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The tunable design of protein redox potentials promises to open a range of applications in biotechnology and catalysis. Here we introduce a method to calculate redox potential changes by combining fluctuation relations with molecular dynamics simulations. It involves the simulation of reduced and oxidized states, followed by the instantaneous conversion between them. Energy differences introduced by the perturbations are obtained using the Kubo-Onsager approach. Using a detailed fluctuation relation coupled with Bayesian inference, these are post-processed into estimates for the redox potentials in an efficient manner. This new method, denoted MD+CB, is tested on a de novo four-helix bundle heme protein (the m4D2 `maquette') and five designed mutants, including some mutants characterized experimentally in this work. The MD+CB approach is found to perform reliably, giving redox potential shifts with reasonably good correlation (0.85) to the experimental values for the mutants. The MD+CB approach also compares well with redox potential shift predictions using a continuum electrostatic method. The estimation method employed within the MD+CB approach is straightforwardly transferable to standard equilibrium MD simulations, and holds promise for redox protein engineering and design applications., Comment: 14 pages, incl. 2 figures and 1 table (+ supplementary information). Accepted version

While proteins have been treated as particles with a spherically symmetric interaction, of course in reality the situation is rather more complex. A simple step towards higher complexity is to treat the proteins as non--spherical particles and that is the approach we pursue here. We investigate the phase behavior of enhanced green fluorescent protein (eGFP) under the addition of a non--adsorbing polymer, polyethylene glycol (PEG). From small angle x-ray scattering we infer that the eGFP undergoes dimerization and we treat the dimers as spherocylinders with aspect ratio $L/D-1 = 1.05$. Despite the complex nature of the proteins, we find that the phase behaviour is similar to that of hard spherocylinders with ideal polymer depletant, exhibiting aggregation and, in a small region of the phase diagram, crystallization. By comparing our measurements of the onset of aggregation with predictions for hard colloids and ideal polymers [S.V. Savenko and M. Dijkstra, J. Chem. Phys 124, 234902 (2006) and F. lo Verso et al., Phys. Rev. E 73, 061407 (2006)] we find good agreement, which suggests that the eGFP proteins are consistent with hard spherocylinders and ideal polymer., Comment: 12 pages

SARS-CoV-2 is the cause of COVID-19 acute respiratory illness that like its predecessors, MERS and SARS, can be severe and fatal 1-4. By April of 2020, COVID-19 infections had become a worldwide pandemic with nearly 3 million infections and over 200,000 deaths. The relative contributions of virus replication and cytopathic effects or immunopathological host responses to the severe and fatal outcomes of COVID-19 lung infections have as yet to be determined. Here we show that SARS-CoV-2 replication and cytopathic effects in type II alveolar pneumocytes causes focal lung injury in an individual with no history of pulmonary symptoms. These findings point to the potential benefit of early effective antiviral treatment to prevent progression to severe and fatal COVID-19 pneumonia., Comment: 19 pages, 4 figures, 3 extended data figures

The implementation of natural and artificial proteins with designer properties and functionalities offers unparalleled opportunity for functional nanoarchitectures formed through self-assembly. However, to exploit the opportunities offered we require the ability to control protein assembly into the desired architecture while avoiding denaturation and therefore retaining protein functionality. Here we address this challenge with a model system of fluorescent proteins. Using techniques of self-assembly manipulation inspired by soft matter where interactions between components are controlled to yield the desired structure, we show that it is possible to assemble networks of proteins of one species which we can decorate with another, whose coverage we can tune. Consequently, the interfaces between domains of each component can also be tuned, with applications for example in energy transfer. Our model system of fluorescent proteins eGFP and mCherry retain their fluorescence throughout the assembly process, thus demonstrating that functionality is preserved.

Classical motion of positronium embedded in a magnetic field is studied, and computation shows the emergence of chaotic orbits. Recent work investigating quantum behavior of this system predicts extremely long lifetimes. Chaos assisted tunneling, however may lead to significant shortening of the lifetime of this system., Comment: 3 pages,4 figures

Impact cratering is a fundamental physical process that has dominated the evolution and modification of nearly every planetary surface in the Solar System. Impact craters serve as a means to probe the subsurface structure of a planetary body and provide hints about target surface properties. By examining small craters on the lunar maria and comparing these to experimental impacts in the laboratory, Oberbeck and Quaide first suggested that crater morphology can be used to estimate the thickness of a regolith layer on top of a more competent unit. Lunar craters show a morphological progression from a simple bowl shape to flat-floored and concentric craters as crater diameter increases for a given regolith thickness. This quantitative relationship is commonly used to estimate regolith thicknesses on the lunar surface and has also been explored via numerical and experimental studies. Here we report on a series of experimental impact craters formed in targets com-posed of a thin layer of loose sand on top of a stronger substrate at the Experimental Impact Laboratory at NASA Johnson Space Center.

AImpact cratering has dominated the evolution and modification of planetary surfaces through-out the history of the solar system. Impact craters can serve as probes to understanding the details of a planetary subsurface; for example, Oberbeck and Quaide, suggested that crater morphology can be used to estimate the thickness of a regolith layer on top of a more competent unit. Lunar craters show a morphological progression from a simple bowl shape to flat-floored and concentric craters as crater diameter in-creases for a given regolith thickness. The final shape of the impact crater is a result of the subsurface flow-field initiated as the projectile transfers its energy and momentum to the target surface at the moment of impact. Therefore, when a regolith layer is present over a stronger substrate, such as is the case on the lunar surface, the substrate modifies the flow-field and thereby the excavation flow of the crater, which is reflected in the morphology of the final crater. Here we report on a series of experimental impacts into targets composed of a thin layer of loose sand on top of a stronger substrate. We use the Ejection-Velocity Measurement System developed to examine the ejecta kinematics during the formation of these craters.

Impact cratering is the dominant geo-logic process affecting the surfaces of solid bodies throughout our solar system. Because large impacts are (luckily) rare on Earth, the process is studied through experiments, observations of existing structures, numerical modeling, and theory, most of which make the simplifying assumptions that the target is homogeneous, with no substantial topography. Craters do not always form on level targets com-posed of homogeneous loose material. Rather (Fig. 1), they often form on sloped surfaces and in layered tar-gets, both of which significantly influence the excavation and ejecta deposition processes. Such craters are common on the Moon and asteroids. We are investigating crater formation in two separate suites of experiments using sloped and layered targets (Fig. 2) at the Experimental Impact Laboratory at NASA Johnson Space Center. An experiment was also performed in a flat, homogenous target to serve as a reference.