GENOMEPOP: a program to simulate genomes in populations.

Die cavity design of near flashless forging process using FEM-based backward simulation

An upper bound elemental technique approach to the process design of axisymmetric forging by forward and backward simulation

In this paper we propose a methodology which combines Forward and Backward Simulation in order to extend discrete-event simulation by the ability to calculate float times. In the case of Backward Simulation, the simulation starts at the virtual completion date of the construction project and runs backwards in time until the start date. To determine float times it is important that the task execution sequence is in the same order for forward and backward simulation. Consequently we present an extension to the simulation concept that controls the execution order of the tasks within the backward simulation. By combining the results of the forward and backward simulation, it is possible to determine float times for each task while taking into account resources. A comprehensive case study illustrates the application of this new approach. One result of this is the determination of detailed float times for each task using discrete-event simulation.

BackgroundThe vast majority of phylogenetic trees are inferred from molecular sequence data (nucleotides or amino acids) using time-reversible evolutionary models which assume that, for any pair of nucleotide or amino acid characters, the relative rate of X to Y substitution is the same as the relative rate of Y to X substitution. However, this reversibility assumption is unlikely to accurately reflect the actual underlying biochemical and/or evolutionary processes that lead to the fixation of substitutions. Here, we use empirical viral genome sequence data to reveal that evolutionary non-reversibility is pervasive among most groups of viruses. Specifically, we consider two non-reversible nucleotide substitution models: (1) a 6-rate non-reversible model (NREV6) in which Watson-Crick complementary substitutions occur at identical relative rates and which might therefor be most applicable to analyzing the evolution of genomes where both complementary strands are subject to the same mutational processes (such as might be expected for double-stranded (ds) RNA or dsDNA genomes); and (2) a 12-rate non-reversible model (NREV12) in which all relative substitution types are free to occur at different rates and which might therefore be applicable to analyzing the evolution of genomes where the complementary genome strands are subject to different mutational processes (such as might be expected for viruses with single-stranded (ss) RNA or ssDNA genomes).ResultsUsing likelihood ratio and Akaike Information Criterion-based model tests, we show that, surprisingly, NREV12 provided a significantly better fit to 21/31 dsRNA and 20/30 dsDNA datasets than did the general time reversible (GTR) and NREV6 models with NREV6 providing a better fit than NREV12 and GTR in only 5/30 dsDNA and 2/31 dsRNA datasets. As expected, NREV12 provided a significantly better fit to 24/33 ssDNA and 40/47 ssRNA datasets. Next, we used simulations to show that increasing degrees of strand-specific substitution bias decrease the accuracy of phylogenetic inference irrespective of whether GTR or NREV12 is used to describe mutational processes. However, in cases where strand-specific substitution biases are extreme (such as in SARS-CoV-2 and Torque teno sus virus datasets) NREV12 tends to yield more accurate phylogenetic trees than those obtained using GTR.ConclusionWe show that NREV12 should, be seriously considered during the model selection phase of phylogenetic analyses involving viral genomic sequences.

Evaluating placental inter-ordinal phylogenies with novel sequences including RAG1, γ-fibrinogen, ND6, and mt-tRNA, plus MCMC-driven nucleotide, amino acid, and codon models

The paper illustrates the use of a forward and backward linkage agricultural production simulation model. CHICKSIM III is a comprehensive, farm-level, and stochastic capital budgeting simulation model which provides an analytical framework for simulating probable consequences of production, marketing, financial, and policy variables on the profitability of a farm or agribusiness firm. The model is applied to evaluate the profitability of a representative farm producing broiler, beef, corn, and kenaf.

A general automaton model for timing-based systems is presented and is used as the context for developing a variety of simulation proof techniques for such systems. As a first step, a comprehensive overview of simulation techniques for simple untimed automata is given. In particular, soundness and completeness results for (1) refinements, (2) forward and backward simulations, (3) forward-backward and backward-forward simulations, and (4) history and prophecy relations are given. History and prophecy relations are new and are abstractions of the history variables of Owicki and Gries and the prophecy variables of Abadi and Lamport, respectively. As a subsequent step, it is shown how most of the results for untimed automata can be carried over to the setting of timed automata. In fact many of the results for the timed case are obtained as consequences of the analogous results for the untimed case.

Nuclear-encoded SSU rDNA sequences have been obtained from 64 strains of conjugating green algae (Zygnemophyceae, Streptophyta, Viridiplantae). Molecular phylogenetic analyses of 90 SSU rDNA sequences of Viridiplantae (inciuding 78 from the Zygnemophyceae) were performed using complex evolutionary models and maximum likelihood, distance, and maximum parsimony methods. The significance of the results was tested by bootstrap analyses, deletion of long-branch taxa, relative rate tests, and Kishino-Hasegawa tests with user-defined trees. All results support the monophyly of the class Zygnemophyceae and of the order Desmidiales. The second order, Zygnematales, forms a series of early-branching clades in paraphyletic succession, with the two traditional families Mesotaeniaceae and Zygnemataceae not recovered as lineages. Instead, a long-branch Spirogyra/Sirogonium clade and the later-diverging Netrium and Roya clades represent independent clades. Within the order Desmidiales, the families Gonatozygaceae and Closteriaceae are monophyletic, whereas the Peniaceae (represented only by Penium margaritaceum) and the Desmidiaceae represent a single weakly supported lineage. Within the Desmidiaceae short internal branches and varying rates of sequence evolution among taxa reduce the phylogenetic resolution significantly. The SSU rDNA-based phylogeny is largely congruent with a published analysis of the rbcL phylogeny of the Zygnemophyceae (McCourt et al. 2000) and is also in general agreement with classification schemes based on cell wall ultrastructure. The extended taxon sampling at the subgenus level provides solid evidence that many genera in the Zygnemophyceae are not monophyletic and that the genus concept in the group needs to be revised.

The development of divergence-time estimation methods has been an active area of research since the early 1960s, when the molecular clock was first postulated by Zuckerkandl and Pauling. Thanks to technological and computational improvements, more powerful and cutting-edge techniques and algorithms have been developed to better understand species evolution at the molecular level. These have led to improved methods for molecular clock dating of speciation events. During the past two decades, the approaches for DNA sequencing have substantially advanced and their costs have decreased, thus enabling large-scale genome-sequencing projects that aim to sequence all species in the tree of life. Being able to access thousands of complete genomes, however, has brought new biological and computational challenges to phylogenomic analyses. We might have more data, but also new questions to answer. Inferring reliable phylogenies and accurately dating them is now the main goal of phylogenomic analyses. Although new computational tools that implement more complex evolutionary models have been developed, there remain challenges in dealing with issues such as polytomies, incomplete lineage sorting, and the uncertainty in the fossil record. This chapter aims to guide the reader through the steps of Bayesian phylogenomic dating analyses, from data collection and processing up to the inference of the species tree and subsequent clock dating analysis. We pay close attention to the Bayesian paradigm in molecular clock dating, focusing on the effects that the prior and the likelihood can have on the estimated divergence times when using phylogenomic data. We describe strategies to speed up computation when using large genomic data sets, such as the approximate-likelihood method, which produces speed-ups of up to 1000× in time-tree inference. We also discuss strategies to improve the efficiency of Markov chain Monte Carlo sampling.

Backward tracing simulation of precision forging process for blade based on 3D FEM

Previous article Next article Haploid Populations Subject to Varying Environment: The Characteristic Values and the Rate of Loss of AllelesKeith GladstienKeith Gladstienhttps://doi.org/10.1137/0132065PDFBibTexSections ToolsAdd to favoritesExport CitationTrack CitationsEmail SectionsAboutAbstractA class of stochastic matrices, arising in genetics, are considered. The characteristic values are obtained and related to the genetic process.[1] C. Cannings, The latent roots of certain Markov chains arising in genetics: a new approach. I. Haploid models, Advances in Appl. Probability, 6 (1974), 260–290 MR0343949 0284.60064 CrossrefGoogle Scholar[2] C. Cannings, The latent roots of certain Markov chains arising in genetics: a new approach. II. Further haploid models, Advances in Appl. Probability, 7 (1975), 264–282 MR0371430 0339.60067 CrossrefISIGoogle Scholar[3] A. B. Chia, Random mating in a population of cyclic size, J. Appl. Probability, 5 (1968), 21–30 MR0225583 0162.51901 CrossrefISIGoogle Scholar[4] William Feller, Diffusion processes in genetics, Proceedings of the Second Berkeley Symposium on Mathematical Statistics and Probability, 1950, University of California Press, Berkeley and Los Angeles, 1951, 227–246 MR0046022 0045.09302 Google Scholar[5] Joseph Felsenstein, The rate of loss of multiple alleles in finite haploid populations, Theoret. Population Biology, 2 (1971), 391–403 10.1016/0040-5809(71)90028-1 MR0332215 0234.92010 CrossrefGoogle Scholar[6] Keith Gladstien, Loss of alleles in a haploid population with varying environment, Theoret. Population Biology, 10 (1976), 383–394 10.1016/0040-5809(76)90025-3 MR0496833 0346.92014 CrossrefISIGoogle Scholar[7] Keith Gladstien, The characteristic values and vectors for a class of stochastic matrices arising in genetics, SIAM J. Appl. Math., 34 (1978), 630–642 10.1137/0134050 MR0475977 0386.92004 LinkISIGoogle Scholar[8] Samuel Karlin, Equilibrium behavior of population genetic models with non-random mating. II. Pedigrees, homozygosity and stochastic models, J. Appl. Probability, 5 (1968), 487–566 MR0246657 0205.49601 CrossrefISIGoogle Scholar[9] S. Karlin, Rates of approach to homozygosity for finite stochastic models with variable population size, Amer. Naturalist, 102 (1968), 443–455 10.1086/282557 CrossrefISIGoogle Scholar[10] S. Wright, Evolution in Mendelain populations, Genetics, 16 (1931), 97–159 Google Scholar Previous article Next article FiguresRelatedReferencesCited ByDetails Looking Forwards and Backwards in the Multi-Allelic Neutral Cannings Population ModelJournal of Applied Probability, Vol. 47, No. 03 | 14 July 2016 Cross Ref Looking Forwards and Backwards in the Multi-Allelic Neutral Cannings Population ModelJournal of Applied Probability, Vol. 47, No. 3 | 14 July 2016 Cross Ref The time back to the most recent common ancestor in exchangeable population modelsAdvances in Applied Probability, Vol. 36, No. 01 | 1 July 2016 Cross Ref The time back to the most recent common ancestor in exchangeable population modelsAdvances in Applied Probability, Vol. 36, No. 1 | 1 July 2016 Cross Ref Robustness results for the coalescentJournal of Applied Probability, Vol. 35, No. 02 | 14 July 2016 Cross Ref Robustness results for the coalescentJournal of Applied Probability, Vol. 35, No. 2 | 14 July 2016 Cross Ref Line-of-descent and genealogical processes, and their applications in population genetics modelsTheoretical Population Biology, Vol. 26, No. 2 | 1 Oct 1984 Cross Ref The Characteristic Values and Vectors for a Class of Stochastic Matrices Arising in GeneticsKeith GladstienSIAM Journal on Applied Mathematics, Vol. 34, No. 4 | 12 July 2006AbstractPDF (1212 KB) Volume 32, Issue 4| 1977SIAM Journal on Applied Mathematics707-895 History Submitted:29 April 1976Published online:12 July 2006 InformationCopyright © 1977 Society for Industrial and Applied MathematicsPDF Download Article & Publication DataArticle DOI:10.1137/0132065Article page range:pp. 778-783ISSN (print):0036-1399ISSN (online):1095-712XPublisher:Society for Industrial and Applied Mathematics

A correction for the vertical gradient of air density has been incorporated into a skewed probability density function formulation for turbulence in the convective boundary layer. The related drift term for Lagrangian stochastic dispersion modelling has been derived based on the well-mixed condition. Furthermore, the formulation has been extended to include unsteady turbulence statistics and the related additional component of the drift term obtained. These formulations are an extension of the drift formulation reported by Luhar et al. (Atmos Environ 30:1407–1418, 1996) following the well-mixed condition proposed by Thomson (J Fluid Mech 180:529–556, 1987). Comprehensive tests were carried out to validate the formulations including consistency between forward and backward simulations and preservation of a well-mixed state with unsteady conditions. The stationary state CBL drift term with density correction was incorporated into the FLEXPART and FLEXPART-WRF Lagrangian models, and included the use of an ad hoc transition function that modulates the third moment of the vertical velocity based on stability parameters. Due to the current implementation of the FLEXPART models, only a steady-state horizontally homogeneous drift term could be included. To avoid numerical instability, in the presence of non-stationary and horizontally inhomogeneous conditions, a re-initialization procedure for particle velocity was used. The criteria for re-initialization and resulting errors were assessed for the case of non-stationary conditions by comparing a reference numerical solution in simplified unsteady conditions, obtained using the non-stationary drift term, and a solution based on the steady drift with re-initialization. Two examples of “real-world” numerical simulations were performed under different convective conditions to demonstrate the effect of the vertical gradient in density on the particle dispersion in the CBL.

Calculating the kinetic rates for rare transitions is an important objective for molecular simulations. Here I prove equalities that relate the transition rates to the equilibrium free energy and the statistics of the transition paths. In particular, the durations of the transition paths within given intervals of the reaction coordinate provide the kinetic pre-factor in the rate formula. Based on the available free energy, the transition rates can further be rigorously calculated by initiating forward and backward simulations and evaluating the duration of each transition path. Validation on a model system confirms that the approach correctly predicts the transition rates from the simulations and demonstrates that whereas the relations here are general and valid for any chosen reaction coordinate, a good reaction coordinate will enable a more efficient sampling of the transition paths and thus a more reliable rate calculation.

Simulations of weighted tree automata (wta) are considered. It is shown how such simulations can be decomposed into simpler functional and dual functional simulations also called forward and backward simulations. In addition, it is shown in several cases (fields, commutative rings, NOETHERIAN semirings, semiring of natural numbers) that all equivalent wta M and N can be joined by a finite chain of simulations. More precisely, in all mentioned cases there is a single wta that simulates both M and N. Those results immediately yield decidability of equivalence provided that the semiring is finitely (and effectively) presented.

Global warming and the urgency of environmental issues have brought the issue of carbon emissions in the shipping industry to the forefront. Taking the government, port enterprises, shipping companies, and social and environmental organizations as research subjects, this study delves into the key challenges of carbon emission reduction in the shipping industry. By constructing a complex and dynamic evolutionary game model and conducting data simulations with the help of MATLAB 2016b, we analyze in detail the strategic choices of each party on the emission reduction issue and explore the impact of these choices on the evolution of the system. In this study, we find that the government plays a crucial role in emission reduction regulation. Regulatory strategy and intensity have far-reaching impacts on the development of the whole system, and a flexible and intelligent regulatory system will promote active emission reduction by all parties. In addition, the reputation mechanism of social and environmental organizations plays a significant role in motivating all parties to take the initiative to adopt emission reduction strategies. In terms of economic incentives, we find that the government needs to provide differentiated support according to the characteristics of different enterprises, so that all parties can work together to move towards the emission reduction target. Through this study, we present a comprehensive game analysis of carbon emission reduction in the shipping industry and propose practical recommendations that are valuable to the shipping industry and environmental managers. These findings provide strong policy and action support for realizing the decarbonization of the shipping industry.