Kinetic modeling of molecular motors: pause model and parameter determination from single-molecule experiments

Single-molecule manipulation experiments of molecular motors provide essential information about the rate and conformational changes of the steps of the reaction located along the manipulation coordinate. This information is not always sufficient to define a particular kinetic cycle. Recent single-molecule experiments with optical tweezers showed that the DNA unwinding activity of a Phi29 DNA polymerase mutant presents a complex pause behavior, which includes short and long pauses. Here we show that different kinetic models, considering different connections between the active and the pause states, can explain the experimental pause behavior. Both the two independent pause model and the two connected pause model are able to describe the pause behavior of a mutated Phi29 DNA polymerase observed in an optical tweezers single-molecule experiment. For the two independent pause model all parameters are fixed by the observed data, while for the more general two connected pause model there is a range of values of the parameters compatible with the observed data (which can be expressed in terms of two of the rates and their force dependencies). This general model includes models with indirect entry and exit to the long-pause state, and also models with cycling in both directions. Additionally, assuming that detailed balance is verified, which forbids cycling, this reduces the ranges of the values of the parameters (which can then be expressed in terms of one rate and its force dependency). The resulting model interpolates between the independent pause model and the indirect entry and exit to the long-pause state model

Low-resolution spectroscopy and spectral energy distributions of selected sources towards σ Orionis

Aims. We study in detail nine sources in the direction of the young σ Orionis cluster, which is considered to be a unique site for studying stellar and substellar formation. The nine sources were selected because of their peculiar properties, such as extremely-red infrared colours or excessively strong Hα emission for their blue optical colours. Methods. We acquired high-quality, low-resolution spectroscopy (R ∼ 500) of the nine targets with ALFOSC at the Nordic Optical Telescope. We also re-analysed [24]-band photometry from MIPS/Spitzer and compiled the highest quality photometric dataset available at the ViJHK_s passbands and the four IRAC/Spitzer channels, for constructing accurate spectral energy distributions between 0.55 and 24 μm. Results. The nine targets were classified into: one Herbig Ae/Be star with a scattering edge-on disc; two G-type stars; one X-ray flaring, early-M, young star with chromospheric Hα emission; one very low-mass, accreting, young spectroscopic binary; two young objects at the brown-dwarf boundary with the characteristics of classical T Tauri stars; and two emission-line galaxies, one undergoing star formation, and another whose spectral energy distribution is dominated by an active galactic nucleus. We also discovered three infrared sources associated with overdensities in a cold cloud of the cluster centre. Conclusions. Low-resolution spectroscopy and spectral energy distributions are a vital tool for measuring the physical properties and evolution of young stars and candidates in the σ Orionis cluster.

Development of data reduction pipelines for GTC instruments at the UCM

The UCM Instrumentation Group (GUAIX) is developing currently Data Reduction Pipelines (DRP) for four instruments of the GTC: EMIR, FRIDA, MEGARA and MIRADAS. The purpose of the DRPs is to provide astronomers scientific quality data, removing instrumental biases, calibrating the images in physical units and providing a estimation of the associated uncertainties.

Stars and brown dwarfs in the σ Orionis cluster (Research Note) III. OSIRIS/GTC low-resolution spectroscopy of variable sources

Context. Although many studies have been performed so far, there are still dozens of low-mass stars and brown dwarfs in the young σ Orionis open cluster without detailed spectroscopic characterisation. Aims. We look for unknown strong accretors and disc hosts that were undetected in previous surveys. Methods. We collected low-resolution spectroscopy (R ~ 700) of ten low-mass stars and brown dwarfs in σ Orionis with OSIRIS at the Gran Telescopio Canarias under very poor weather conditions. These objects display variability in the optical, infrared, Hα, and/or X-rays on time scales of hours to years. We complemented our spectra with optical and near-/mid-infrared photometry. Results. For seven targets, we detected lithium in absorption, identified Hα, the calcium doublet, and forbidden lines in emission, and/or determined spectral types for the first time. We characterise in detail a faint, T Tauri-like brown dwarf with an 18 h-period variability in the optical and a large Hα equivalent width of –125  ±  15 Å, as well as two M1-type, X-ray-flaring, low-mass stars, one with a warm disc and forbidden emission lines, the other with a previously unknown cold disc with a large inner hole. Conclusions. New unrevealed strong accretors and disc hosts, even below the substellar limit, await discovery among the list of known σ Orionis stars and brown dwarfs that are variable in the optical and have no detailed spectroscopic characterisation yet.