Elevated Electron Temperatures in the Auroral E Layer Measured With the Chatanika Radar

An extensive series of spectral measurements has been made in the auroral E region with the Chatanika incoherent scatter radar. Becasue of the small scale length for variations of electron density, temperatures, and ion-neutral collisions we used the operating mode with the best possible range resolution—9 km. About 5% of the time the data exhibited an unusual spectral shape that was most pronounced at 105 and 110 km. Instead of being almost Gaussian with only a small hint of two peaks, the spectra are much wider, with two well-developed peaks. After carefully considering the validity of the measurements and their interpretation, we conclude that the unusual spectra are due to greatly enhanced electron temperatures. At 110 km, the electron temperature may increase from 250 K to 800 K, while the ion temperature remains near 250 K. This enhancement of the electron temperature extends from 99 km to at least 116 km. We show that the temperature increase is too large to be accounted for by auroral particle precipitation, though it coincides in time with ion temperature enhancements at altitudes above 125 km. Because these latter enhancements are believed to be due to joule heating, we deduce that electric fields of 24-40 mV/m are present and that the electrons are moving through the ions and neutrals at speeds of 500-800 m/s. Despite these velocities, we find that joule heating of the electrons also cannot account for the elevated electron temperatures. Several consequences of the elevated electron temperatures are discussed. One is that the rate constants for molecular recombination are reduced. Another is that during periods of significant joule heating, the deduced electron density profile, when fully corrected for temperatures, has a significantly lower peak altitude and greater density than that deduced under the usual assumption of equal electron and ion temperatures. Since conductivities, currents, ionization rates, and differential energy spectra are dependent upon the density profile, care must be taken to account properly for the temperature effects when deriving these quantities

Gated Diffusion-controlled Reactions

The binding and active sites of proteins are often dynamically occluded by motion of the nearby polypeptide. A variety of theoretical and computational methods have been developed to predict rates of ligand binding and reactivity in such cases. Two general approaches exist, "protein centric" approaches that explicitly treat only the protein target, and more detailed dynamical simulation approaches in which target and ligand are both treated explicitly. This mini-review describes recent work in this area and some of the biological implications

Mechanism of MicroRNA-Target Interaction: Molecular Dynamics Simulations and Thermodynamics Analysis

MicroRNAs (miRNAs) are endogenously produced ∼21-nt riboregulators that associate with Argonaute (Ago) proteins to direct mRNA cleavage or repress the translation of complementary RNAs. Capturing the molecular mechanisms of miRNA interacting with its target will not only reinforce the understanding of underlying RNA interference but also fuel the design of more effective small-interfering RNA strands. To address this, in the present work the RNA-bound (Ago-miRNA, Ago-miRNA-target) and RNA-free Ago forms were analyzed by performing both molecular dynamics simulations and thermodynamic analysis. Based on the principal component analysis results of the simulation trajectories as well as the correlation analysis in fluctuations of residues, we discover that: 1) three important (PAZ, Mid and PIWI) domains exist in Argonaute which define the global dynamics of the protein; 2) the interdomain correlated movements are so crucial for the interaction of Ago-RNAs that they not only facilitate the relaxation of the interactions between residues surrounding the RNA binding channel but also induce certain conformational changes; and 3) it is just these conformational changes that expand the cavity of the active site and open putative pathways for both the substrate uptake and product release. In addition, by thermodynamic analysis we also discover that for both the guide RNA 5′-end recognition and the facilitated site-specific cleavage of the target, the presence of two metal ions (of Mg2+) plays a predominant role, and this conclusion is consistent with the observed enzyme catalytic cleavage activity in the ternary complex (Ago-miRNA-mRNA). Our results find that it is the set of arginine amino acids concentrated in the nucleotide-binding channel in Ago, instead of the conventionally-deemed seed base-paring, that makes greater contributions in stabilizing the binding of the nucleic acids to Ago