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- Wiedenhoeft, John, 1982, et al.
(författare)
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Bayesian localization of CNV candidates in WGS data within minutes
- 2019
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Ingår i: Algorithms for Molecular Biology. - : Springer Science and Business Media LLC. - 1748-7188. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- Background Full Bayesian inference for detecting copy number variants (CNV) from whole-genome sequencing (WGS) data is still largely infeasible due to computational demands. A recently introduced approach to perform Forward-Backward Gibbs sampling using dynamic Haar wavelet compression has alleviated issues of convergence and, to some extent, speed. Yet, the problem remains challenging in practice. Results In this paper, we propose an improved algorithmic framework for this approach. We provide new space-efficient data structures to query sufficient statistics in logarithmic time, based on a linear-time, in-place transform of the data, which also improves on the compression ratio. We also propose a new approach to efficiently store and update marginal state counts obtained from the Gibbs sampler. Conclusions Using this approach, we discover several CNV candidates in two rat populations divergently selected for tame and aggressive behavior, consistent with earlier results concerning the domestication syndrome as well as experimental observations. Computationally, we observe a 29.5-fold decrease in memory, an average 5.8-fold speedup, as well as a 191-fold decrease in minor page faults. We also observe that metrics varied greatly in the old implementation, but not the new one. We conjecture that this is due to the better compression scheme. The fully Bayesian segmentation of the entire WGS data set required 3.5 min and 1.24 GB of memory, and can hence be performed on a commodity laptop.
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| 2. |
- Bessarab, Pavel F., et al.
(författare)
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Stability and lifetime of antiferromagnetic skyrmions
- 2019
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Ingår i: Physical Review B. - : American Physical Society. - 2469-9950 .- 2469-9969. ; 99:14
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Tidskriftsartikel (refereegranskat)abstract
- The two-dimensional Heisenberg exchange model with out-of-plane anisotropy and a Dzyaloshinskii-Moriya interaction is employed to investigate the lifetime and stability of antiferromagnetic (AFM) skyrmions as a function of temperature and external magnetic field. An isolated AFM skyrmion is metastable at zero temperature in a certain parameter range set by two boundaries separating the skyrmion state from the uniform AFM phase and a stripe domain phase. The distribution of the energy barriers for the AFM skyrmion decay into the uniform AFM state complements the zero-temperature stability diagram and demonstrates that the skyrmion stability region is significantly narrowed at finite temperatures. We show that the AFM skyrmion stability can be enhanced by an application of magnetic field, whose strength is comparable to the spin-flop field. This stabilization of AFM skyrmions in external magnetic fields is in sharp contrast to the behavior of their ferromagnetic counterparts. Furthermore, we demonstrate that the AFM skyrmions are stable on timescales of milliseconds below 50 K for realistic material parameters, making it feasible to observe them in modern experiments.
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| 3. |
- Johansson, Magnus, 1965-, et al.
(författare)
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Nonlinear gap modes and compactons in a lattice model for spin-orbit coupled exciton-polaritons in zigzag chains
- 2019
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Ingår i: Journal of Physics Communications. - : Institute of Physics Publishing (IOPP). - 2399-6528. ; 3:1, s. 1-17
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Tidskriftsartikel (refereegranskat)abstract
- We consider a system of generalized coupled Discrete Nonlinear Schrödinger (DNLS) equations, derived as a tight-binding model from the Gross-Pitaevskii-type equations describing a zigzag chain of weakly coupled condensates of exciton-polaritons with spin-orbit (TE-TM) coupling. We focus on the simplest case when the angles for the links in the zigzag chain are ±π/4 with respect to the chain axis, and the basis (Wannier) functions are cylindrically symmetric (zero orbital angular momenta). We analyze the properties of the fundamental nonlinear localized solutions, with particular interest in the discrete gap solitons appearing due to the simultaneous presence of spin–orbit coupling and zigzag geometry, opening a gap in the linear dispersion relation. In particular, their linear stability is analyzed. We also find that the linear dispersion relation becomes exactly flat at particular parameter values, and obtain corresponding compact solutions localized on two neighboring sites, with spin-up and spin-down parts π/2 out of phase at each site. The continuation of these compact modes into exponentially decaying gap modes for generic parameter values is studied numerically, and regions of stability are found to exist in the lower or upper half of the gap, depending on the type of gap modes.
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