Publications

The 2024 New York City Integrative Structural Biology Symposium focused on understanding the challenges and opportunities of applying integrative structural biology techniques to biomedical research. To foster connections across different fields and disciplines, this symposium offered hands-on workshops. These workshops provided attendees an opportunity to use state-of-the-art instrumentation and software programs in the structural biology sciences that they may not have access to in their own laboratories. Moreover, the symposium provided a vibrant environment for scientific discourse where cutting-edge research talks presented the trends in integrative structural biology in the New York City area. In this TrendsTalk, the symposium organizers bring to you the highlights of the workshops and scientific sections from this event.

Notwithstanding the evidence against them, classical variational phase-field models continue to be used and pursued in an attempt to describe fracture nucleation in elastic brittle materials. In this context, the main objective of this paper is to provide a comprehensive review of the existing evidence against such a class of models as descriptors of fracture nucleation. To that end, a review is first given of the plethora of experimental observations of fracture nucleation in nominally elastic brittle materials under quasi-static loading conditions, as well as of classical variational phase-field models, without and with energy splits. These models are then confronted with the experimental observations. The conclusion is that they cannot possibly describe fracture nucleation in general. This because classical variational phase-field models cannot account for material strength as an independent macroscopic material property. The last part of the paper includes a brief summary of a class of phase-field models that can describe fracture nucleation. It also provides a discussion of how pervasively material strength has been overlooked in the analysis of fracture at large, as well as an outlook into the modeling of fracture nucleation beyond the basic setting of elastic brittle materials.

The two-dimensional (2D) homogeneous electron gas (HEG) is a fundamental model in quantum many-body physics. It is important to theoretical and computational studies, where exchange-correlation energies computed in it serve as the foundation for density-functional calculations. It is also of direct relevance to a variety of experimental settings, especially with the rapid recent growth in 2D materials and moiré systems. In these experiments, metallic gates are often present, which screen the Coulomb interaction between electrons. The effect of the screening can qualitatively change the behavior of the 2D HEG, and requires accurate many-body computations to capture. In this work, we perform state-of-the-art diffusion Monte Carlo (DMC) calculations in the 2D HEG subjected to symmetric dual-gate screening. We systematically compute the correlation energy across a range of densities and gate separations for both spin unpolarized and fully polarized systems. A global fit is obtained for the correlation energy, using these data and imposing various limiting behaviors obtained from perturbation analysis. The new functional will allow density-functional calculations to be performed for a variety of realistic experimental setups which can accurately account for the presence of gates. We also investigate how the gate screening affects the bulk modulus, pair correlation function, and the structure factor of the 2D HEG, which can potentially be probed in experiments.

The two-dimensional (2D) homogeneous electron gas (HEG) is a fundamental model in quantum many-body physics. It is important to theoretical and computational studies, where exchange-correlation energies computed in it serve as the foundation for density-functional calculations. It is also of direct relevance to a variety of experimental settings, especially with the rapid recent growth in 2D materials and moiré systems. In these experiments, metallic gates are often present, which screen the Coulomb interaction between electrons. The effect of the screening can qualitatively change the behavior of the 2D HEG, and requires accurate many-body computations to capture. In this work, we perform state-of-the-art diffusion Monte Carlo (DMC) calculations in the 2D HEG subjected to symmetric dual-gate screening. We systematically compute the correlation energy across a range of densities and gate separations for both spin unpolarized and fully polarized systems. A global fit is obtained for the correlation energy, using these data and imposing various limiting behaviors obtained from perturbation analysis. The new functional will allow density-functional calculations to be performed for a variety of realistic experimental setups which can accurately account for the presence of gates. We also investigate how the gate screening affects the bulk modulus, pair correlation function, and the structure factor of the 2D HEG, which can potentially be probed in experiments.

We introduce a Fourier-based fast algorithm for Gaussian process regression in low dimensions. It approximates a translationally invariant covariance kernel by complex exponentials on an equispaced Cartesian frequency grid of \(M\) nodes. This results in a weight-space \(M\times M\) system matrix with Toeplitz structure, which can thus be applied to a vector in \({\mathcal O}(M \log{M})\) operations via the fast Fourier transform (FFT), independent of the number of data points \(N\). The linear system can be set up in \({\mathcal O}(N+M \log{M})\) operations using nonuniform FFTs. This enables efficient massive-scale regression via an iterative solver, even for kernels with fat-tailed spectral densities (large \(M\)). We provide bounds on both kernel approximation and posterior mean errors. Numerical experiments for squared-exponential and Matérn kernels in one, two, and three dimensions often show 1–2 orders of magnitude acceleration over state-of-the-art rank-structured solvers at comparable accuracy. Our method allows two-dimensional Matérn-\(\frac{3}{2}\) regression from \(N=10^9\) data points to be performed in two minutes on a standard desktop, with posterior mean accuracy \(10^{-3}\). This opens up spatial statistics applications 100 times larger than previously possible.

Extracting conformational heterogeneity from cryo-electron microscopy (cryo-EM) images is particularly challenging for flexible biomolecules, where traditional 3D classification approaches often fail. Over the past few decades, advancements in experimental and computational techniques have been made to tackle this challenge, especially Bayesian-based approaches that provide physically interpretable insights into cryo-EM heterogeneity. To reduce the computational cost for Bayesian approaches, and building upon previously developed Fourier–Bessel image-representation methods, we created CryoLike, computationally efficient software for evaluating image-to-structure (or image-to-volume) likelihoods across large image data sets, packaged in a user-friendly Python workflow.

Notwithstanding the evidence against them, classical variational phase-field models continue to be used and pursued in an attempt to describe fracture nucleation in elastic brittle materials. In this context, the main objective of this paper is to provide a comprehensive review of the existing evidence against such a class of models as descriptors of fracture nucleation. To that end, a review is first given of the plethora of experimental observations of fracture nucleation in nominally elastic brittle materials under quasi-static loading conditions, as well as of classical variational phase-field models, without and with energy splits. These models are then confronted with the experimental observations. The conclusion is that they cannot possibly describe fracture nucleation in general. This because classical variational phase-field models cannot account for material strength as an independent macroscopic material property. The last part of the paper includes a brief summary of a class of phase-field models that can describe fracture nucleation. It also provides a discussion of how pervasively material strength has been overlooked in the analysis of fracture at large, as well as an outlook into the modeling of fracture nucleation beyond the basic setting of elastic brittle materials.

The discovery of superconductivity in twisted bilayer and twisted trilayer graphene has generated tremendous interest. The key feature of these systems is an interplay between interlayer coupling and a moiré superlattice that gives rise to low-energy flat bands with strong correlations. Flat bands can also be induced by moiré patterns in lattice-mismatched and or twisted heterostructures of other two-dimensional materials such as transition metal dichalcogenides (TMDs). Although a wide range of correlated phenomenon have indeed been observed in the moiré TMDs, robust demonstration of superconductivity has remained absent. Here we report superconductivity in 5 degree twisted bilayer WSe

We solve a model of electrons with Hubbard-U Coulomb repulsion and a random Yukawa coupling to a two-dimensional bosonic bath, using an extended dynamical mean field theory scheme. Our model exhibits a quantum critical point, at which the repulsive component of the electron interactions strongly enhances the effects of the quantum critical bosonic fluctuations on the electrons, leading to a breakdown of Fermi liquid physics and the formation of a strange metal with `Planckian' (O(k

We present a generalization of the phaseless auxiliary-field quantum Monte Carlo (AFQMC) method to cavity quantum-electrodynamical (QED) matter systems. The method can be formulated in both the Coulomb and the dipole gauge. We verify its accuracy by benchmarking calculations on a set of small molecules against full configuration interaction and state-of-the-art QED coupled cluster (QED-CCSD) calculations. Our results show that (i) gauge invariance can be achieved within correlation-consistent Gaussian basis sets, (ii) the accuracy of QED-CCSD can be enhanced significantly by adding the standard perturbative triples correction without light-matter coupling, and (iii) there is a straightforward way to evaluate the differential expression for the photon occupation number that works in any gauge. The high accuracy and favorable computational scaling of our AFQMC approach will enable a broad range of applications. Besides polaritonic chemistry, the method opens a way to simulate extended QED matter systems.