Search results for "Monte Carlo method"
showing 10 items of 1234 documents
A comparison of two indirect methods for estimating average levels of gene flow using microsatellite data.
1999
We compare the performance of Nm estimates based on FST and RST obtained from microsatellite data using simulations of the stepwise mutation model with range constraints in allele size classes. The results of the simulations suggest that the use of microsatellite loci can lead to serious overestimations of Nm, particularly when population sizes are large (N5000) and range constraints are high (K20). The simulations also indicate that, when population sizes are small (N/= 500) and migration rates are moderate (Nm approximately 2), violations to the assumption used to derive the Nm estimators lead to biased results. Under ideal conditions, i.e. large sample sizes (ns/= 50) and many loci (nl/=…
Social relations in older adults: Secular trends and longitudinal changes over a 16-year follow-up.
2010
Abstract Drawing on population studies in Finland, we investigated secular trends and longitudinal changes in social relations. The cohort comparison data comprised on 974 persons aged 65–69 years from three cohorts born between 1919 and 1939 and interviewed in 1988, 1996 and 2004. Longitudinal analyses were conducted for 635 persons aged 65–74 years over a 16-year follow-up at three measurement points. Social relations were studied on the basis of frequency seeing one's offspring, perceptions of the sufficiency of these contacts, and by asking whom the participants considered as their closest person and how often and in how many tasks they helped someone. The cohort comparisons showed that…
Phase behaviour of heteronuclear dimers in three-dimensional systems—a Monte Carlo study
2008
Monte Carlo simulation in the grand canonical ensemble, the histogram reweighting technique and finite size scaling are used to study the phase behaviour of dimers in three-dimensional systems. A single molecule is composed of two segments A and B, and the bond between them cannot be broken. The phase diagrams have been estimated for a set of model systems. Different structures formed by heteronuclear dimers have been found. The results show a great variety of vapour–liquid coexistence behaviour depending on the strength of the interactions between segments.
Analyzing Protein-Protein Spatial-Temporal Dependencies from Image Sequences Using Fuzzy Temporal Random Sets
2008
Total Internal Reflection Fluorescence Microscopy (TIRFM) allows us to image fluorescenttagged proteins near the plasma membrane of living cells with high spatial-temporal resolution. Using TIRFM imaging of GFP-tagged clathrin endocytic proteins, areas of fluorescence are observed as overlapping spots of different sizes and durations. Standard procedures to measure protein-protein colocalization of dual labeled samples threshold the original graylevel images to segment areas covered by different proteins. This binary logic is not appropriate as it leaves a free tuning parameter which can influence the conclusions. Moreover, these procedures rely on simple statistical analysis based on corre…
A generic TG-186 shielded applicator for commissioning model-based dose calculation algorithms for high-dose-rate Ir-192 brachytherapy
2017
PurposeA joint working group was created by the American Association of Physicists in Medicine (AAPM), the European Society for Radiotherapy and Oncology (ESTRO), and the Australasian Brachytherapy Group (ABG) with the charge, among others, to develop a set of well-defined test case plans and perform calculations and comparisons with model-based dose calculation algorithms (MBDCAs). Its main goal is to facilitate a smooth transition from the AAPM Task Group No. 43 (TG-43) dose calculation formalism, widely being used in clinical practice for brachytherapy, to the one proposed by Task Group No. 186 (TG-186) for MBDCAs. To do so, in this work a hypothetical, generic high-dose rate (HDR) Ir-19…
Enhanced sampling in simulations of dense systems
2002
In the simulations of a variety of systems we encounter the problem of large relaxation times due to the dense packing of the systems constituents. We propose an algorithm to overcome this slowing down by temporarily allowing the constituents of a 3d systems to escape into a 4th space coordinate. The idea will be exemplified for the problem of a homopolymer collapse.
SIMULATING SPIN MODELS ON GPU: A TOUR
2012
The use of graphics processing units (GPUs) in scientific computing has gathered considerable momentum in the past five years. While GPUs in general promise high performance and excellent performance per Watt ratios, not every class of problems is equally well suitable for exploiting the massively parallel architecture they provide. Lattice spin models appear to be prototypic examples of problems suitable for this architecture, at least as long as local update algorithms are employed. In this review, I summarize our recent experience with the simulation of a wide range of spin models on GPU employing an equally wide range of update algorithms, ranging from Metropolis and heat bath updates,…
QPO emission from moving hot spots on the surface of neutron stars: a model
2009
We present recent results of 3D magnetohydrodynamic simulations of neutron stars with small misalignment angles, as regards the features in lightcurves produced by regular movements of the hot spots during accretion onto the star. In particular, we show that the variation of position of the hot spot created by the infalling matter, as observed in 3D simulations, can produce high frequency Quasi Periodic Oscillations with frequencies associated with the inner zone of the disk. Previously reported simulations showed that the usual assumption of a fixed hot spot near the polar region is valid only for misalignment angles relatively large. Otherwise, two phenomena challenge the assumption: one …
Fractal Spacetime Structure in Asymptotically Safe Gravity
2005
Four-dimensional Quantum Einstein Gravity (QEG) is likely to be an asymptotically safe theory which is applicable at arbitrarily small distance scales. On sub-Planckian distances it predicts that spacetime is a fractal with an effective dimensionality of 2. The original argument leading to this result was based upon the anomalous dimension of Newton's constant. In the present paper we demonstrate that also the spectral dimension equals 2 microscopically, while it is equal to 4 on macroscopic scales. This result is an exact consequence of asymptotic safety and does not rely on any truncation. Contact is made with recent Monte Carlo simulations.
Challenges of the ATLAS Monte Carlo production during run 1 and beyond
2013
In this paper we will review the ATLAS Monte Carlo production setup including the different production steps involved in full and fast detector simulation. A report on the Monte Carlo production campaigns during run 1 and long shutdown 1 will be presented, including details on various performance aspects. Important improvements in the work flow and software will be highlighted. Besides standard Monte Carlo production for data analyses at 7 and 8 TeV, the production accommodates for various specialised activities. These ranges from extended Monte Carlo validation, Geant4 validation, pileup simulation using zero bias data and production for various upgrade studies. The challenges of these act…