Computer Simulations of the interaction between SARS-CoV-2 spike glycoprotein and different surfaces

A prominent feature of coronaviruses is the presence of a large glycoprotein spike protruding from a lipidic membrane. This glycoprotein spike determines the interaction of coronaviruses with the environment and the host. In this paper, we perform all atomic molecular dynamics simulations of the interaction between the SARS-CoV-2 trimeric glycoprotein spike and surfaces of materials. We considered a material with high hydrogen bonding capacity (cellulose) and a material capable of strong hydrophobic interactions (graphite). Initially, the spike adsorbs to both surfaces through essentially the same residues belonging to the receptor binding subunit of its three monomers. Adsorption onto cellulose stabilizes in this configuration, with the help of a large number of hydrogen bonds developed between cellulose and the three receptor-binding domains of the glycoprotein spike. In the case of adsorption onto graphite, the initial adsorption configuration is not stable and the surface induces a substantial deformation of the glycoprotein spike with a large number of adsorbed residues not pertaining to the binding subunits of the spike monomers.This work was supported by the Spanish Ministry of Science and Innovation through grant RTI2018-096273-B-I00 and the “Severo Ochoa” Grant SEV-2015-0496 for Centres of Excellence in R&D awarded to ICMAB. We thank the CESGA supercomputing center for computer time and technical support at the Finisterrae supercomputer. D. C. Malaspina is supported by the European Union Horizon 2020 research and innovation programme under Marie Sklodowska-Curie grant agreement No. 6655919.Peer reviewe

The water supercooled regime as described by four common water models

The temperature scale of simple water models in general does not coincide with the natural one. Therefore, in order to make a meaningful evaluation of different water models a temperature rescaling is necessary. In this paper we introduce a rescaling using the melting temperature and the temperature corresponding to the maximum of the heat capacity to evaluate four common water models (TIP4P-Ew, TIP4P-2005, TIP5P-Ew and Six-Sites) in the supercooled regime. Although all the models show the same general qualitative behavior, the TIP5P-Ew appears as the best representation of the supercooled regime when the rescaled temperature is used. We also analyze, using thermodynamic arguments, the critical nucleus size for ice growth. Finally, we speculate on the possible reasons why atomistic models do not usually crystalize while the coarse grained mW model do crystallize.Comment: 8 pages, 8 figure

Observations of Energetic-particle Population Enhancements along Intermittent Structures near the Sun from the Parker Solar Probe

Observations at 1 au have confirmed that enhancements in measured energetic-particle (EP) fluxes are statistically associated with "rough" magnetic fields, i.e., fields with atypically large spatial derivatives or increments, as measured by the Partial Variance of Increments (PVI) method. One way to interpret this observation is as an association of the EPs with trapping or channeling within magnetic flux tubes, possibly near their boundaries. However, it remains unclear whether this association is a transport or local effect; i.e., the particles might have been energized at a distant location, perhaps by shocks or reconnection, or they might experience local energization or re-acceleration. The Parker Solar Probe (PSP), even in its first two orbits, offers a unique opportunity to study this statistical correlation closer to the corona. As a first step, we analyze the separate correlation properties of the EPs measured by the Integrated Science Investigation of the Sun (IS⊙IS) instruments during the first solar encounter. The distribution of time intervals between a specific type of event, i.e., the waiting time, can indicate the nature of the underlying process. We find that the IS⊙IS observations show a power-law distribution of waiting times, indicating a correlated (non-Poisson) distribution. Analysis of low-energy (~15 – 200 keV/nuc) IS⊙IS data suggests that the results are consistent with the 1 au studies, although we find hints of some unexpected behavior. A more complete understanding of these statistical distributions will provide valuable insights into the origin and propagation of solar EPs, a picture that should become clear with future PSP orbits

Interplanetary mesoscale observatory (InterMeso): A mission to untangle dynamic mesoscale structures throughout the heliosphere

Mesoscale dynamics are a fundamental process in space physics, but fall within an observational gap of current and planned missions. Particularly in the solar wind, measurements at the mesoscales (100s RE to a few degrees heliographic longitude at 1 au) are crucial for understanding the connection between the corona and an observer anywhere within the heliosphere. Mesoscale dynamics may also be key to revealing the currently unresolved physics regulating particle acceleration and transport, magnetic field topology, and the causes of variability in the composition and acceleration of solar wind plasma. Studies using single-point observations do not allow for investigations into mesoscale solar wind dynamics and plasma variability, nor do they allow for the exploration of the sub-structuring of large-scale solar wind structures like coronal mass ejections (CMEs), co-rotating/stream interaction regions (CIR/SIRs), and the heliospheric plasma sheet. To address this fundamental gap in our knowledge of the heliosphere at these scales, the Interplanetary Mesoscale Observatory (InterMeso) concept employs a multi-point approach using four identical spacecraft in Earth-trailing orbits near 1 au. Varying drift speeds of the InterMeso spacecraft enable the mission to span a range of mesoscale separations in the solar wind, achieving significant and innovative science return. Simultaneous, longitudinally-separated measurements of structures co-rotating over the spacecraft also allow for disambiguation of spatiotemporal variability, tracking of the evolution of solar wind structures, and determination of how the transport of energetic particles is impacted by these variabilities

Small-scale Magnetic Flux Ropes in the First two Parker Solar Probe Encounters

Small-scale magnetic flux ropes (SFRs) are a type of structures in the solar wind that possess helical magnetic field lines. In a recent report (Chen & Hu 2020), we presented the radial variations of the properties of SFR from 0.29 to 8 au using in situ measurements from the Helios, ACE/Wind, Ulysses, and Voyager spacecraft. With the launch of the Parker Solar Probe (PSP), we extend our previous investigation further into the inner heliosphere. We apply a Grad-Shafranov-based algorithm to identify SFRs during the first two PSP encounters. We find that the number of SFRs detected near the Sun is much less than that at larger radial distances, where magnetohydrodynamic (MHD) turbulence may act as the local source to produce these structures. The prevalence of Alfvenic structures significantly suppresses the detection of SFRs at closer distances. We compare the SFR event list with other event identification methods, yielding a dozen well-matched events. The cross-section maps of two selected events confirm the cylindrical magnetic flux rope configuration. The power-law relation between the SFR magnetic field and heliocentric distances seems to hold down to 0.16 au.Comment: Accepted by ApJ on 2020 Sep 1

The Future of Heliophysics Research through Targeted use of Constellations

This white paper seeks to outline the benefits and challenges of constellations, ranging from the Heliophysics System Observatory, to constellations consisting of a small number of spacecraft, to large-number constellations. In moving toward this constellation era, investments are required by our sponsors to best enable our continued scientific advancement in Solar and Space Physics

Parker Solar Probe observations of proton beams simultaneous with ion-scale waves

Parker Solar Probe (PSP), NASA's latest and closest mission to the Sun, is on a journey to investigate fundamental enigmas of the inner heliosphere. This paper reports initial observations made by the Solar Probe Analyzer for Ions (SPAN-I), one of the instruments in the Solar Wind Electrons Alphas and Protons (SWEAP) instrument suite. We address the presence of secondary proton beams in concert with ion-scale waves observed by FIELDS, the electromagnetic fields instrument suite. We show two events from PSP's 2nd orbit that demonstrate signatures consistent with wave-particle interactions. We showcase 3D velocity distribution functions (VDFs) measured by SPAN-I during times of strong wave power at ion-scales. From an initial instability analysis, we infer that the VDFs departed far enough away from local thermodynamic equilibrium (LTE) to provide sufficient free energy to locally generate waves. These events exemplify the types of instabilities that may be present and, as such, may guide future data analysis characterizing and distinguishing between different wave-particle interactions.Comment: 24 pages, 9 figures, 2 table