Publications

An important component of many image alignment methods is the calculation of inner products (correlations) between an image of $n\times n$ pixels and another image translated by some shift and rotated by some angle. For robust alignment of an image pair, the number of considered shifts and angles is typically high, thus the inner product calculation becomes a bottleneck. Existing methods, based on fast Fourier transforms (FFTs), compute all such inner products with computational complexity $\mathcal{O}(n^3 \log n)$ per image pair, which is reduced to $\mathcal{O}(N n^2)$ if only $N$ distinct shifts are needed. We propose to use a factorization of the translation kernel (FTK), an optimal interpolation method which represents images in a Fourier--Bessel basis and uses a rank-$H$ approximation of the translation kernel via an operator singular value decomposition (SVD). Its complexity is $\mathcal{O}(Hn(n + N))$ per image pair. We prove that $H = \mathcal{O}((W + \log(1/\epsilon))^2)$, where $2W$ is the magnitude of the maximum desired shift in pixels and $\epsilon$ is the desired accuracy. For fixed $W$ this leads to an acceleration when $N$ is large, such as when sub-pixel shift grids are considered. Finally, we present numerical results in an electron cryomicroscopy application showing speedup factors of $3$-$10$ with respect to the state of the art.

Single-particle electron cryomicroscopy is an essential tool for high-resolution 3D reconstruction of proteins and other biological macromolecules. An important challenge in cryo-EM is the reconstruction of non-rigid molecules with parts that move and deform. Traditional reconstruction methods fail in these cases, resulting in smeared reconstructions of the moving parts. This poses a major obstacle for structural biologists, who need high-resolution reconstructions of entire macromolecules, moving parts included. To address this challenge, we present a new method for the reconstruction of macromolecules exhibiting continuous heterogeneity. The proposed method uses projection images from multiple viewing directions to construct a graph Laplacian through which the manifold of three-dimensional conformations is analyzed. The 3D molecular structures are then expanded in a basis of Laplacian eigenvectors, using a novel generalized tomographic reconstruction algorithm to compute the expansion coefficients. These coefficients, which we name spectral volumes, provide a high-resolution visualization of the molecular dynamics. We provide a theoretical analysis and evaluate the method empirically on several simulated data sets.

We present near-infrared interferometric data on the Seyfert 2 galaxy NGC 1068, obtained with the GRAVITY instrument on the European Southern Observatory Very Large Telescope Interferometer. The extensive baseline coverage from 5 to 60 M\lambda allowed us to reconstruct a continuum image of the nucleus with an unrivaled 0.2 pc resolution in the K-band. We find a thin ring-like structure of emission with a radius r = 0.24+/-0.03 pc, inclination i = 70+/-5 deg, position angle PA = -50+/-4 deg, and h/r < 0.14, which we associate with the dust sublimation region. The observed morphology is inconsistent with the expected signatures of a geometrically and optically thick torus. Instead, the infrared emission shows a striking resemblance to the 22 GHz maser disc, which suggests they share a common region of origin. The near-infrared spectral energy distribution indicates a bolometric luminosity of (0.4-4.7) x 10^45 erg/s, behind a large A_K ~ 5.5 (A_V ~ 90) screen of extinction that also appears to contribute significantly to obscuring the broad line region.

We discuss the construction of low-energy tight-binding Hamiltonians for condensed matter systems with a strong coupling to the quantum electromagnetic field. Such Hamiltonians can be obtained by projecting the continuum theory on a given set of Wannier orbitals. However, different representations of the continuum theory lead to different low-energy formulations, because different representations may entangle light and matter, transforming orbitals into light-matter hybrid states before the projection. In particular, a multi-center Power-Zienau-Woolley transformation yields a dipolar Hamiltonian which incorporates the light-matter coupling via both Peierls phases and a polarization density. We compare this dipolar gauge Hamiltonian and the straightforward Coulomb gauge Hamiltonian for a one-dimensional solid, to describe sub-cycle light-driven electronic motion in the semiclassical limit, and a coupling of the solid to a quantized cavity mode which renormalizes the band-structure into electron-polariton bands. Both descriptions yield the same result when many bands are taken into account, but the dipolar Hamiltonian is more accurate when the model is restricted to few electronic bands, while the Coulomb Hamiltonian requires fewer electromagnetic modes.

Understanding how gene expression programs are controlled requires identifying regulatory relationships between transcription factors and target genes. Gene regulatory networks are typically constructed from gene expression data acquired following genetic perturbation or environmental stimulus. Single-cell RNA sequencing (scRNAseq) captures the gene expression state of thousands of individual cells in a single experiment, offering advantages in combinatorial experimental design, large numbers of independent measurements, and accessing the interaction between the cell cycle and environmental responses that is hidden by population-level analysis of gene expression. To leverage these advantages, we developed a method for scRNAseq in budding yeast (Saccharomyces cerevisiae). We pooled diverse transcriptionally barcoded gene deletion mutants in 11 different environmental conditions and determined their expression state by sequencing 38,285 individual cells. We benchmarked a framework for learning gene regulatory networks from scRNAseq data that incorporates multitask learning and constructed a global gene regulatory network comprising 12,228 interactions.

We present an algorithm for supervised learning using tensor networks, employing a step of preprocessing the data by coarse-graining through a sequence of wavelet transformations. We represent these transformations as a set of tensor network layers identical to those in a multi-scale entanglement renormalization ansatz (MERA) tensor network, and perform supervised learning and regression tasks through a model based on a matrix product state (MPS) tensor network acting on the coarse-grained data. Because the entire model consists of tensor contractions (apart from the initial non-linear feature map), we can adaptively fine-grain the optimized MPS model backwards through the layers with essentially no loss in performance. The MPS itself is trained using an adaptive algorithm based on the density matrix renormalization group (DMRG) algorithm. We test our methods by performing a classification task on audio data and a regression task on temperature time-series data, studying the dependence of training accuracy on the number of coarse-graining layers and showing how fine-graining through the network may be used to initialize models with access to finer-scale features.

In this paper, a topological classification of molecules and their chemical reactions on a single particle level is proposed. We consider 0-dimensional electronic Hamiltonians in a real-space tight-binding basis with spinless time-reversal symmetry and an additional spatial reflection symmetry. The symmetry gives rise to a perplectic structure and suggests a ℤ2 invariant in form of a pfaffian, which can be captured by an entanglement cut. We apply our findings to a class of chemical reactions studied by Woodward and Hoffmann, where a reflection symmetry is preserved during a one-dimensional reaction path and argue that the topological classification should contribute to the rate constants of these reactions. More concretely, we find that a reaction takes place experimentally whenever the reactants and products can be adiabatically deformed into each other, while reactions that require a change of topological invariants have not been observed experimentally.

We study two-dimensional charge-imbalanced electron-hole systems embedded in an optical microcavity. We find that strong coupling to photons favors states with pairing at zero or small center of mass momentum, leading to a condensed state with spontaneously broken time-reversal and rotational symmetry, and unpaired carriers that occupy an anisotropic crescent-shaped sliver of momentum space. The crescent state is favoured at moderate charge imbalance, while a Fulde--Ferrel--Larkin--Ovchinnikov-like state --- with pairing at large center of mass momentum --- occurs instead at strong imbalance. The crescent state stability results from long-range Coulomb interactions in combination with extremely long-range photon-mediated interactions.

Artificial atom qubits in diamond have emerged as leading candidates for a range of solid-state quantum systems, from quantum sensors to repeater nodes in memory-enhanced quantum communication. Inversion-symmetric group IV vacancy centers, comprised of Si, Ge, Sn and Pb dopants, hold particular promise as their neutrally charged electronic configuration results in a ground-state spin triplet, enabling long spin coherence above cryogenic temperatures. However, despite the tremendous interest in these defects, a theoretical understanding of the electronic and spin structure of these centers remains elusive. In this context, we predict the ground- and excited-state properties of the neutral group IV color centers from first principles. We capture the product Jahn-Teller effect found in the excited state manifold to second order in electron-phonon coupling, and present a non-perturbative treatment of the effect of spin-orbit coupling. Importantly, we find that spin-orbit splitting is strongly quenched due to the dominant Jahn-Teller effect, with the lowest optically-active 3Eu state weakly split into ms-resolved states. The predicted complex vibronic spectra of the neutral group IV color centers are essential for their experimental identification and have key implications for use of these systems in quantum information science.

In recent years significant experimental advances in nano-scale fabrication techniques and in available light sources have opened the possibility to study a vast set of novel light-matter interaction scenarios, including strong coupling cases. In many situations nowadays, classical electromagnetic modeling is insufficient as quantum effects, both in matter and light, start to play an important role. Instead, a fully self-consistent and microscopic coupling of light and matter becomes necessary. We provide here a critical review of current approaches for electromagnetic modeling, highlighting their limitations. We show how to overcome these limitations by introducing the theoretical foundations and the implementation details of a density-functional approach for coupled photons, electrons, and effective nuclei in non-relativistic quantum electrodynamics. Starting point of the formalism is a generalization of the Pauli–Fierz field theory for which we establish a one-to-one correspondence between external fields and internal variables. Based on this correspondence, we introduce a Kohn-Sham construction which provides a computationally feasible approach for ab-initio light-matter interactions. In the mean-field limit, the formalism reduces to coupled Ehrenfest–Maxwell–Pauli–Kohn–Sham equations. We present an implementation of the approach in the real-space real-time code Octopus using the Riemann–Silberstein formulation of classical electrodynamics to rewrite Maxwell's equations in Schrödinger form. This allows us to use existing very efficient time-evolution algorithms developed for quantum-mechanical systems also for Maxwell's equations. We show how to couple the time-evolution of the electromagnetic fields self-consistently with the quantum time-evolution of the electrons and nuclei. This approach is ideally suited for applications in nano-optics, nano-plasmonics, (photo) electrocatalysis, light-matter coupling in 2D materials, cases where laser pulses carry orbital angular momentum, or light-tailored chemical reactions in optical cavities just to name but a few.