functions and the thermodynamics are obtained from the solution of two coupled partial differential equations. The theory provides a comprehensive and accurate description of the phase diagram in all regions, including the wing boundaries in non-zero magnetic field. In particular, the coordinates of the tricritical point are in very good agreement with the best estimates from simulation or series expansion. Numerical and analytical analysis strongly suggest that the theory predicts a universal Ising-like critical behavior along the $\lambda$-line and the wing critical lines, and a tricritical behavior governed by mean-field exponents.Comment: 11 figures. to appear in Physical Review

Retinal Biomarker Discovery for Dementia in an Elderly Diabetic Population

Dementia is a devastating disease, and has severe implications on affected individuals, their family and wider society. A growing body of literature is studying the association of retinal microvasculature measurement with dementia. We present a pilot study testing the strength of groups of conventional (semantic) and texture-based (non-semantic) measurements extracted from retinal fundus camera images to classify patients with and without dementia. We performed a 500-trial bootstrap analysis with regularized logistic regression on a cohort of 1,742 elderly diabetic individuals (median age 72.2). Age was the strongest predictor for this elderly cohort. Semantic retinal measurements featured in up to 81% of the bootstrap trials, with arterial caliber and optic disk size chosen most often, suggesting that they do complement age when selected together in a classifier. Textural features were able to train classifiers that match the performance of age, suggesting they are potentially a rich source of information for dementia outcome classification