Publications

We present a low-scaling algorithm for the random phase approximation (RPA) with

The Holstein Hamiltonian describes itinerant electrons whose site density couples to local phonon degrees of freedom. In the single site limit, at half-filling, the electron-phonon coupling results in a double well structure for the lattice displacement, favoring empty or doubly occupied sites. In two dimensions, and on a bipartite lattice in d ≥2, an intersite hopping causes these doubly occupied and empty sites to alternate in a charge density wave (CDW) pattern when the temperature is lowered. Because a discrete symmetry is broken, this occurs in a conventional second-order transition at finite T

We introduce the time-dependent ghost Gutzwiller approximation (td-gGA), a non-equilibrium extension of the ghost Gutzwiller approximation (gGA), a powerful variational approach which systematically improves on the standard Gutzwiller method by including auxiliary degrees of freedom. We demonstrate the effectiveness of td-gGA by studying the quench dynamics of the single-band Hubbard model as a function of the number of auxiliary parameters. Our results show that td-gGA captures the relaxation of local observables, in contrast with the time-dependent Gutzwiller method. This systematic and qualitative improvement leads to an accuracy comparable with time-dependent Dynamical Mean-Field Theory which comes at a much lower computational cost. These findings suggest that td-gGA has the potential to enable extensive and accurate theoretical investigations of multi-orbital correlated electron systems in nonequilibrium situations, with potential applications in the field of quantum control, Mott solar cells, and other areas where an accurate account of the non-equilibrium properties of strongly interacting quantum systems is required.

Angle-resolved photoemission spectroscopy (ARPES) is a method that measures orbital and band structure contrast through the momentum distribution of photoelectrons. Its simplest interpretation is obtained in the plane-wave approximation, according to which photoelectrons propagate freely to the detector.

Single-particle cryo-electron microscopy (cryo-EM) is a technique that takes projection images of biomolecules frozen at cryogenic temperatures. A major advantage of this technique is its ability to image single biomolecules in heterogeneous conformations. While this poses a challenge for data analysis, recent algorithmic advances have enabled the recovery of heterogeneous conformations from the noisy imaging data. Here, we review methods for the reconstruction and heterogeneity analysis of cryo-EM images, ranging from linear-transformation-based methods to nonlinear deep generative models. We overview the dimensionality-reduction techniques used in heterogeneous 3D reconstruction methods and specify what information each method can infer from the data. Then, we review the methods that use cryo-EM images to estimate probability distributions over conformations in reduced subspaces or predefined by atomistic simulations. We conclude with the ongoing challenges for the cryo-EM community.

Single-particle cryo-electron microscopy (cryo-EM) is a technique that takes projection images of biomolecules frozen at cryogenic temperatures. A major advantage of this technique is its ability to image single biomolecules in heterogeneous conformations. While this poses a challenge for data analysis, recent algorithmic advances have enabled the recovery of heterogeneous conformations from the noisy imaging data. Here, we review methods for the reconstruction and heterogeneity analysis of cryo-EM images, ranging from linear-transformation-based methods to nonlinear deep generative models. We overview the dimensionality-reduction techniques used in heterogeneous 3D reconstruction methods and specify what information each method can infer from the data. Then, we review the methods that use cryo-EM images to estimate probability distributions over conformations in reduced subspaces or predefined by atomistic simulations. We conclude with the ongoing challenges for the cryo-EM community.

Quantum computers have emerged as a promising platform to simulate the strong electron correlation that is crucial to catalysis and photochemistry. However, owing to the choice of a trial wave function employed in the popular hybrid quantum-classical variational quantum eigensolver (VQE) algorithm, the accurate simulation is restricted to certain classes of correlated phenomena. Herein, we combine the spin-flip (SF) formalism with the unitary coupled cluster with singles and doubles (UCCSD) method via the quantum equation-of-motion (qEOM) approach to allow for an efficient simulation of a large family of strongly correlated problems. In particular, we show that the developed qEOM-SF-UCCSD/VQE method outperforms its UCCSD/VQE counterpart for simulation of the cis-trans isomerization of ethylene and the automerization of cyclobutadiene. The predicted qEOM-SF-UCCSD/VQE barrier heights for these two problems are in a good agreement with the experimentally determined values. The methodological developments presented herein will further stimulate investigation of this approach for the simulation of other types of correlated/entangled phenomena on a quantum computer.

Sparse high-dimensional functions have arisen as a rich framework to study the behavior of gradient-descent methods using shallow neural networks, showcasing their ability to perform feature learning beyond linear models. Amongst those functions, the simplest are single-index models $f(x) = \phi( x \cdot \theta^*)$, where the labels are generated by an arbitrary non-linear scalar link function $\phi$ applied to an unknown one-dimensional projection $\theta^*$ of the input data. By focusing on Gaussian data, several recent works have built a remarkable picture, where the so-called information exponent (related to the regularity of the link function) controls the required sample complexity. In essence, these tools exploit the stability and spherical symmetry of Gaussian distributions. In this work, building from the framework of \cite{arous2020online}, we explore extensions of this picture beyond the Gaussian setting, where both stability or symmetry might be violated. Focusing on the planted setting where $\phi$ is known, our main results establish that Stochastic Gradient Descent can efficiently recover the unknown direction $\theta^*$ in the high-dimensional regime, under assumptions that extend previous works \cite{yehudai2020learning,wu2022learning}.

In this paper, we introduce a sketching algorithm for constructing a tensor train representation of a probability density from its samples. Our method deviates from the standard recursive SVD-based procedure for constructing a tensor train. Instead, we formulate and solve a sequence of small linear systems for the individual tensor train cores. This approach can avoid the curse of dimensionality that threatens both the algorithmic and sample complexities of the recovery problem. Specifically, for Markov models under natural conditions, we prove that the tensor cores can be recovered with a sample complexity that scales logarithmically in the dimensionality. Finally, we illustrate the performance of the method with several numerical experiments.

Resolving chromatin-remodeling-linked gene expression changes at cell-type resolution is important for understanding disease states. Here we describe MAGICAL (Multiome Accessibility Gene Integration Calling and Looping), a hierarchical Bayesian approach that leverages paired single-cell RNA sequencing and single-cell transposase-accessible chromatin sequencing from different conditions to map disease-associated transcription factors, chromatin sites, and genes as regulatory circuits. By simultaneously modeling signal variation across cells and conditions in both omics data types, MAGICAL achieved high accuracy on circuit inference. We applied MAGICAL to study Staphylococcus aureus sepsis from peripheral blood mononuclear single-cell data that we generated from subjects with bloodstream infection and uninfected controls. MAGICAL identified sepsis-associated regulatory circuits predominantly in CD14 monocytes, known to be activated by bacterial sepsis. We addressed the challenging problem of distinguishing host regulatory circuit responses to methicillin-resistant and methicillin-susceptible S. aureus infections. Although differential expression analysis failed to show predictive value, MAGICAL identified epigenetic circuit biomarkers that distinguished methicillin-resistant from methicillin-susceptible S. aureus infections.