Publications

The interplay between electron-electron correlations and disorder has been a central theme of condensed matter physics over the last several decades, with particular interest in the possibility that interactions might cause delocalization of an Anderson insulator into a metallic state, and the disrupting effects of randomness on magnetic order and the Mott phase. Here we extend this physics to explore electron-phonon interactions and show, via exact quantum Monte Carlo simulations, that the suppression of the charge density wave correlations in the half-filled Holstein model by disorder can stabilize a superconducting phase. Our simulations thus capture qualitatively the suppression of charge ordered phases and emergent superconductivity recently seen experimentally.

We present accurate many-body results of the electronic densities in several solid materials, including Si, NaCl, and Cu. These results are obtained using the ab initio auxiliary-field quantum Monte Carlo (AFQMC) method working in a plane-wave basis with norm-conserving, multiple-projector pseudopotentials. AFQMC has been shown to be an excellent many-body total energy method. Computation of observables and correlation functions other than the ground-state energy requires back-propagation, whose adaption and implementation in the plane-wave basis AFQMC framework are discussed in the present paper. This development allows us to compute correlation functions, electronic densities and interatomic forces, paving the way for geometry optimizations and calculations of thermodynamic properties in solids. Finite supercell size effects are considerably more subtle in the many-body framework than in independent-electron calculations. We analyze the convergence of the electronic density, and obtain best estimates for the thermodynamic limit. The densities from several typical density functionals are benchmarked against our near-exact results. The electronic densities we have obtained can also be used to help construct improved density functionals.

Modern studies of embryogenesis are increasingly quantitative, powered by rapid advances in imaging, sequencing, and genome manipulation technologies. Deriving mechanistic insights from the complex datasets generated by these new tools requires systematic approaches for data-driven analysis of the underlying developmental processes. Here we use data from our work on signal-dependent gene repression in the fruit fly, Drosophila melanogaster, to illustrate how computational models can compactly summarize quantitative results of live imaging, chromatin immunoprecipitation, and optogenetic perturbation experiments. The presented computational approach is ideally suited for integrating rapidly accumulating quantitative data and for guiding future studies of embryogenesis.

In vivo calcium imaging through microendoscopic lenses enables imaging of neuronal populations deep within the brains of freely moving animals. Previously, a constrained matrix factorization approach (CNMF-E) has been suggested to extract single-neuronal activity from microendoscopic data. However, this approach relies on offline batch processing of the entire video data and is demanding both in terms of computing and memory requirements. These drawbacks prevent its applicability to the analysis of large datasets and closed-loop experimental settings. Here we address both issues by introducing two different online algorithms for extracting neuronal activity from streaming microendoscopic data. Our first algorithm, OnACID-E, presents an online adaptation of the CNMF-E algorithm, which dramatically reduces its memory and computation requirements. Our second algorithm proposes a convolution-based background model for microendoscopic data that enables even faster (real time) processing. Our approach is modular and can be combined with existing online motion artifact correction and activity deconvolution methods to provide a highly scalable pipeline for microendoscopic data analysis. We apply our algorithms on four previously published typical experimental datasets and show that they yield similar high-quality results as the popular offline approach, but outperform it with regard to computing time and memory requirements. They can be used instead of CNMF-E to process pre-recorded data with boosted speeds and dramatically reduced memory requirements. Further, they newly enable online analysis of live-streaming data even on a laptop.

The mRNA-1273 vaccine was recently determined to be effective against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from interim Phase 3 results. Human studies, however, cannot provide the controlled response to infection and complex immunological insight that are only possible with preclinical studies. Hamsters are the only model that reliably exhibit more severe SARS-CoV-2 disease similar to hospitalized patients, making them pertinent for vaccine evaluation. We demonstrate that prime or prime-boost administration of mRNA-1273 in hamsters elicited robust neutralizing antibodies, ameliorated weight loss, suppressed SARS-CoV-2 replication in the airways, and better protected against disease at the highest prime-boost dose. Unlike in mice and non-human primates, mRNA-1273- mediated immunity was non-sterilizing and coincided with an anamnestic response. Single-cell RNA sequencing of lung tissue permitted high resolution analysis which is not possible in vaccinated humans. mRNA-1273 prevented inflammatory cell infiltration and the reduction of lymphocyte proportions, but enabled antiviral responses conducive to lung homeostasis. Surprisingly, infection triggered transcriptome programs in some types of immune cells from vaccinated hamsters that were shared, albeit attenuated, with mock-vaccinated hamsters. Our results support the use of mRNA-1273 in a two-dose schedule and provides insight into the potential responses within the lungs of vaccinated humans who are exposed to SARS-CoV-2.

We present a method to construct pseudo-BCS wave functions from the one-body density matrix. The resulting many-body wave function, which can be produced for any fermion systems, including those with purely repulsive interactions, has the form of a number-projected BCS form, or antisymmetrized germinal power (AGP). Such wave functions provide a better ansatz for correlated fermion systems than a single Slater determinant, and often better than a linear combination of Slater determinants (for example from a truncated active space calculation). We describe a procedure to build such a wave function conveniently from a given reduced density matrix of the system, rather than from a mean-field solution (which gives a Slater determinant for repulsive interactions). The pseudo-BCS wave function thus obtained reproduces the density matrix or minimizes the difference between the input and resulting density matrices. One application of the pseudo-BCS wave function is in auxiliary-field quantum Monte Carlo (AFQMC) calculations as the trial wave function to control the sign/phase problem. AFQMC is often among the most accurate general methods for correlated fermion systems. We show that the pseudo-BCS form further reduces the constraint bias and leads to improved accuracy compared to the usual Slater determinant trial wave functions, using the two-dimensional Hubbard model as an example. Furthermore, the pseudo-BCS trial wave function allows a new systematically improvable self-consistent approach, with pseudo-BCS trial wave function iteratively generated by AFQMC via the one-body density matrix.

Adhesion-mediated cell sorting has long been considered an organizing principle in developmental biology. While most computational models have emphasized the dynamics of segregation to fully sorted structures, cell sorting can also generate a plethora of transient, incompletely sorted states. The timescale of such states in experimental systems is unclear: if they are long-lived, they can be harnessed by development or engineered in synthetic tissues. Here, we use experiments and computational modeling to demonstrate how such structures can be systematically designed by quantitative control of cell composition. By varying the number of highly adhesive and less adhesive cells in multicellular aggregates, we find the cell-type ratio and total cell count control pattern formation, with resulting structures maintained for several days. Our work takes a step toward mapping the design space of self-assembling structures in development and provides guidance to the emerging field of shape engineering with synthetic biology.

Despite the strong genetic basis of psychiatric disorders, the underlying molecular mechanisms are largely unmapped. RNA-binding proteins (RBPs) are responsible for most post-transcriptional regulation, from splicing to translation to localization. RBPs thus act as key gatekeepers of cellular homeostasis, especially in the brain. However, quantifying the pathogenic contribution of noncoding variants impacting RBP target sites is challenging. Here, we leverage a deep learning approach that can accurately predict the RBP target site dysregulation effects of mutations and discover that RBP dysregulation is a principal contributor to psychiatric disorder risk. RBP dysregulation explains a substantial amount of heritability not captured by large-scale molecular quantitative trait loci studies and has a stronger impact than common coding region variants. We share the genome-wide profiles of RBP dysregulation, which we use to identify DDHD2 as a candidate schizophrenia risk gene. This resource provides a new analytical framework to connect the full range of RNA regulation to complex disease.

Despite the strong genetic basis of psychiatric disorders, the underlying molecular mechanisms are largely unmapped. RNA-binding proteins (RBPs) are responsible for most post-transcriptional regulation, from splicing to translation to localization. RBPs thus act as key gatekeepers of cellular homeostasis, especially in the brain. However, quantifying the pathogenic contribution of noncoding variants impacting RBP target sites is challenging. Here, we leverage a deep learning approach that can accurately predict the RBP target site dysregulation effects of mutations and discover that RBP dysregulation is a principal contributor to psychiatric disorder risk. RBP dysregulation explains a substantial amount of heritability not captured by large-scale molecular quantitative trait loci studies and has a stronger impact than common coding region variants. We share the genome-wide profiles of RBP dysregulation, which we use to identify DDHD2 as a candidate schizophrenia risk gene. This resource provides a new analytical framework to connect the full range of RNA regulation to complex disease.

Numerical methods for approximately solving partial differential equations (PDE) are at the core of scientific computing. Often, this requires high-resolution or adaptive discretization grids to capture relevant spatio-temporal features in the PDE solution, e.g., in applications like turbulence, combustion, and shock propagation. Numerical approximation also requires knowing the PDE in order to construct problem-specific discretizations. Systematically deriving such solution-adaptive discrete operators, however, is a current challenge. Here we present STENCIL-NET, an artificial neural network architecture for data-driven learning of problem- and resolution-specific local discretizations of nonlinear PDEs. STENCIL-NET achieves numerically stable discretization of the operators in an unknown nonlinear PDE by spatially and temporally adaptive parametric pooling on regular Cartesian grids, and by incorporating knowledge about discrete time integration. Knowing the actual PDE is not necessary, as solution data is sufficient to train the network to learn the discrete operators. A once-trained STENCIL-NET model can be used to predict solutions of the PDE on larger spatial domains and for longer times than it was trained for, hence addressing the problem of PDE-constrained extrapolation from data. To support this claim, we present numerical experiments on long-term forecasting of chaotic PDE solutions on coarse spatio-temporal grids. We also quantify the speed-up achieved by substituting base-line numerical methods with equation-free STENCIL-NET predictions on coarser grids with little compromise on accuracy.