512 research outputs found
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 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 , 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 is determined as (12)
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