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

Achtergrondinformatie over HDI: gebruik, voorkomen in het leefmilieu en gedrag in het lichaam

Dit rapport maakt onderdeel uit van een serie van acht rapporten over het onderzoek naar HDI uit CARC op de POMS-locaties van Defensie. Dit rapport bevat geen afzonderlijke publiekssamenvatting. Een overkoepelende publiekssamenvatting van de acht rapporten is te vinden op de website van het RIVM: "CARC op de POMS-locaties van Defensie: blootstelling en gezondheidsrisico's. Bevindingen uit het onderzoek op hoofdlijnen, met speciale aandacht voor het bestanddeel HDI" RIVM rapport 2020-0017.Ministerie van Defensi

FluxSimulator: An R Package to Simulate Isotopomer Distributions in Metabolic Networks

The representation of biochemical knowledge in terms of fluxes (transformation rates) in a metabolic network is often a crucial step in the development of new drugs and efficient bioreactors. Mass spectroscopy (MS) and nuclear magnetic resonance spectroscopy (NMRS) in combination with ^13C labeled substrates are experimental techniques resulting in data that may be used to quantify fluxes in the metabolic network underlying a process. The massive amount of data generated by spectroscopic experiments increasingly requires software which models the dynamics of the underlying biological system. In this work we present an approach to handle isotopomer distributions in metabolic networks using an object-oriented programming approach, implemented using S4 classes in R. The developed package is called FluxSimulator and provides a user friendly interface to specify the topological information of the metabolic network as well as carbon atom transitions in plain text files. The package automatically derives the mathematical representation of the formulated network, and assembles a set of ordinary differential equations (ODEs) describing the change of each isotopomer pool over time. These ODEs are subsequently solved numerically. In a case study FluxSimulator was applied to an example network. Our results indicate that the package is able to reproduce exact changes in isotopomer compositions of the metabolite pools over time at given flux rates.

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

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

SEQATOMS: a web tool for identifying missing regions in PDB in sequence context.

doi:10.1093/nar/gkn23

Diffusive Thermal Dynamics for the Ising Ferromagnet

We introduce a thermal dynamics for the Ising ferromagnet where the energy variations occurring within the system exhibit a diffusive character typical of thermalizing agents such as e.g. localized excitations. Time evolution is provided by a walker hopping across the sites of the underlying lattice according to local probabilities depending on the usual Boltzmann weight at a given temperature. Despite the canonical hopping probabilities the walker drives the system to a stationary state which is not reducible to the canonical equilibrium state in a trivial way. The system still exhibits a magnetic phase transition occurring at a finite value of the temperature larger than the canonical one. The dependence of the model on the density of walkers realizing the dynamics is also discussed. Interestingly the differences between the stationary state and the Boltzmann equilibrium state decrease with increasing number of walkers.Comment: 9 pages, 14 figures. Accepted for publication on PR

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

Monte Carlo computation of correlation times of independent relaxation modes at criticality

We investigate aspects of universality of Glauber critical dynamics in two dimensions. We compute the critical exponent $z$ and numerically corroborate its universality for three different models in the static Ising universality class and for five independent relaxation modes. We also present evidence for universality of amplitude ratios, which shows that, as far as dynamic behavior is concerned, each model in a given universality class is characterized by a single non-universal metric factor which determines the overall time scale. This paper also discusses in detail the variational and projection methods that are used to compute relaxation times with high accuracy

The Dynamic Exponent of the Two-Dimensional Ising Model and Monte Carlo Computation of the Sub-Dominant Eigenvalue of the Stochastic Matrix

We introduce a novel variance-reducing Monte Carlo algorithm for accurate determination of autocorrelation times. We apply this method to two-dimensional Ising systems with sizes up to $15 \times 15$, using single-spin flip dynamics, random site selection and transition probabilities according to the heat-bath method. From a finite-size scaling analysis of these autocorrelation times, the dynamical critical exponent $z$ is determined as $z=2.1665$ (12)