Characterizing the conformational free-energy landscape of RNA using single-molecule field-effect transistors

We have developed and used high-time-resolution, single-molecule field-effect transistors (smFETs) to characterize the con-formational free-energy landscape of RNA stem-loops. Stem-loops are some of the most common RNA structural motifs and serve as building blocks for the formation of more complex RNA structures. Given their prevalence and integral role in RNA folding, the kinetics of stem-loop (un)folding has been extensively characterized using both experimental and computational approaches. Interestingly, these studies have reported vastly disparate timescales of (un)folding, which has been recently in-terpreted as evidence that (un)folding of even simple stem-loops occurs on a highly rugged conformational energy landscape. Because smFETs do not rely on fluorophore reporters of conformation or on the application of mechanical (un)folding forces, they provide a unique and complementary approach that has allowed us to directly monitor tens of thousands of (un)folding events of individual stem-loops at a 200 μs time resolution. Our results show that under our experimental conditions, stem-loops fold and unfold over a 1-200 ms timescale during which they transition between ensembles of unfolded and folded conformations, the latter of which is composed of at least two sub-populations. The 1-200 ms timescale of (un)folding we observe here indicates that smFETs report on complete (un)folding trajectories in which relatively extended unfolded con-formations of the RNA spend long periods of time wandering the free-energy landscape before sampling one of several mis-folded conformations or, alternatively, the natively folded conformation. Our findings demonstrate how the combination of single-molecule sensitivity and high time resolution makes smFETs unique and powerful tools for characterizing the con-formational free-energy landscape of RNA and highlight the extremely rugged landscape on which even the simplest RNA structural elements fold.

Advanced scintillation materials for calorimetry at circular colliders

The most probable scenario for the development of experimental high-energy physics in the next 50 years is the creation of a family of Future Circular Colliders (FCC) at CERN, a Circular Electron–Positron Collider at China, and a Future Electron-Ion Collider at Brookhaven (USA), which continue the Large Hadron Collider (LHC) scientific program within the framework of the Standard Model and beyond it. The first generation of colliders to be put into operation will utilize the electron beam as one of the colliding species to provide precise mass spectroscopy in a wide energy range. Similarly to the measurements at the high luminosity phase of the LHC operation, the most important property of the detectors to be used in the experimental setup is a combination of the short response of the detectors and their high time resolution. The radiation tolerance to a harsh irradiation environment remains mandatory but not the main factor of the collider’s experiments using electronic beams. A short response in combination with high time resolution ensures minimization of the influence of the pile-up and spill-over effects at the high frequency of collisions (higher than 50 MGz). The radiation hardness of the materials maintains the long-term high accuracy of the detector calibration. This paper discusses the prospects for using modern inorganic scintillation materials for calorimetric detectors at future colliders.

Systemic liquidity contagion in the European interbank market

Systemic liquidity risk, defined by the International Monetary Fund as “the risk of simultaneous liquidity difficulties at multiple financial institutions,” is a key topic in financial stability studies and macroprudential policy-making. In this context, the complex web of interconnections of the interbank market plays the crucial role of allowing funding liquidity shortages to propagate between financial institutions. Here, we introduce a simple yet effective model of the interbank market in which liquidity shortages propagate through an epidemic-like contagion mechanism on the network of interbank loans. The model is defined by using aggregate balance sheet information of European banks, and it exploits country and bank-specific risk features to account for the heterogeneity of financial institutions. Moreover, in order to obtain the European-wide topology of the interbank network, we define a block reconstruction method based on the exchange flows between the various countries. We show that the proposed contagion model is able to estimate systemic liquidity risk across different years and countries. Results suggest that our effective contagion approach can be successfully used as a viable alternative to more realistic but complicated models, which not only require more specific balance sheet variables with high time resolution but also need assumptions on how banks respond to liquidity shocks.

Predicting Pulsars from Imbalanced Dataset with Hybrid Resampling Approach

Pulsar stars, usually neutron stars, are spherical and compact objects containing a large quantity of mass. Each pulsar star possesses a magnetic field and emits a slightly different pattern of electromagnetic radiation which is used to identify the potential candidates for a real pulsar star. Pulsar stars are considered an important cosmic phenomenon, and scientists use them to study nuclear physics, gravitational waves, and collisions between black holes. Defining the process of automatic detection of pulsar stars can accelerate the study of pulsar stars by scientists. This study contrives an accurate and efficient approach for true pulsar detection using supervised machine learning. For experiments, the high time-resolution (HTRU2) dataset is used in this study. To resolve the data imbalance problem and overcome model overfitting, a hybrid resampling approach is presented in this study. Experiments are performed with imbalanced and balanced datasets using well-known machine learning algorithms. Results demonstrate that the proposed hybrid resampling approach proves highly influential to avoid model overfitting and increase the prediction accuracy. With the proposed hybrid resampling approach, the extra tree classifier achieves a 0.993 accuracy score for true pulsar star prediction.

Design of Interplanetary Observation Terminal based on All Programmable System-on-Chip

The drastic changes in the solar wind will cause serious harm to human life. Monitoring interplanetary scintillation (IPS) can predict solar wind activity, thereby effectively reducing the harm caused by space weather. Aiming at the problem of the lack of the ability to observe IPS phenomenon of the 40-meter radio telescope at the Yunnan Astronomical Observatory of China in the frequency band around 300MHz, an IPS real-time acquisition and processing scheme based on all programmable system-on-chip(APSoC) was proposed. The system calculates the average power of 10ms IPS signal in PL-side and transmits it to the system memory through AXI4 bus. PS-side reads the data, takes logarithms, packages it, and finally transmits it to the LabVIEW host computer through gigabit Ethernet UDP mode for display and storage. Experimental tests show that the system functions correctly, and the PL-side power consumption is only 1.955 W, with a high time resolution of 10ms, and no data is lost in 24 hours of continuous observation, with good stability. The system has certain application value in IPS observation.

Plant Cryptochromes Illuminated: A Spectroscopic Perspective on the Mechanism

Plant cryptochromes are central blue light receptors for the control of land plant and algal development including the circadian clock and the cell cycle. Cryptochromes share a photolyase homology region with about 500 amino acids and bind the chromophore flavin adenine dinucleotide. Characteristic for plant cryptochromes is a conserved aspartic acid close to flavin and an exceptionally long C-terminal extension. The mechanism of activation by excitation and reduction of the chromophore flavin adenine dinucleotide has been controversially discussed for many years. Various spectroscopic techniques have contributed to our understanding of plant cryptochromes by providing high time resolution, ambient conditions and even in-cell approaches. As a result, unifying and differing aspects of photoreaction and signal propagation have been revealed in comparison to members from other cryptochrome subfamilies. Here, we review the insight from spectroscopy on the flavin photoreaction in plant cryptochromes and present the current models on the signal propagation from flavin reduction to dissociation of the C-terminal extension.

The Vector Electric Field Investigation (VEFI) on the C/NOFS Satellite

The Vector Electric Field Investigation (VEFI) on the C/NOFS satellite comprises a suite of sensors controlled by one central electronics box. The primary measurement consists of a vector DC and AC electric field detector which extends spherical sensors with embedded pre-amps at the ends of six, 9.5-m booms forming three orthogonal detectors with baselines of 20 m tip-to-tip each. The primary VEFI measurement is the DC electric field at 16 vectors/sec with an accuracy of 0.5 mV/m. The electric field receiver also measures the broad spectra of irregularities associated with equatorial spread-F and related ionospheric processes that create the scintillations responsible for the communication and navigation outages for which the C/NOFS mission is designed to understand and predict. The AC electric field measurements range from ELF to HF frequencies.VEFI includes a flux-gate magnetometer providing DC measurements at 1 vector/sec and AC-coupled measurements at 16 vector/sec, as well as a fast, fixed-bias Langmuir probe that serves as the input signal to trigger the VEFI burst memory collection of high time resolution wave data when plasma density depletions are encountered in the low latitude nighttime ionosphere. A bi-directional optical lightning detector designed by the University of Washington (UW) provides continuous average lightning counts at different irradiance levels as well as high time resolution optical lightning emissions captured in the burst memory. The VEFI central electronics box receives inputs from all of the sensors and includes a configurable burst memory with 1–8 channels at sample rates as high as 32 ks/s per channel. The VEFI instrument is thus one experiment with many sensors. All of the instruments were designed, built, and tested at the NASA/Goddard Space Flight Center with the exception of the lightning detector which was designed at UW. The entire VEFI instrument was delivered on budget in less than 2 years.VEFI included a number of technical advances and innovative features described in this article. These include: (1) Two independent sets of 3-axis, orthogonal electric field double probes; (2) Motor-driven, pre-formed cylinder booms housing signal wires that feed pre-amps within tip-mounted spherical sensors; (3) Extended shadow equalizers (2.5 times the sphere diameter) to mitigate photoelectron shadow mismatch for sun angles along the boom directions, particularly important at sunrise/sunset for a low inclination satellite; (4) DC-coupled electric field channels with “boosted” or pre-emphasized amplitude response at ELF frequencies; (5) Miniature multi-channel spectrum analyzers using hybrid technology; (6) Dual-channel optical lightning detector with on-board comparators and counters for 7 irradiance levels with high-time-resolution data capture; (7) Spherical Langmuir probe with Titanium Nitride-coated sensor element and guard; (8) Selectable data rates including 200 kbps (fast), 20 kbps (nominal), and 2 kbps (low for real-time TDRSS communication); and (9) Highly configurable burst memory with selectable channels, sample rates and number, duration, and precursor length of bursts, chosen based on best triggering algorithm “score”.This paper describes the various sensors that constitute the VEFI experiment suite and discusses their operation during the C/NOFS mission. Examples of data are included to illustrate the performance of the different sensors in space.