Deciphering the universe of RNA structures and trans RNA-RNA interactions of transcriptomes in vivo: from experimental protocols to computational analyses

The last few years have seen an explosion of experimental and computational methods for investigating RNA structures of entire transcriptomes in vivo. Very recent experimental protocols now also allow trans RNA–RNA interactions to be probed in a transcriptome-wide manner. All of the experimental strategies require comprehensive computational pipelines for analysing the raw data and converting it back into actual RNA structure features or trans RNA–RNA interactions. The overall performance of these methods thus strongly depends on the experimental and the computational protocols employed. In order to get the best out of both worlds, both aspects need to be optimised simultaneously. This review introduced the methods and proposes ideas how they could be further improved

Weighted coupling for geographical networks: Application to reducing consensus time in sensor networks

Although many complex real-world networks are weighted, unweighted networks are used in many applications such as sensor networks. In this Letter it is shown using properly weighted networks the performance can be greatly enhanced by reducing the time necessary for the average consensus. Random geographical models are adapted as network models and a method based on mutually coupled phase oscillators is used for providing average consensus over the network. The consensus time is calculated by numerically solving the network's differential equations and monitoring the average error. The simulation results on some sample networks show that the consensus time is dramatically reduced when the proposed weights are used for the links of the underlying network

Three-dimensional operando optical imaging of particle and electrolyte heterogeneities inside Li-ion batteries

Understanding (de)lithiation heterogeneities in battery materials is key to ensure optimal electrochemical performance. However, this remains challenging due to the three-dimensional morphology of electrode particles, the involvement of both solid- and liquid-phase reactants and a range of relevant timescales (seconds to hours). Here we overcome this problem and demonstrate the use of confocal microscopy for the simultaneous three-dimensional operando measurement of lithium-ion dynamics in individual agglomerate particles, and the electrolyte in batteries. We examine two technologically important cathode materials: Li xCoO2 and Li xNi0.8Mn0.1Co0.1O2. The surface-to-core transport velocity of Li-phase fronts and volume changes are captured as a function of cycling rate. Additionally, we visualize heterogeneities in the bulk and at agglomerate surfaces during cycling, and image microscopic liquid electrolyte concentration gradients. We discover that surface-limited reactions and intra-agglomerate competing rates control (de)lithiation and structural heterogeneities in agglomerate-based electrodes. Importantly, the conditions under which optical imaging can be performed inside the complex environments of battery electrodes are outlined