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All proteins in living organisms are produced in ribosomes that facilitate the translation of genetic information into a sequence of amino acid residues. During translation, the ribosome undergoes stages of initialization, elongation, termination, and recycling. In fact, peptide bonds are formed only during the elongation stage, which comprises periodic association of transfer RNAs and multiple auxiliary proteins with the ribosome, and the addition of an amino acid to the nascent polypeptide one at a time. The protein spends a considerable amount of time attached to the ribosome. Here, we conceptually divide this portion of the protein lifetime into three epochs. We define the epochs on the basis of the position of the N-terminus of the nascent polypeptide within the ribosome exit tunnel and the context of the catalytic center. We argue that nascent polypeptides experience a variety of forces that determine how they translocate through the tunnel and interact with the tunnel walls. We review current knowledge about translocation and identify several white spots in our understanding of the birth of proteins., Comment: 20 pages, 3 figures

In living organisms, proteins and peptides are often under the influence of mechanical forces, especially in confined spaces such as membrane channels, ribosome exit tunnel, or proteasome gate. Due to the directional nature of proteins as polymers with distinct ends, forces have the potential to influence protein conformational dynamics in a direction-dependent manner. In this study, we employed force-probe molecular dynamics simulations to investigate the impact of pulling a peptide through a confined environment versus pushing it in the same direction. Our model involves a carbon nanotube and one of three decapeptides with varying amino acid sequences. The simulations reveal that the difference between pulling the C-terminus and pushing the N-terminus is relatively minor when considering the conformational ensembles of the peptides. The loading rate of the force probe and the amino acid sequence of the peptide play a more important role. However, the application of force to the peptide significantly influences the relative motion of the peptides with respect to the nanotube. Pulling the peptide results in a smoother translocation through the nanotube compared to pushing, although the internal conformational dynamics of the peptide add complexity in either case. Our findings shed light on how short peptides navigate confined spaces within the cellular environment, emphasizing the importance of force-probe simulation studies in understanding these processes., Comment: 16 pages, 8 figures, added GitHub repo, updated Acknowledgment

We show evidence of particle acceleration at GEV energies associated directly with protons from the prompt emission of a long-duration M6-class solar flare on July 17, 2023, rather than from protons acceleration by shocks from its associated Coronal Mass Ejection (CME), which erupted with a speed of 1342 km/s. Solar Energetic Particles (SEP) accelerated by the blast have reached Earth, up to an almost S3 (strong) category of a radiation storm on the NOAA scale. Also, we show a temporal correlation between the fast rising of GOES-16 proton and muon excess at ground level in the count rate of the New-Tupi muon detector at the central SAA region. A Monte Carlo spectral analysis based on muon excess at New-Tupi is consistent with the acceleration of electrons and protons (ions) up to relativistic energies (GeV energy range) in the impulsive phase of the flare. In addition, we present another two marginal particle excesses (with low confidence) at ground-level detectors in correlation with the solar flare prompt emission., Comment: 8 pages,8 figures

With the construction of the European Spallation Source, a remarkable opportunity has emerged to conduct high sensitivity searches for neutron oscillations, including a first search for thirty years for free neutrons converting to antineutrons. Furthermore, searches can be made for transitions of neutrons and antineutrons to sterile neutron states. Upgrades to the ESS infrastructure allow an improved HIBEAM design that would provide an increase in sensitivity by an order of magnitude compared to previous work. The HIBEAM program focuses on processes that violate baryon number by one or two units. The observation of a process satisfying one of the Sakharov conditions addresses the open question of the origin of the matter-antimatter asymmetry in the Universe. Sterile neutron states would belong to a `dark' sector of particles which may explain dark matter. As electrically neutral, meta-stable objects that can be copiously produced and studied, neutrons represent an attractive portal to a `dark' sector. The HIBEAM instrument can also be utilised for other purposes such as direct searches for ultralight axion dark matter. This paper describes the capability, design, infrastructure, and potential of the HIBEAM program. This includes a dedicated beamline, neutron optical system, magnetic shielding and control, and detectors for neutrons and antineutrons., Comment: 58 pages, 23 figures

The European Spallation Source, currently under construction in Lund, Sweden, is a multidisciplinary international laboratory. Once completed to full specifications, it will operate the world's most powerful pulsed neutron source. Supported by a 3 million Euro Research and Innovation Action within the EU Horizon 2020 program, a design study (HighNESS) has been completed to develop a second neutron source located below the spallation target. Compared to the first source, designed for high cold and thermal brightness, the new source has been optimized to deliver higher intensity, and a shift to longer wavelengths in the spectral regions of cold (CN, 2--20\,\AA), very cold (VCN, 10--120\,\AA), and ultracold (UCN, ${>}\,{500}$\,\AA) neutrons. The second source comprises a large liquid deuterium moderator designed to produce CN and support secondary VCN and UCN sources. Various options have been explored in the proposed designs, aiming for world-leading performance in neutronics. These designs will enable the development of several new instrument concepts and facilitate the implementation of a high-sensitivity neutron-antineutron oscillation experiment (NNBAR). This document serves as the Conceptual Design Report for the HighNESS project, representing its final deliverable., Comment: 269 pages, 255 figures. Volume I of the final deliverable of the HighNESS Project (HORIZON 2020 grant agreement ID: 951782)

Despite their importance in a wide variety of applications, the estimation of ionization cross sections for large molecules continues to present challenges for both experiment and theory. Machine learning algorithms have been shown to be an effective mechanism for estimating cross section data for atomic targets and a select number of molecular targets. We present an efficient machine learning model for predicting ionization cross sections for a broad array of molecular targets. Our model is a 3-layer neural network that is trained using published experimental datasets. There is minimal input to the network, making it widely applicable. We show that with training on as few as 10 molecular datasets, the network is able to predict the experimental cross sections of additional molecules with an accuracy similar to experimental uncertainties in existing data. As the number of training molecular datasets increased, the network's predictions became more accurate and, in the worst case, were within 30% of accepted experimental values. In many cases, predictions were within 10% of accepted values. Using a network trained on datasets for 25 different molecules, we present predictions for an additional 27 molecules, including alkanes, alkenes, molecules with ring structures, and DNA nucleotide bases.

We look for a diurnal anisotropy in the cosmic ray flow, using the Mexico-City Neutron Monitor (NM) detector, due to the Earth's orbital motion and predicted by Compton-Getting (C-G) in 1935, as a first-order relativistic effect. The Mexico-City NM's geographic latitude is not very high ($19.33^{\circ}$N), and it has a high cutoff geomagnetic rigidity (8.2 GV) and mountain altitude (2274 m asl) favoring the observation of the C-G effect. Furthermore, during the solar cycle minima, the galactic cosmic ray flux is maxima, and the solar magnetic field gets weakened, with a dipolar pattern. Its influence on cosmic rays reaching Earth is the smallest. Analysis of the combined counting rate during two solar minima, 2008 and 2019, from Mexico-city NM's data yields the C-G effect with an amplitude variation of (0.043$\pm$ 0.019)\%, and phase of (6.15$\pm$ 1.71) LT. The expected amplitude variation is 0.044\%, and the phase of 6.00 LT., Comment: 8 pages, 6 figures

We study the first gravitational wave, GW150914, detected by advanced LIGO and constructed from the data of measurement of strain relative deformation of the fabric of spacetime. We show that the time series from the gravitational wave obeys Tsallis's $q$-Gaussian distribution as a probability density and its dynamics evolve of the three associated Tsallis' indices named $q$-triplet. This fact strongly suggests that these black hole merger systems behave in a non-extensive manner. Furthermore, our results point out that the entropic indexes obtained as a function of frequency are useful statistical parameters to determine the dominant frequency when black hole coalescence is achieved., Comment: 7 pages, 6 figures

We show that the energy-weighted angular (zenith, azimuth) distribution of extensive air showers (EAS), produced by Ultra High Energy (UHE) cosmic rays at the Pierre Auger Observatory (PAO), has a thrust axis almost transverse to the interplanetary magnetic field (IMF), with a thrust value $Tp \geq 0.64$ ( where 1.0 means a perfect alignment and 0.5 isotropy). This behavior strongly suggests an effect of the IMF on the charged shower particles, producing additional lateral scattering. We discuss the weakening of the Earth's magnetic field during geomagnetic storms (30\% of observational time) when the IMF becomes preponderant, strengthening the alignment., Comment: 6 pages, 6 figures