Supplementary data are available at Bioinformatics online.
Summary: Likelihood-free methods are often required for inference in systems biology. While Approximate Bayesian Computation (ABC) provides a theoretical solution, its practical application has often been challenging due to its high computational demands. To scale likelihood-free inference to computationally demanding stochastic models we developed pyABC: a distributed and scalable ABC-Sequential Monte Carlo (ABC-SMC) framework. It implements computation-minimizing and scalable, runtime-minimizing parallelization strategies for multi-core and distributed environments scaling to thousands of cores. The framework is accessible to non-expert users and also enables advanced users to experiment with and to custom implement many options of ABC-SMC schemes, such as acceptance threshold schedules, transition kernels and distance functions without alteration of pyABC's source code. pyABC includes a web interface to visualize ongoing and finished ABC-SMC runs and exposes an API for data querying and post-processing. Availability and Implementation: pyABC is written in Python 3 and is released under the GPLv3 license. The source code is hosted on https://github.com/neuralyzer/pyabc and the documentation on http://pyabc.readthedocs.io. It can be installed from the Python Package Index (PyPI).
In this letter we study magnetic circular dichroism in alkali atoms exhibiting asymmetric behaviour of magnetically induced transitions. The magnetic field B k induces transitions between ΔF = ±2 hyperfine levels of alkali atoms and in the range of ∼0.1-3 kG magnetic field, the intensities of these transitions experience significant enhancement. We have inferred a general rule applicable for the D2 lines of all alkali atoms, that is the transition intensity enhancement is around four times larger for the case of σ + than for σ − excitation for ΔF = +2, whereas it is several hundreds of thousand times larger in the case of σ − than that for σ + polarization for ΔF = −2. This asymmetric behaviour results in circular dichroism. For experimental verification we employed half-wavelength-thick atomic vapor nanocells using a derivative of the selective reflection technique, which provides a sub-Doppler spectroscopic linewidth (∼50 MHz). The presented theoretical curves well describe the experimental results. This effect can find applications particularly in parity violation experiments.
Decoupling of total electronic and nuclear spin moments of Cs atoms in external magnetic field for the case of atomic D 1 line, leading to onset of the hyperfine Paschen-Back regime has been studied theoretically and experimentally. Selective reflection of laser radiation from an interface of dielectric window and atomic vapor confined in a nanocell with 300 nm gap thickness was implemented for the experimental studies. The real time derivative of selective reflection signal with a frequency position coinciding with atomic transitions was used in measurements, providing ∼ 40 MHz spectral resolution and linearity of signal response in respect to transition probability. Behavior of 28 individual Zeeman transitions in a wide range of longitudinal magnetic field (0 -6 kG) has been tracked under excitation of Cs vapor by a low-intensity σ + -polarized cw laser radiation. For B ≥ 6 kG, only 8 transitions with nearly equal probabilities and the same frequency slope remained in the spectrum, which is a manifestation of the hyperfine Paschen-Back regime. The obtained experimental results are consistent with numerical modeling. Due to small divergence of selective reflection signal, as well as sub-wavelength thickness and sub-Doppler spectral linewidth inherent to nanocell, the employed technique can be used for distant remote sensing of magnetic field with high spatial and B-field resolution. I IntroductionOptical nanometric thin cell (nanocell) containing atomic vapor of alkali metal (Rb, Cs, K, Na) is proven to be efficient and convenient spectroscopic tool for magneto-optical studies of optical atomic transitions between the hyperfine levels in strong external magnetic fields. Two interconnected effects develop with the increase of Bfield: strong deviation of Zeeman splitting of hyperfine transitions from linear dependence, and significant change in probability of individual Zeeman transitions [1,2,3]. The efficiency of nanocell technique for quantitative spectroscopy of the Rb atomic transitions in strong magnetic field (up to 7 kG) resulting in onset of the hyperfine Paschen-Back regime was demonstrated in [4,5,6]. The presence of specific "guiding" transitions foretelling characteristics of all other transitions between magnetic sublevels of alkali atoms D 1 line excited by π-polarized radiation in a strong transversal magnetic field was recently shown in [7]. Micro-and nanocells were used in [8] to study the onset of hyperfine Paschen-Back regime for Cs D 2 line in magnetic fields up to 9 kG. Realization of 1 arXiv:1610.09807v1 [physics.atom-ph]
Magnetic field-induced giant modification of the probabilities of five transitions of 5S 1/2 , Fg = 2 → 5P 3/2 , Fe = 4 of 85 Rb and three transitions of 5S 1/2 , Fg = 1 → 5P 3/2 , Fe = 3 of 87 Rb forbidden by selection rules for zero magnetic field has been observed experimentally and described theoretically for the first time. For the case of excitation with circularly-polarized (σ + ) laser radiation, the probability of Fg = 2, mF = −2 → Fe = 4, mF = −1 transition becomes the largest among the seventeen transitions of 85 Rb Fg = 2 → Fe = 1, 2, 3, 4 group, and the probability of Fg = 1, mF = −1 → Fe = 3, mF = 0 transition becomes the largest among the nine transitions of 87 Rb Fg = 1 → Fe = 0, 1, 2, 3 group, in a wide range of magnetic field 200 -1000 G. Complete frequency separation of individual Zeeman components was obtained by implementation of derivative selective reflection technique with a 300 nm-thick nanocell filled with Rb, allowing formation of narrow optical resonances. Possible applications are addressed. The theoretical model is perfectly consistent with the experimental results.
Selective reflection of a laser radiation from an interface formed by a dielectric window and a potassium atomic vapour confined in a nano-cell with 350 nm gap thickness is implemented for the first time to study the atomic transitions of K D 2 line in external magnetic fields. In moderate B-fields, there are 44 individual Zeeman transitions which reduce to two groups (one formed by σ + the other one by σ − circularly-polarised light), each containing eight atomic transitions, as the magnetic field increases. Each of these groups contains one so-called "guiding" transition whose particularities are to have a probability (intensity) as well as a frequency shift slope (in MHz/G) that are constant in the whole range of 0 -10 kG magnetic fields. In the case of π-polarised laser radiation, among eight transitions two are forbidden at B = 0, yet their probabilities undergo a giant modification under the influence of a magnetic field. We demonstrate that for B-fields > 165 G a complete hyperfine Paschen-Back regime is observed. Other peculiarities of K D 2 line behaviour in magnetic field are also presented. We show a very good agreement between theoretical calculations and experiments. The recording of the hyperfine Paschen-Back regime of K D 2 line with high spectral resolution is demonstrated for the first time.
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