Coarse Graining RNA Nanostructures for Molecular Dynamics Simulations

A series of coarse-grained models have been developed for the study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural information. Such a treatment allows us to reach, for the systems of thousands of nucleotides, a time scale of microseconds (i.e. by three orders of magnitude longer than in the full atomistic modelling) and thus to enable simulations of large RNA polymers in the context of bionanotechnology. We find that the 3-beads-per-nucleotide models, described by a set of just a few universal parameters, are able to describe different RNA conformations and are comparable in structural precision to the models where detailed values of the backbone P-C4' dihedrals taken from a reference structure are included. These findings are discussed in the context of the RNA conformation classes

Oscillation of solar radio emission at coronal acoustic cut-off frequency

Recent SECCHI COR2 observations on board STEREO-A spacecraft have detected density structures at a distance of 2.5--15~R propagating with periodicity of about 90~minutes. The observations show that the density structures probably formed in the lower corona. We used the large Ukrainian radio telescope URAN-2 to observe type IV radio bursts in the frequency range of 8--32~MHz during the time interval of 08:15--11:00~UT on August 1, 2011. Radio emission in this frequency range originated at the distance of 1.5--2.5 R according to the Baumbach-Allen density model of the solar corona. Morlet wavelet analysis showed the periodicity of 80~min in radio emission intensity at all frequencies, which demonstrates that there are quasi-periodic variations of coronal density at all heights. The observed periodicity corresponds to the acoustic cut-off frequency of stratified corona at a temperature of 1~MK. We suggest that continuous perturbations of the coronal base in the form of jets/explosive events generate acoustic pulses, which propagate upwards and leave the wake behind oscillating at the coronal cut-off frequency. This wake may transform into recurrent shocks due to the density decrease with height, which leads to the observed periodicity in the radio emission. The recurrent shocks may trigger quasi-periodic magnetic reconnection in helmet streamers, where the opposite field lines merge and consequently may generate periodic density structures observed in the solar wind.Comment: 10 pages, 6 figures, accepted in A&

A Simulation Study of the Effect of Powerful High-Frequency Radio Waves on the Behavior of Super-Small-Scale Irregularities in the F-layer Ionospheric

Magnetic field aligned super-small-scale irregularities in the concentration of charged particles are often observed in the Earthrsquos ionosphere and magnetosphere. Earlier, the time evolution of such irregularities was studied with the help of the mathematical model, developed in the Polar Geophysical Institute. This model is based on a numerical solution of the Vlasov-Poisson system of equations. This mathematical model is used in the present paper. The purpose of the present paper is to examine numerically how high-power high-frequency radio waves, utilized for artificial heating experiments and pumped into the ionosphere by ground-based ionospheric heaters, influence on the time evolution of the super-small-scale irregularities present naturally in the F-layer ionospheric plasma. The results of simulation indicate that a presence of high-power high-frequency radio wave ought to influence essentially on the behavior of physically significant parameters of the plasma inside and in the vicinity of the irregularity.nbs