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The very first transcriptome sequencing files research into the Javan mahseer (Tor tambra).
Direct-coupling analysis is a statistical learning method for protein contact prediction based on sequence information alone. The maximum entropy principle leads to an effective inverse Potts model. Predictions on contacts are based on fitted local fields and couplings from an empirical multiple sequence alignment. Typically, the l_2 norm of the resulting two-body couplings is used for contact prediction. However, this procedure discards important information. In this paper we show that the usage of the full fields and coupling information improves prediction accuracy.Dark solitons are some of the most interesting nonlinear excitations and are considered to be the one-dimensional topological analogs of vortices. However, in contrast to their two-dimensional vortex counterparts, the topological characteristics of a dark soliton are far from fully understood because the topological charge defined according to the phase jump cannot reflect its essential property. Here, similar to the complex extension used in the exploration of the partition-function zeros to depict thermodynamic states, we extend the complex coordinate space to explore the density zeros of dark solitons. Surprisingly we find that these zeros constitute some pointlike magnetic fields, each of which has a quantized magnetic flux of elementary π. The corresponding vector potential fields demonstrate the topology of the Wess-Zumino term and can depict the essential characteristics of dark solitons. Then we classify the dark solitons according to the Euler characteristic of the topological manifold of the vector potential fields. Our study not only reveals the topological features of dark solitons but can also be applied to explore and identify new dark solitons with high topological complexity.We show that viscoelastic effects play a crucial role in the damping of vibrational modes in harmonic amorphous solids. The relaxation of a given plane elastic wave is described by a memory function of a semi-infinite one-dimensional mass-spring chain. The initial vibrational energy spreads from the first site of the chain to infinity. In the beginning of the chain, there is a barrier, which significantly reduces the decay of vibrational energy below the Ioffe-Regel frequency. To obtain the parameters of the chain, we present a numerically stable method, based on the Chebyshev expansion of the local vibrational density of states.We focus on studying the opacity of iron, chromium, and nickel plasmas at conditions relevant to experiments carried out at Sandia National Laboratories [J. E. Bailey et al., Nature (London) 517, 56 (2015)NATUAS0028-083610.1038/nature14048]. We calculate the photoabsorption cross sections and subsequent opacity for plasmas using linear-response time-dependent density functional theory (TD-DFT). Our results indicate that the physics of channel mixing accounted for in linear-response TD-DFT leads to an increase in the opacity in the bound-free quasicontinuum, where the Sandia experiments indicate that models underpredict iron opacity. However, the increase seen in our calculations is only in the range of 5%-10%. Further, we do not see any change in this trend for chromium and nickel. This behavior indicates that channel mixing effects do not explain the trends in opacity observed in the Sandia experiments.We investigate the relaxation dynamics of open nonintegrable quantum many-body systems in the thermodynamic limit by using a tensor-network formalism. We simulate the Lindblad quantum master equation (LQME) of infinite systems by making use of the uniform matrix product operators (MPO) as the ansatz of their density matrices. Furthermore, we establish a method to measure the thermodynamic equivalence between two states described by the uniform MPOs. We numerically show that when an initial state of the LQME is a thermal Gibbs state, a time evolved state is always indistinguishable from a Gibbs state with a time-dependent effective temperature in the weak-dissipation and thermodynamic limit.We perform an experimental parametric study of the chaos generated by a laser diode subjected to phase-conjugate feedback. selleck chemicals In addition to the typical figure of merit, i.e., chaos bandwidth, the corresponding spectral flatness and permutation entropy at delay is analyzed. Our experimental observations reveal that the chaos can be generated with a bandwidth of ≈29 GHz, a spectral flatness up to 0.75, and a permutation entropy at delay of up to 0.99. These optimized performances are maintained over a large range of parameters and have not been achieved in the conventional optical feedback configuration. Interestingly, reducing the pump current reduces the chaos bandwidth while keeping the spectral flatness and the permutation entropy at delay the same as observed for increased pump current. Our experimental findings are consistent with the presented numerical simulations produced using the Lang-Kobayashi model.We study the Brownian motion of a charged colloid, confined between two charged walls, for small separation between the colloid and the walls. The system is embedded in an ionic solution. The combined effect of electrostatic repulsion and reduced diffusion due to hydrodynamic forces results in a specific motion in the direction perpendicular to the confining walls. The apparent diffusion coefficient at short times as well as the diffusion characteristic time are shown to follow a sigmoid curve as a function of a dimensionless parameter. This parameter depends on the electrostatic properties and can be controlled by tuning the solution ionic strength. At low ionic strength, the colloid moves faster and is localized, while at high ionic strength it moves slower and explores a wider region between the walls, resulting in a larger diffusion characteristic time.We present experimental and theoretical results for the fluctuation properties in the incomplete spectra of quantum systems with symplectic symmetry and a chaotic dynamics in the classical limit. To obtain theoretical predictions, we extend the random-matrix theory (RMT) approach introduced in Bohigas and Pato [O. Bohigas and M. P. Pato, Phys. Rev. E 74, 036212 (2006)PLEEE81539-375510.1103/PhysRevE.74.036212] for incomplete spectra of quantum systems with orthogonal symmetry. We validate these RMT predictions by randomly extracting a fraction of levels from complete sequences obtained numerically for quantum graphs and experimentally for microwave networks with symplectic symmetry and then apply them to incomplete experimental spectra to demonstrate their applicability. Independently of their symmetry class, quantum graphs exhibit nongeneric features which originate from nonuniversal contributions. Part of the associated eigenfrequencies can be identified in the level dynamics of parameter-dependent quantum graphs and extracted, thereby yielding spectra with systematically missing eigenfrequencies.
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