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In this paper we report the detection of five strong Gamma-Ray Bursts (GRBs) by the High-Energy Particle Detector (HEPD-01) mounted on board the China Seismo-Electromagnetic Satellite (CSES-01), operational since 2018 on a Sun-synchronous polar orbit at a $\sim$ 507 km altitude and 97$^\circ$ inclination. HEPD-01 was designed to detect high-energy electrons in the energy range 3 - 100 MeV, protons in the range 30 - 300 MeV, and light nuclei in the range 30 - 300 MeV/n. Nonetheless, Monte Carlo simulations have shown HEPD-01 is sensitive to gamma-ray photons in the energy range 300 keV - 50 MeV, even if with a moderate effective area above $\sim$ 5 MeV. A dedicated time correlation analysis between GRBs reported in literature and signals from a set of HEPD-01 trigger configuration masks has confirmed the anticipated detector sensitivity to high-energy photons. A comparison between the simultaneous time profiles of HEPD-01 electron fluxes and photons from GRB190114C, GRB190305A, GRB190928A, GRB200826B and GRB211211A has shown a remarkable similarity, in spite of the different energy ranges. The high-energy response, with peak sensitivity at about 2 MeV, and moderate effective area of the detector in the actual flight configuration explain why these five GRBs, characterised by a fluence above $\sim$ 3 $\times$ 10$^{-5}$ erg cm$^{-2}$ in the energy interval 300 keV - 50 MeV, have been detected., Comment: Accepted for publication in The Astrophysical Journal (ApJ)

We present 294 pulsars found in GeV data from the Large Area Telescope (LAT) on the Fermi Gamma-ray Space Telescope. Another 33 millisecond pulsars (MSPs) discovered in deep radio searches of LAT sources will likely reveal pulsations once phase-connected rotation ephemerides are achieved. A further dozen optical and/or X-ray binary systems co-located with LAT sources also likely harbor gamma-ray MSPs. This catalog thus reports roughly 340 gamma-ray pulsars and candidates, 10% of all known pulsars, compared to $\leq 11$ known before Fermi. Half of the gamma-ray pulsars are young. Of these, the half that are undetected in radio have a broader Galactic latitude distribution than the young radio-loud pulsars. The others are MSPs, with 6 undetected in radio. Overall, >235 are bright enough above 50 MeV to fit the pulse profile, the energy spectrum, or both. For the common two-peaked profiles, the gamma-ray peak closest to the magnetic pole crossing generally has a softer spectrum. The spectral energy distributions tend to narrow as the spindown power $\dot E$ decreases to its observed minimum near $10^{33}$ erg s$^{-1}$, approaching the shape for synchrotron radiation from monoenergetic electrons. We calculate gamma-ray luminosities when distances are available. Our all-sky gamma-ray sensitivity map is useful for population syntheses. The electronic catalog version provides gamma-ray pulsar ephemerides, properties and fit results to guide and be compared with modeling results., Comment: 142 pages. Accepted by the Astrophysical Journal Supplement

The DArk Matter Particle Explorer (DAMPE) is well suitable for searching for monochromatic and sharp $\gamma$-ray structures in the GeV$-$TeV range thanks to its unprecedented high energy resolution. In this work, we search for $\gamma$-ray line structures using five years of DAMPE data. To improve the sensitivity, we develop two types of dedicated data sets (including the BgoOnly data which is the first time to be used in the data analysis for the calorimeter-based gamma-ray observatories) and adopt the signal-to-noise ratio optimized regions of interest (ROIs) for different DM density profiles. No line signals or candidates are found between 10 and 300 GeV in the Galaxy. The constraints on the velocity-averaged cross section for $\chi\chi \to \gamma\gamma$ and the decay lifetime for $\chi \to \gamma\nu$, both at 95% confidence level, have been calculated and the systematic uncertainties have been taken into account. Comparing to the previous Fermi-LAT results, though DAMPE has an acceptance smaller by a factor of $\sim 10$, similar constraints on the DM parameters are achieved and below 100 GeV the lower limits on the decay lifetime are even stronger by a factor of a few. Our results demonstrate the potential of high-energy-resolution observations on dark matter detection., Comment: 14 pages, 8 figures. Update the content to keep up with the published version

The Forbush Decrease (FD) represents the rapid decrease of the intensities of charged particles accompanied with the coronal mass ejections (CMEs) or high-speed streams from coronal holes. It has been mainly explored with ground-based neutron monitors network which indirectly measure the integrated intensities of all species of cosmic rays by counting secondary neutrons produced from interaction between atmosphere atoms and cosmic rays. The space-based experiments can resolve the species of particles but the energy ranges are limited by the relative small acceptances except for the most abundant particles like protons and helium. Therefore, the FD of cosmic ray electrons and positrons have just been investigated by the PAMELA experiment in the low energy range ($<5$ GeV) with limited statistics. In this paper, we study the FD event occurred in September, 2017, with the electron and positron data recorded by the Dark Matter Particle Explorer. The evolution of the FDs from 2 GeV to 20 GeV with a time resolution of 6 hours are given. We observe two solar energetic particle events in the time profile of the intensity of cosmic rays, the earlier and weak one has not been shown in the neutron monitor data. Furthermore, both the amplitude and recovery time of fluxes of electrons and positrons show clear energy-dependence, which is important in probing the disturbances of the interplanetary environment by the coronal mass ejections., Comment: This article is dedicated to the 72nd anniversary of People's Republic of China

We present a new multiscale method to study the N-Methyl-D-Aspartate (NMDA) neuroreceptor starting from the reconstruction of its crystallographic structure. Thanks to the combination of homology modelling, Molecular Dynamics and Lattice Boltzmann simulations, we analyse the allosteric transition of NDMA upon ligand binding and compute the receptor response to ionic passage across the membrane., Comment: 22 pages, 5 figures

The High-Energy Particle Detector (HEPD) is one of the payloads of the CSES space mission. The CSES (China Seismo-Electromagnetic Satellite) mission will investigate the structure and the dynamic of the topside ionosphere, will monitor electric and magnetic field and high energy particle fluctuations, searching for their correlations with the geophysical activity, in order to contribute to the monitoring of earthquakes from space. The HEPD is built by the Italian collaboration and has different goals. It will study the temporal stability of the inner Van Allen radiation belts, the precipitation of trapped particles in the atmosphere and the low energy component of the cosmic rays (5 - 100 MeV for electrons and 15 - 300 MeV for protons). Here is presented a study of the performance of the apparatus to separate electrons and protons and identify nuclei up to iron., Comment: XXV ECRS 2016 Proceedings - eConf C16-09-04.3

Riboswitches are cis-acting regulatory RNA elements prevalently located in the leader sequences of bacterial mRNA. An adenine sensing riboswitch cis-regulates adeninosine deaminase gene (add) in Vibrio vulnificus. The structural mechanism regulating its conformational changes upon ligand binding mostly remains to be elucidated. In this open framework it has been suggested that the ligand stabilizes the interaction of the distal "kissing loop" complex. Using accurate full-atom molecular dynamics with explicit solvent in combination with enhanced sampling techniques and advanced analysis methods it could be possible to provide a more detailed perspective on the formation of these tertiary contacts. In this work, we used umbrella sampling simulations to study the thermodynamics of the kissing loop complex in the presence and in the absence of the cognate ligand. We enforced the breaking/formation of the loop-loop interaction restraining the distance between the two loops. We also assessed the convergence of the results by using two alternative initialization protocols. A structural analysis was performed using a novel approach to analyze base contacts. Our simulations qualitatively indicated that the ligand could stabilize the kissing loop complex. We also compared with previously published simulation studies. Kissing complex stabilization given by the ligand was compatible with available experimental data. However, the dependence of its value on the initialization protocol of the umbrella sampling simulations posed some questions on the quantitative interpretation of the results and called for better converged enhanced sampling simulations., Comment: Accepted for publication on BMC Bioinformatics

RNA is a fundamental class of biomolecules that mediate a large variety of molecular processes within the cell. Computational algorithms can be of great help in the understanding of RNA structure-function relationship. One of the main challenges in this field is the development of structure-prediction algorithms, which aim at the prediction of the three-dimensional (3D) native fold from the sole knowledge of the sequence. In a recent paper, we have introduced a scoring function for RNA structure prediction. Here, we analyze in detail the performance of the method, we underline strengths and shortcomings, and we discuss the results with respect to state-of-the-art techniques. These observations provide a starting point for improving current methodologies, thus paving the way to the advances of more accurate approaches for RNA 3D structure prediction., Comment: Accepted for publication on RNA & Disease

The intricate network of interactions observed in RNA three-dimensional structures is often described in terms of a multitude of geometrical properties, including helical parameters, base pairing/stacking, hydrogen bonding and backbone conformation. We show that a simple molecular representation consisting in one oriented bead per nucleotide can account for the fundamental structural properties of RNA. In this framework, canonical Watson-Crick, non-Watson-Crick base-pairing and base-stacking interactions can be unambiguously identified within a well-defined interaction shell. We validate this representation by performing two independent, complementary tests. First, we use it to construct a sequence-independent, knowledge-based scoring function for RNA structural prediction, which compares favorably to fully atomistic, state-of-the-art techniques. Second, we define a metric to measure deviation between RNA structures that directly reports on the differences in the base-base interaction network. The effectiveness of this metric is tested with respect to the ability to discriminate between structurally and kinetically distant RNA conformations, performing better compared to standard techniques. Taken together, our results suggest that this minimalist, nucleobase-centric representation captures the main interactions that are relevant for describing RNA structure and dynamics., Comment: Accepted for publication on Nucleic Acids Research

Riboswitches are structured mRNA elements that modulate gene expression. They undergo conformational changes triggered by highly specific interactions with sensed metabolites. Among the structural rearrangements engaged by riboswitches, the forming and melting of the aptamer terminal helix, the so-called P1 stem, is essential for genetic control. The structural mechanisms by which this conformational change is modulated upon ligand binding mostly remain to be elucidated. Here, we used pulling molecular dynamics simulations to study the thermodynamics of the P1 stem in the add adenine riboswitch. The P1 ligand-dependent stabilization was quantified in terms of free energy and compared with thermodynamic data. This comparison suggests a model for the aptamer folding in which direct P1-ligand interactions play a minor role on the conformational switch when compared with those related to the ligand-induced aptamer preorganization., Comment: Accepted on RNA Journal

Neutrino telescopes are moving steadily toward the goal of detecting astrophysical neutrinos from the most powerful galactic and extragalactic sources. Here we describe analysis methods to search for high energy point-like neutrino sources using detectors deep in the ice or sea. We simulate an ideal cubic kilometer detector based on real world performance of existing detectors such as AMANDA, IceCube, and ANTARES. An unbinned likelihood ratio method is applied, making use of the point spread function and energy distribution of simulated neutrino signal events to separate them from the background of atmospheric neutrinos produced by cosmic ray showers. The unbinned point source analyses are shown to perform better than binned searches and, depending on the source spectral index, the use of energy information is shown to improve discovery potential by almost a factor of two., Comment: pdfLaTeX, 16 pages, 12 figures. Submitted to Astroparticle Physics