Publications

Male sex is a major risk factor for SARS-CoV-2 infection severity. To understand the basis for this sex difference, we studied SARS-CoV-2 infection in a young adult cohort of United States Marine recruits. Among 2,641 male and 244 female unvaccinated and seronegative recruits studied longitudinally, SARS-CoV-2 infections occurred in 1,033 males and 137 females. We identified sex differences in symptoms, viral load, blood transcriptome, RNA splicing, and proteomic signatures. Females had higher pre-infection expression of antiviral interferon-stimulated gene (ISG) programs. Causal mediation analysis implicated ISG differences in number of symptoms, levels of ISGs, and differential splicing of CD45 lymphocyte phosphatase during infection. Our results indicate that the antiviral innate immunity set point causally contributes to sex differences in response to SARS-CoV-2 infection. A record of this paper’s transparent peer review process is included in the supplemental information.

We propose an algorithm for optimizations in which the gradients contain stochastic noise. This arises, for example, in structural optimizations when computations of forces and stresses rely on methods involving Monte Carlo sampling, such as quantum Monte Carlo or neural network states, or are performed on quantum devices which have intrinsic noise. Our proposed algorithm is based on the combination of two key ingredients: an update rule derived from the steepest descent method, and a staged scheduling of the targeted statistical error and step-size, with position averaging. We compare it with commonly applied algorithms, including some of the latest machine learning optimization methods, and show that the algorithm consistently performs efficiently and robustly under realistic conditions. Applying this algorithm, we achieve full-degree optimizations in solids using ab initio many-body computations, by auxiliary-field quantum Monte Carlo with planewaves and pseudopotentials. A new metastable structure in Si was discovered in a mixed geometry and lattice relaxing simulation. In addition to structural optimization in materials, our algorithm can potentially be useful in other problems in various fields where optimization with noisy gradients is needed.

The advent of ultrafast laser science offers the unique opportunity to combine Floquet engineering with extreme time resolution, further pushing the optical control of matter into the petahertz domain. However, what is the shortest driving pulse for which Floquet states can be realised remains an unsolved matter, thus limiting the application of Floquet theory to pulses composed by many optical cycles. Here we ionized Ne atoms with few-femtosecond pulses of selected time duration and show that a Floquet state can be established already within 10 cycles of the driving field. For shorter pulses, down to 2 cycles, the finite lifetime of the driven state can still be explained using an analytical model based on Floquet theory. By demonstrating that the population of the Floquet sidebands can be controlled not only with the driving laser pulse intensity and frequency, but also by its duration, our results add a new lever to the toolbox of Floquet engineering.

The recently introduced classification of two-dimensional insulators in terms of topological crystalline invariants has been applied so far to "obstructed" atomic insulators characterized by a mismatch between the centers of the electronic Wannier functions and the ionic positions. We extend this notion to quantum spin Hall insulators in which the ground state cannot be described in terms of time-reversal symmetric localized Wannier functions. A system equivalent to graphene in all its relevant electronic and topological properties except for a real-space obstruction is identified and studied via symmetry analysis as well as with density functional theory. The low-energy model comprises a local spin-orbit coupling and a non-local symmetry breaking potential, which turn out to be the essential ingredients for an obstructed quantum spin Hall insulator. An experimental fingerprint of the obstruction is then measured in a large-gap triangular quantum spin Hall material.

Background Accurate high-resolution EEG source reconstruction (localization) is important for several tasks, including rigorous and rapid mental health screening.Objective The present study has developed, validated, and applied a new source localization algorithm utilizing a charge-based boundary element fast multipole method (BEM-FMM) coupled with the Helmholtz reciprocity principle and the transcranial electrical stimulation (TES) forward solution.Methods The unknown cortical dipole density is reconstructed over the entire cortical surface by expanding into global basis functions in the form of cortical fields of active TES electrode pairs. These pairs are constructed from the reading electrodes. An analog of the minimum norm estimation (MNE) equation is obtained after substituting this expansion into the reciprocity principle written in terms of measured electrode voltages. Delaunay (geometrically balanced) triangulation of the electrode cap is introduced first. Basis functions for all electrode pairs connected by the edges of a triangular mesh are precomputed and stored in memory. A smaller set of independent basis functions is then selected and employed at every time instant. This set is based on the highest voltage differences measured.Results The method is validated against the classic, yet challenging problem of median nerve stimulation and the tangential cortical sources located at the posterior wall of the central sulcus for an N20/P20 peak (2 scanned subjects). The method is further applied to perform source reconstruction of synthesized tangential cortical sources located at the posterior wall of the central sulcus (12 different subjects). In the second case, an average source reconstruction error of 7 mm is reported for the best possible noiseless scenario.Conclusions Once static preprocessing with TES electrodes has been done (the basis functions have been computed), our method requires fractions of a second to complete the accurate high-resolution source localization.Competing Interest StatementThe authors have declared no competing interest.

We address the problem of analytic continuation of imaginary-frequency Green's functions, which is crucial in many-body physics, using machine learning based on a multi-level residual neural network. We specifically address potential biases that can be introduced due to the use of artificially created spectral functions that are employed to train the neural network. We also implement an uncertainty estimation of the predicted spectral function, based on Monte Carlo dropout, which allows to identify frequency regions where the prediction might not be accurate, and we study the effect of noise, in particular also for situations where the noise level during training is different from that in the actual data. Our analysis demonstrates that this method can indeed achieve a high quality of prediction, comparable or better than the widely used maximum entropy method, but that further improvement is currently limited by the lack of true data that can be used for training. We also benchmark our approach by applying it to the case of SrVO

We study the performance of spin-component-scaled second-order Møller-Plesset perturbation theory (SCS-MP2) for the prediction of the lattice constant, bulk modulus, and cohesive energy of 12 simple, three-dimensional, covalent and ionic semiconductors and insulators. We find that SCS-MP2 and the simpler scaled opposite-spin MP2 (SOS-MP2) yield predictions that are significantly improved over the already good performance of MP2. Specifically, when compared to experimental values with zero-point vibrational corrections, SCS-MP2 (SOS-MP2) yields mean absolute errors of 0.015 (0.017) Å for the lattice constant, 3.8 (3.7) GPa for the bulk modulus, and 0.06 (0.08) eV for the cohesive energy, which are smaller than those of leading density functionals by about a factor of two or more. We consider a reparameterization of the spin scaling parameters and find that the optimal parameters for these solids are very similar to those already in common use in molecular quantum chemistry, suggesting good transferability and reliable future applications to surface chemistry on insulators.

We introduce libdlr, a library implementing the recently introduced discrete Lehmann representation (DLR) of imaginary time Green's functions. The DLR basis consists of a collection of exponentials chosen by the interpolative decomposition to ensure stable and efficient recovery of Green's functions from imaginary time or Matsubara frequency samples. The library provides subroutines to build the DLR basis and grids, and to carry out various standard operations. The simplicity of the DLR makes it straightforward to incorporate into existing codes as a replacement for less efficient representations of imaginary time Green's functions, and libdlr is intended to facilitate this process. libdlr is written in Fortran, provides a C header interface, and contains a Python module pydlr. We also introduce a stand-alone Julia implementation, Lehmann.jl

Two groups have visualized actin — the protein polymer that gives cells their shape — at high resolution. The structures provide in-depth views of the polymer as it adopts fleeting states and undergoes conformational changes.

Optical spectroscopy of ultimately thin materials has significantly enhanced our understanding of collective excitations in low-dimensional semiconductors. This is particularly reflected by the rich physics of excitons in atomically thin crystals which uniquely arises from the interplay of strong Coulomb correlation, spin-orbit coupling (SOC), and lattice geometry. Here we extend the field by reporting the observation of room temperature excitons in a material of non-trivial global topology. We study the fundamental optical excitation spectrum of a single layer of bismuth atoms epitaxially grown on a SiC substrate (hereafter bismuthene or Bi/SiC) which has been established as a large-gap, two-dimensional (2D) quantum spin Hall (QSH) insulator. Strongly developed optical resonances are observed to emerge around the direct gap at the K and K’ points of the Brillouin zone, indicating the formation of bound excitons with considerable oscillator strength. These experimental findings are corroborated, concerning both the character of the excitonic resonances as well as their energy scale, by ab-initio GW and Bethe-Salpeter equation calculations, confirming strong Coulomb interaction effects in these optical excitations. Our observations provide evidence of excitons in a 2D QSH insulator at room temperature, with excitonic and topological physics deriving from the very same electronic structure.