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Single-stranded RNA viruses co-assemble their capsid with the genome and variations in capsid structures can have significant functional relevance. In particular, viruses need to respond to a dehydrating environment to prevent genomic degradation and remain active upon rehydration. Theoretical work has predicted low-energy buckling transitions in icosahedral capsids which could protect the virus from further dehydration. However, there has been no direct experimental evidence, nor molecular mechanism, for such behaviour. Here we observe this transition using X-ray single particle imaging of MS2 bacteriophages after aerosolization. Using a combination of machine learning tools, we classify hundreds of thousands of single particle diffraction patterns to learn the structural landscape of the capsid morphology as a function of time spent in the aerosol phase. We found a previously unreported compact conformation as well as intermediate structures which suggest an incoherent buckling transition which does not preserve icosahedral symmetry. Finally, we propose a mechanism of this buckling, where a single 19-residue loop is destabilised, leading to the large observed morphology change. Our results provide experimental evidence for a mechanism by which viral capsids protect themselves from dehydration. In the process, these findings also demonstrate the power of single particle X-ray imaging and machine learning methods in studying biomolecular structural dynamics., Comment: 10 pages, 4 figures plus 9 pages supplementary information

Realizing tunable functional materials with built-in nanoscale heat flow directionality represents a significant challenge with the potential to enable novel thermal management strategies. Here we use spatiotemporally-resolved thermoreflectance to visualize lateral thermal transport anisotropy in self-assembled supercrystals of anisotropic Au nanocrystals. Correlative electron and thermoreflectance microscopy reveal that heat predominantly flows along the long-axis of the anisotropic nanocrystals, and does so across grain boundaries and curved assemblies while voids disrupt heat flow. We finely control the anisotropy via the aspect ratio of constituent nanorods, and it exceeds the aspect ratio for nano-bipyramid supercrystals and certain nanorod arrangements. Finite element simulations and effective medium modeling rationalize the emergent anisotropic behavior in terms of a simple series resistance model, further providing a framework for estimating thermal anisotropy as a function of material and structural parameters. Self-assembly of colloidal nanocrystals promises a novel route to direct heat flow in a wide range of applications that utilize this important class of materials.

Nanoparticles, exhibiting functionally relevant structural heterogeneity, are at the forefront of cutting-edge research. Now, high-throughput single-particle imaging (SPI) with x-ray free-electron lasers (XFELs) creates unprecedented opportunities for recovering the shape distributions of millions of particles that exhibit functionally relevant structural heterogeneity. To realize this potential, three challenges have to be overcome: (1) simultaneous parametrization of structural variability in real and reciprocal spaces; (2) efficiently inferring the latent parameters of each SPI measurement; (3) scaling up comparisons between $10^5$ structural models and $10^6$ XFEL-SPI measurements. Here, we describe how we overcame these three challenges to resolve the non-equilibrium shape distributions within millions of gold nanoparticles imaged at the European XFEL. These shape distributions allowed us to quantify the degree of asymmetry in these particles, discover a relatively stable `shape envelope' amongst nanoparticles, discern finite-size effects related to shape-controlling surfactants, and extrapolate nanoparticles' shapes to their idealized thermodynamic limit. Ultimately, these demonstrations show that XFEL SPI can help transform nanoparticle shape characterization from anecdotally interesting to statistically meaningful.

One of the outstanding analytical problems in X-ray single particle imaging (SPI) is the classification of structural heterogeneity, which is especially difficult given the low signal-to-noise ratios of individual patterns and that even identical objects can yield patterns that vary greatly when orientation is taken into consideration. We propose two methods which explicitly account for this orientation-induced variation and can robustly determine the structural landscape of a sample ensemble. The first, termed common-line principal component analysis (PCA) provides a rough classification which is essentially parameter-free and can be run automatically on any SPI dataset. The second method, utilizing variation auto-encoders (VAEs) can generate 3D structures of the objects at any point in the structural landscape. We implement both these methods in combination with the noise-tolerant expand-maximize-compress (EMC) algorithm and demonstrate its utility by applying it to an experimental dataset from gold nanoparticles with only a few thousand photons per pattern and recover both discrete structural classes as well as continuous deformations. These developments diverge from previous approaches of extracting reproducible subsets of patterns from a dataset and open up the possibility to move beyond studying homogeneous sample sets and study open questions on topics such as nanocrystal growth and dynamics as well as phase transitions which have not been externally triggered., Comment: 29 pages, 9 figures

We present measurements of the electron helicity asymmetry in quasi-elastic proton knockout from $^{2}$H and $^{12}$C nuclei by polarized electrons. This asymmetry depends on the fifth structure function, is antisymmetric with respect to the scattering plane, and vanishes in the absence of final-state interactions, and thus it provides a sensitive tool for their study. Our kinematics cover the full range in off-coplanarity angle $\phi_{pq}$, with a polar angle $\theta_{pq}$ coverage up to about 8 degrees. The missing energy resolution enabled us to determine the asymmetries for knock-out resulting in different states of the residual $^{11}$B system. We find that the helicity asymmetry for $p$-shell knockout from $^{12}$C depends on the final state of the residual system and is relatively large (up to $\approx 0.16$), especially at low missing momentum. It is considerably smaller (up to $\approx 0.01$) for $s$-shell knockout from both $^{12}$C and $^2$H. The data for $^2$H are in very good agreement with theoretical calculations, while the predictions for $^{12}$C exhibit differences with respect to the data.

We report measurements of the induced polarization $\vec P$ of protons knocked out from $^2$H and $^{12}$C via the $A(e,e'\vec p\,)$ reaction. We have studied the dependence of $\vec P$ on two kinematic variables: the missing momentum $p_{\rm miss}$ and the "off-coplanarity" angle $\phi_{pq}$ between the scattering and reaction planes. For the full 360$\degree$ range in $\phi_{pq}$, both the normal ($P_y$) and, for the first time, the transverse ($P_x$) components of the induced polarization were measured with respect to the coordinate system associated with the scattering plane. $P_x$ vanishes in coplanar kinematics, however in non-coplanar kinematics, it is on the same scale as $P_y$. We find that the dependence on $\phi_{pq}$ is sine-like for $P_x$ and cosine-like for $P_y$. For carbon, the magnitude of the induced polarization is especially large when protons are knocked out from the $p_{3/2}$ shell at very small $p_{\rm miss}$. For the deuteron, the induced polarization is near zero at small $|p_{\rm miss}|$, and its magnitude increases with $|p_{\rm miss}|$. For both nuclei such behavior is reproduced qualitatively by theoretical results, driven largely by the spin-orbit part of the final-state interactions. However, for both nuclei, sizeable discrepancies exist between experiment and theory.

We report the 3D structure determination of gold nanoparticles (AuNPs) by X-ray single particle imaging (SPI). Around 10 million diffraction patterns from gold nanoparticles were measured in less than 100 hours of beam time, more than 100 times the amount of data in any single prior SPI experiment, using the new capabilities of the European X-ray free electron laser which allow measurements of 1500 frames per second. A classification and structural sorting method was developed to disentangle the heterogeneity of the particles and to obtain a resolution of better than 3 nm. With these new experimental and analytical developments, we have entered a new era for the SPI method and the path towards close-to-atomic resolution imaging of biomolecules is apparent., Comment: 25 pages, 5 main figures, 6 supplementary figures, 2 supplementary movies (link in document)

We report the measurements of the transverse ($P'x$) and longitudinal ($P'z$) components of the polarization transfer to a bound proton in carbon via the quasi-free $^{12}{\rm C}(\vec e,e'\vec p)$ reaction, over a wide range of missing momenta. We determine these polarization-transfers separately for protons knocked out from the $s$- and $p$-shells. The electron-beam polarization was measured to determine the individual components with systematic uncertainties which allow a detailed comparison with theoretical calculations.

Tip-enhanced Raman spectroscopy (TERS) has reached nanometer spatial resolution for measurements performed at ambient conditions and sub-nanometer resolution at ultra high vacuum. Super-resolution (beyond the tip apex diameter) TERS has been obtained, mostly in the gap mode configuration, where a conductive substrate localizes the electric fields. Here we present experimental and theoretical TERS to explore the field distribution responsible for spectral enhancement. We use gold tips of $40\pm 10 \ \text{nm}$ apex diameter to measure TERS on graphene, a spatially delocalized two-dimensional sample, sitting on different substrates: (i) glass, (ii) a thin layer of gold and (iii) a surface covered with $12\ \text{nm}$ diameter gold spheres, for which $6\ \text{nm}$ resolution is achieved at ambient conditions. The super-resolution is due to the field configuration resulting from the coupled tip-sample-substrate system, exhibiting a non-trivial spatial surface distribution. The field distribution and the symmetry selection rules are different for non-gap vs. gap mode configurations. This influences the overall enhancement which depends on the Raman mode symmetry and substrate structure., Comment: 8 pages, 7 figures

We report on a comprehensive reinterpretation of the existing cross-section data for elastic electron-proton scattering obtained by the initial-state radiation technique, resulting in a significantly improved accuracy of the extracted proton charge radius. By refining the external energy corrections we have achieved an outstanding description of the radiative tail, essential for a detailed investigation of the proton finite-size effects on the measured cross-sections. This development, together with a novel framework for determining the radius, based on a regression analysis of the cross-sections employing a polynomial model for the form factor, led us to a new value for the charge radius, which is $(0.870 \pm 0.014_\mathrm{stat.}\pm 0.024_\mathrm{sys.} \pm 0.003_\mathrm{mod.})\,\mathrm{fm}$.

We present measurements of the polarization-transfer components in the $^2$H$(\vec e,e'\vec p)$ reaction, covering a previously unexplored kinematic region with large positive (anti-parallel) missing momentum, $p_{\rm miss}$, up to 220 MeV$/c$, and $Q^2=0.65$ $({\rm GeV}/c)^2$. These measurements, performed at the Mainz Microtron (MAMI), were motivated by theoretical calculations which predict small final-state interaction (FSI) effects in these kinematics, making them favorable for searching for medium modifications of bound nucleons in nuclei. We find in this kinematic region that the measured polarization-transfer components $P_x$ and $P_z$ and their ratio agree with the theoretical calculations, which use free-proton form factors. Using this, we establish upper limits on possible medium effects that modify the bound proton's form factor ratio $G_E/G_M$ at the level of a few percent. We also compare the measured polarization-transfer components and their ratio for $^2$H to those of a free (moving) proton. We find that the universal behavior of $^2$H, $^4$He and $^{12}$C in the double ratio $\frac{(P_x/P_z)^A}{(P_x/P_z)^{^1\rm H}}$ is maintained in the positive missing-momentum region.