Publications

An important but missing component in the application of the kernel independent fast multipole method (KIFMM) is the capability for flexibly and efficiently imposing singly, doubly, and triply periodic boundary conditions. In most popular packages such periodicities are imposed with the hierarchical repetition of periodic boxes, which may give an incorrect answer due to the conditional convergence of some kernel sums. Here we present an efficient method to properly impose periodic boundary conditions using a near-far splitting scheme. The near-field contribution is directly calculated with the KIFMM method, while the far-field contribution is calculated with a multipole-to-local (M2L) operator which is independent of the source and target point distribution. The M2L operator is constructed with the far-field portion of the kernel function to generate the far-field contribution with the downward equivalent source points in KIFMM. This method guarantees the sum of the near-field & far-field converge pointwise to results satisfying periodicity and compatibility conditions. The computational cost of the far-field calculation observes the same O(N) complexity as FMM and is designed to be small by reusing the data computed by KIFMM for the near-field. The far-field calculations require no additional control parameters, and observes the same theoretical error bound as KIFMM. We present accuracy and timing test results for the Laplace kernel in singly periodic domains and the Stokes velocity kernel in doubly and triply periodic domains.

We study the large source asymptotics of the generating functional in quantum field theory using the holographic renormalization group, and draw comparisons with the asymptotics of the Hopf characteristic function in fractal geometry. Based on the asymptotic behavior, we find a correspondence relating the Weyl anomaly and the fractal dimension of the Euclidean path integral measure. We are led to propose an equivalence between the logarithmic ultraviolet divergence of the Shannon entropy of this measure and the integrated Weyl anomaly, reminiscent of a known relation between logarithmic divergences of entanglement entropy and a central charge. It follows that the information dimension associated with the Euclidean path integral measure satisfies a c-theorem.

Two-dimensional materials equipped with strong spin–orbit coupling can display novel electronic, spintronic, and topological properties originating from the breaking of time or inversion symmetry. A lot of interest has focused on the valley degrees of freedom that can be used to encode binary information. By performing ab initio time-dependent density functional simulation on MoS2, here we show that the spin is not only locked to the valley momenta but strongly coupled to the optical E′′ phonon that lifts the lattice mirror symmetry. Once the phonon is pumped so as to break time-reversal symmetry, the resulting Floquet spectra of the phonon-dressed spins carry a net out-of-plane magnetization (≈0.024μB for single-phonon quantum) even though the original system is non-magnetic. This dichroic magnetic response of the valley states is general for all 2H semiconducting transition-metal dichalcogenides and can be probed and controlled by infrared coherent laser excitation.

The compositions of stars are a critical diagnostic tool for many topics in astronomy such as the evolution of our Galaxy, the formation of planets, and the uniqueness of the Sun. Previous spectroscopic measurements indicate a large intrinsic variation in the elemental abundance patterns of stars with similar overall metal content. However, systematic errors arising from inaccuracies in stellar models are known to be a limiting factor in such studies, and thus it is uncertain to what extent the observed diversity of stellar abundance patterns is real. Here we report the abundances of 30 elements with precisions of 2% for 79 Sun-like stars within 100 parsecs. Systematic errors are minimized in this study by focusing on solar twin stars and performing a line-by-line differential analysis using high-resolution, high-signal-to-noise spectra. We resolve [X/Fe] abundance trends in galactic chemical evolution at precisions of 10^-3 dex Gyr^-1 and reveal that stars with similar ages and metallicities have nearly identical abundance patterns. Contrary to previous results, we find that the ratios of carbon-to-oxygen and magnesium-to-silicon are homogeneous to within 10% throughout the solar neighborhood, implying that exoplanets may exhibit much less compositional diversity than previously thought. Finally, we demonstrate that the Sun has a subtle deficiency in refractory material relative to ~95% of solar twins, suggesting a possible signpost for planetary systems like our own.

Particle picking is a crucial first step in the computational pipeline of single-particle cryo-electron microscopy (cryo-EM). Selecting particles from the micrographs is difficult especially for small particles with low contrast. As high-resolution reconstruction typically requires hundreds of thousands of particles, manually picking that many particles is often too time-consuming. While semi-automated particle picking is currently a popular approach, it may suffer from introducing manual bias into the selection process. In addition, semi-automated particle picking is still somewhat time-consuming. This paper presents the APPLE (Automatic Particle Picking with Low user Effort) picker, a simple and novel approach for fast, accurate, and fully automatic particle picking. While our approach was inspired by template matching, it is completely template-free. This approach is evaluated on publicly available datasets containing micrographs of β-galactosidase and keyhole limpet hemocyanin projections.

The number of microbial and metagenomic studies has increased drastically due to advancements in next-generation sequencing-based measurement techniques. Statistical analysis and the validity of conclusions drawn from (time series) 16S rRNA and other metagenomic sequencing data is hampered by the presence of significant amount of noise and missing data (sampling zeros). Accounting uncertainty in microbiome data is often challenging due to the difficulty of obtaining biological replicates. Additionally, the compositional nature of current amplicon and metagenomic data differs from many other biological data types adding another challenge to the data analysis. To address these challenges in human microbiome research, we introduce a novel probabilistic approach to explicitly model overdispersion and sampling zeros by considering the temporal correlation between nearby time points using Gaussian Processes. The proposed Temporal Gaussian Process Model for Compositional Data Analysis (TGP-CODA) shows superior modeling performance compared to commonly used Dirichlet-multinomial, multinomial, and non-parametric regression models on real and synthetic data. We demonstrate that the nonreplicative nature of human gut microbiota studies can be partially overcome by our method with proper experimental design of dense temporal sampling. We also show that different modeling approaches have a strong impact on ecological interpretation of the data, such as stationarity, persistence, and environmental noise models. A Stan implementation of the proposed method is available under MIT license at

We present a theoretical investigation of the effects of correlations on the electronic structure of the Mott insulator Sr2IrO4 upon electron doping. A rapid collapse of the Mott gap upon doping is found, and the electronic structure displays a strong momentum-space differentiation at low doping level: The Fermi surface consists of pockets centered around (π/2,π/2), while a pseudogap opens near (π,0). Its physical origin is shown to be related to short-range spin correlations. The pseudogap closes upon increasing doping, but a differentiated regime characterized by a modulation of the spectral intensity along the Fermi surface persists to higher doping levels. These results, obtained within the cellular dynamical mean-field theory framework, are discussed in comparison to recent photoemission experiments and an overall good agreement is found.

Multiple stellar systems are ubiquitous in the Milky Way, but are often unresolved and seen as single objects in spectroscopic, photometric, and astrometric surveys. Yet, modeling them is essential for developing a full understanding of large surveys such as Gaia, and connecting them to stellar and Galactic models. In this paper we address this problem by jointly fitting the Gaia and 2MASS photometric and astrometric data using a data-driven Bayesian hierarchical model that includes populations of binary and trinary systems. This allows us to classify observations into singles, binaries, and trinaries, in a robust and efficient manner, without resorting to external models. We are able to identify multiple systems and, in some cases, make strong predictions for the properties of its unresolved stars. We will be able to compare such predictions with Gaia Data Release 4, which will contain astrometric identification and analysis of binary systems.