Parallel Computing of Edwards—Anderson Model

A scheme for parallel computation of the two-dimensional Edwards—Anderson model based on the transfer matrix approach is proposed. Free boundary conditions are considered. The method may find application in calculations related to spin glasses and in quantum simulators. Performance data are given. The scheme of parallelisation for various numbers of threads is tested. Application to a quantum computer simulator is considered in detail. In particular, a parallelisation scheme of work of quantum computer simulator.

AliSim: A Fast and Versatile Phylogenetic Sequence Simulator For the Genomic Era

Sequence simulators play an important role in phylogenetics. Simulated data has many applications, such as evaluating the performance of different methods, hypothesis testing with parametric bootstraps, and, more recently, generating data for training machine-learning applications. Many sequence simulation programs exist, but the most feature-rich programs tend to be rather slow, and the fastest programs tend to be feature-poor. Here, we introduce AliSim, a new tool that can efficiently simulate biologically realistic alignments under a large range of complex evolutionary models. To achieve high performance across a wide range of simulation conditions, AliSim implements an adaptive approach that combines the commonly-used rate matrix and probability matrix approach. AliSim takes 1.3 hours and 1.3 GB RAM to simulate alignments with one million sequences or sites, while popular software Seq-Gen, Dawg, and INDELible require two to five hours and 50 to 500 GB of RAM. We provide AliSim as an extension of the IQ-TREE software version 2.2, freely available at www.iqtree.org, and a comprehensive user tutorial at http://www.iqtree.org/doc/AliSim.

Advances in identifying GM plants: current frame of the detection of transgenic GMOs

Transgenic GMOs were welcomed in the 1990s due to the difficulties distinguishing genetic and epigenetic modifications from random mutagenesis and their ability to insert new nucleic sequences more rapidly but still randomly. Their marketing in Europe has been accompanied by health and environmental risk assessments, specific monitoring and traceability procedures to preserve the free choice of consumers and allow the coexistence of different supply chains. This chapter reviews the regulations, detection techniques, strategies and standards that have been put in place in the European Union since 1996 to ensure the analytical traceability of these GMOs. The capacity of the matrix approach, initially targeted at transgenic GMOs, to trace other types of GMOs is discussed in an accompanying chapter.

Investigation of the lightest hybrid meson candidate with a coupled-channel analysis of $${{\bar{p}}p}$$-, $$\pi ^- p$$- and $${\pi \pi }$$-Data

A sophisticated coupled-channel analysis is presented that combines different processes: the channels $${\pi ^0\pi ^0\eta }$$ π 0 π 0 η , $${\pi ^0\eta \eta }$$ π 0 η η and $${K^+K^-\pi ^0}$$ K + K - π 0 from $${{\bar{p}}p}$$ p ¯ p annihilations, the P- and D-wave amplitudes of the $$\pi \eta $$ π η and $$\pi \eta ^\prime $$ π η ′ systems produced in $$\pi ^-p$$ π - p scattering, and data from $${\pi \pi }$$ π π -scattering reactions. Hence our analysis combines the data sets used in two independent previous analyses published by the Crystal Barrel experiment and by the JPAC group. Based on the new insights from these studies, this paper aims at a better understanding of the spin-exotic $$\pi _1$$ π 1 resonances in the light-meson sector. By utilizing the K-matrix approach and realizing the analyticity via Chew-Mandelstam functions the amplitude of the spin-exotic wave can be well described by a single $$\pi _1$$ π 1 pole for both systems, $$\pi \eta $$ π η and $$\pi \eta ^\prime $$ π η ′ . The mass and the width of the $$\pi _1$$ π 1 -pole are measured to be $$(1623 \, \pm \, 47 \, ^{+24}_{-75})\, \mathrm {MeV/}c^2$$ ( 1623 ± 47 - 75 + 24 ) MeV / c 2 and $$(455 \, \pm 88 \, ^{+144}_{-175})\, \mathrm {MeV}$$ ( 455 ± 88 - 175 + 144 ) MeV .