Local RNA structure alignment with incomplete sequence

Motivation: Accuracy of automated structural RNA alignment is improved by using models that consider not only primary sequence but also secondary structure information. However, current RNA structural alignment approaches tend to perform poorly on incomplete sequence fragments, such as single reads from metagenomic environmental surveys, because nucleotides that are expected to be base paired are missing

Laboratory demonstration of an alternative laser guide stars wavefront sensing technique—projected pupil plane pattern

Adaptive optics (AO) is widely used in optical/near-infrared telescopes to remove the effects of atmospheric distortion, and laser guide stars (LGSs) are commonly used to ease the requirement for a bright, natural reference source close to the scientific target in an AO system. However, focus anisoplanatism renders single LGS AO useless for the next generation of extremely large telescopes. Here, we describe proof-of-concept experimental demonstrations of a LGS alternative configuration, which is free of focus anisoplanatism, with the corresponding wavefront sensing and reconstruction method, termed projected pupil plane pattern (PPPP). This laboratory experiment is a critical milestone between the simulation and on-sky experiment, for demonstrating the feasibility of PPPP technique and understanding technical details, such as extracting the signal and calibrating the system. Three major processes of PPPP are included in this laboratory experiment: the upward propagation, return path, and reconstruction process. From the experimental results, it has been confirmed that the PPPP signal is generated during the upward propagation and the return path is a reimaging process whose effect can be neglected (if the images of the backscattered patterns are binned to a certain size). Two calibration methods are used: the theoretical calibration is used for the wavefront measurement, and the measured calibration is used for closed-loop control. From both the wavefront measurement and closed-loop results, we show that PPPP achieves equivalent performance to a Shack–Hartmann wavefront sensor

Durham adaptive optics real-time controller

The Durham adaptive optics (AO) real-time controller was initially a proof of concept design for a generic AO control system. It has since been developed into a modern and powerful central-processing-unit-based real-time control system, capable of using hardware acceleration (including field programmable gate arrays and graphical processing units), based primarily around commercial off-the-shelf hardware. It is powerful enough to be used as the real-time controller for all currently planned 8 m class telescope AO systems. Here we give details of this controller and the concepts behind it, and report on performance, including latency and jitter, which is less than 10 μs for small AO systems

Full LQG control with vibration mitigation: from theory to first on-sky validation on the CANARY MOAO demonstrator

International audienc

First on-sky validation of full LQG control with vibration mitigation on the CANARY MOAO pathfinder

International audienceWe present in this paper the very first on-sky results of full Multi-Object Adaptive Optics (MOAO) LQG control (i.e. all modes, with coupling, controlled with an LQG regulator), obtained in Spring 2013 on the CANARY demonstrator at the William Herschel Telescope (La Palma, Spain). The MOAO on-sky pathfinder CANARY features two AO configurations that have both been tested: single-conjugated AO and multi-object AO with NGS and NGS+LGS, together with vibration mitigation on tip and tilt modes. The successful MOAO results are presented and shortly analyzed in terms of performance and tuning

CHOUGH: implementation and performance of a high-order 4m AO demonstrator

CHOUGH is a small, fast project to provide an experimental on-sky high-order SCAO capability to the 4.2m WHT telescope. The basic goal has r0-sized sub- apertures with the aim of achieving high-Strehl ratios (> 0:5) in the visible (> 650 nm). It achieves this by including itself into the CANARY experiment: CHOUGH is mounted as a breadboard and intercepts the beam within CANARY via a periscope. In doing so, it takes advantage of the mature CANARY infrastructure, but add new AO capabilities. The key instruments that CHOUGH brings to CANARY are: an atmospheric dispersion compensator; a 32 × 32 (1000 actuator) MEMS deformable mirror; 31 × 31 wavefront sensor; and a complementary (narrow-field) imager. CANARY provides a 241-actuator DM, tip/tilt mirror, and comprehensive off-sky alignment facility together with a RTC. In this work, we describe the CHOUGH sub-systems: backbone, ADC, MEMS-DM, HOWFS, CAWS, and NFSI