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Monte Carlo Computer Simulation (monte + carlo_computer_simulation)
Selected AbstractsProspects for inferring pairwise relationships with single nucleotide polymorphismsMOLECULAR ECOLOGY, Issue 4 2003Jeffrey C. Glaubitz Abstract An extraordinarily large number of single nucleotide polymorphisms (SNPs) are now available in humans as well as in other model organisms. Technological advancements may soon make it feasible to assay hundreds of SNPs in virtually any organism of interest. One potential application of SNPs is the determination of pairwise genetic relationships in populations without known pedigrees. Although microsatellites are currently the marker of choice for this purpose, the number of independently segregating microsatellite markers that can be feasibly assayed is limited. Thus, it can be difficult to distinguish reliably some classes of relationship (e.g. full-sibs from half-sibs) with microsatellite data alone. We assess, via Monte Carlo computer simulation, the potential for using a large panel of independently segregating SNPs to infer genetic relationships, following the analytical approach of Blouin et al. (1996). We have explored a ,best case scenario' in which 100 independently segregating SNPs are available. For discrimination among single-generation relationships or for the identification of parent,offspring pairs, it appears that such a panel of moderately polymorphic SNPs (minor allele frequency of 0.20) will provide discrimination power equivalent to only 16,20 independently segregating microsatellites. Although newly available analytical methods that can account for tight genetic linkage between markers will, in theory, allow improved estimation of relationships using thousands of SNPs in highly dense genomic scans, in practice such studies will only be feasible in a handful of model organisms. Given the comparable amount of effort required for the development of both types of markers, it seems that microsatellites will remain the marker of choice for relationship estimation in nonmodel organisms, at least for the foreseeable future. [source] Optimal selection method for establishing an inbred strain of laboratory animals with high performance for litter size at weaningANIMAL SCIENCE JOURNAL, Issue 2 2008Masahiro SATOH ABSTRACT The optimal selection method was investigated for establishing an inbred strain of laboratory animals with high performance for litter size at weaning (LSW). A Monte Carlo computer simulation was used to assess the effects of our selection methods on the genetic change of LSW under the continuous use of full-sib mating for 20 generations. Smaller number of growing animals of each sex per litter and genetic evaluation for selection using a BLUP animal model increased LSW. Use of information on another trait genetically related to LSW, larger population size, and greater number of generations for random selection before starting full-sib mating were useful for establishing an inbred strain of laboratory animals with high performance for LSW. It was concluded that LSW can be increased by directional selection when establishing inbred strains. [source] Comparison of genetic improvement for litter size at birth by direct and indirect selection in swine herdANIMAL SCIENCE JOURNAL, Issue 6 2006Masahiro SATOH ABSTRACT Responses to selection for number of piglets born alive (NBA) by the total number of piglets born (TNB), the NBA, and the NBA plus number of piglets born dead (NBD) were compared using the accuracy of selection and expected genetic gain calculated from the selection index with family information and the real response to selection, using data generated by Monte Carlo computer simulation. The accuracy of selection for NBA selected by TNB was higher than that by NBA only if the genetic correlation between TNB and NBA was close to 1.0, or the value of heritability for the TNB was much larger than that for the NBA. The accuracy of selection for the NBA selected by the combination of the TNB and the NBA was generally highest in the three selection methods in each family structure. Selection by the TNB resulted in the greatest expected genetic gain for the TNB among the selection methods. In the best linear unbiased prediction (BLUP) selection, the genetic gain for the NBA accumulated by the NBA tended to be similar to that accumulated by the combination of the NBA and the NBD, and both genetic gains at generation 10 were significantly larger than that by the TNB (P < 0.001). The accumulated responses selected by the two-trait animal model BLUP estimated from genetic parameters with errors were similar to those estimated from the true parameters, and there was no significant difference between them. These results indicate that selection by the NBA or by the NBA and the NBD gives more genetic improvement in the NBA than that by the TNB. [source] Effect of electric field on diffusion in disordered materialsANNALEN DER PHYSIK, Issue 12 2009F. Jansson Abstract The effect of electric field on diffusion of charge carriers in disordered materials is studied by Monte Carlo computer simulations and analytical calculations. It is shown how an electric field enhances the diffusion coefficient in the hopping transport mode. The enhancement essentially depends on the temperature and on the energy scale of the disorder potential. It is shown that in one-dimensional hopping the diffusion coefficient depends linearly on the electric field, while for hopping in three dimensions the dependence is quadratic. [source] Complex 1H,13C-NMR relaxation and computer simulation study of side-chain dynamics in solid polylysineBIOPOLYMERS, Issue 3 2005Alexey Krushelnitsky Abstract The side-chain dynamics of solid polylysine at various hydration levels was studied by means of proton spin,lattice relaxation times measurements in the laboratory and tilted (off-resonance) rotating frames at several temperatures as well as Monte Carlo computer simulations. These data were analyzed together with recently measured carbon relaxation data (A. Krushelnitsky, D. Faizullin, and D. Reichert, Biopolymers, 2004, Vol. 73, pp. 1,15). The analysis of the whole set of data performed within the frame of the model-free approach led us to a conclusion about three types of the side-chain motion. The first motion consists of low amplitude rotations of dihedral angles of polylysine side chains on the nanosecond timescale. The second motion is cis,trans conformational transitions of the side chains with correlation times in the microsecond range for dry polylysine. The third motion is a diffusion of dilating defects described in (W. Nusser, R. Kimmich, and F. Winter, Journal of Physical Chemistry, 1988, Vol. 92, pp. 6808,6814). This diffusion causes almost no reorientation of chemical bonds but leads to a sliding motion of side chains with respect to each other in the nanosecond timescale. This work evidently demonstrates the advantages of the simultaneous quantitative analysis of data obtained from different experiments within the frame of the same mathematical formalism, providing for the detailed description of the nature and geometry of the internal molecular dynamics. © 2005 Wiley Periodicals, Inc. Biopolymers 78: 129,139, 2005 This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] | ||||||||||