Publications

DNA methylation comprises a cumulative record of lifetime exposures superimposed on genetically determined markers. Little is known about methylation dynamics in humans following an acute perturbation, such as infection. We characterized the temporal trajectory of blood epigenetic remodeling in 133 participants in a prospective study of young adults before, during, and after asymptomatic and mildly symptomatic SARS-CoV-2 infection. The differential methylation caused by asymptomatic or mildly symptomatic infections was indistinguishable. While differential gene expression largely returned to baseline levels after the virus became undetectable, some differentially methylated sites persisted for months of follow-up, with a pattern resembling autoimmune or inflammatory disease. We leveraged these responses to construct methylation-based machine learning models that distinguished samples from pre-, during-, and postinfection time periods, and quantitatively predicted the time since infection. The clinical trajectory in the young adults and in a diverse cohort with more severe outcomes was predicted by the similarity of methylation before or early after SARS-CoV-2 infection to the model-defined postinfection state. Unlike the phenomenon of trained immunity, the postacute SARS-CoV-2 epigenetic landscape we identify is antiprotective.

Recently, the stochastic Polyak step size (SPS) has emerged as a competitive adaptive step size scheme for stochastic gradient descent. Here we develop ProxSPS, a proximal variant of SPS that can handle regularization terms. Developing a proximal variant of SPS is particularly important, since SPS requires a lower bound of the objective function to work well. When the objective function is the sum of a loss and a regularizer, available estimates of a lower bound of the sum can be loose. In contrast, ProxSPS only requires a lower bound for the loss which is often readily available. As a consequence, we show that ProxSPS is easier to tune and more stable in the presence of regularization. Furthermore for image classification tasks, ProxSPS performs as well as AdamW with little to no tuning, and results in a network with smaller weight parameters. We also provide an extensive convergence analysis for ProxSPS that includes the non-smooth, smooth, weakly convex and strongly convex setting.

Deep neural networks can learn powerful prior probability models for images, as evidenced by the high-quality generations obtained with recent score-based diffusion methods. But the means by which these networks capture complex global statistical structure, apparently without suffering from the curse of dimensionality, remain a mystery. To study this, we incorporate diffusion methods into a multi-scale decomposition, reducing dimensionality by assuming a stationary local Markov model for wavelet coefficients conditioned on coarser-scale coefficients. We instantiate this model using convolutional neural networks (CNNs) with local receptive fields, which enforce both the stationarity and Markov properties. Global structures are captured using a CNN with receptive fields covering the entire (but small) low-pass image. We test this model on a dataset of face images, which are highly non-stationary and contain large-scale geometric structures. Remarkably, denoising, super-resolution, and image synthesis results all demonstrate that these structures can be captured with significantly smaller conditioning neighborhoods than required by a Markov model implemented in the pixel domain. Our results show that score estimation for large complex images can be reduced to low-dimensional Markov conditional models across scales, alleviating the curse of dimensionality.

Life is a nonequilibrium phenomenon: Metabolism provides a continuous supply of energy that drives nearly all cellular processes. However, very little is known about how much energy different cellular processes use, i.e., their energetic costs. The most direct experimental measurements of these costs involve modulating the activity of cellular processes and determining the resulting changes in energetic fluxes. In this review, we present a flux balance framework to aid in the design and interpretation of such experiments and discuss the challenges associated with measuring the relevant metabolic fluxes. We then describe selected techniques that enable measurement of these fluxes. Finally, we review prior experimental and theoretical work that has employed techniques from biochemistry and nonequilibrium physics to determine the energetic costs of cellular processes.

Deep neural networks can learn powerful prior probability models for images, as evidenced by the high-quality generations obtained with recent score-based diffusion methods. But the means by which these networks capture complex global statistical structure, apparently without suffering from the curse of dimensionality, remain a mystery. To study this, we incorporate diffusion methods into a multi-scale decomposition, reducing dimensionality by assuming a stationary local Markov model for wavelet coefficients conditioned on coarser-scale coefficients. We instantiate this model using convolutional neural networks (CNNs) with local receptive fields, which enforce both the stationarity and Markov properties. Global structures are captured using a CNN with receptive fields covering the entire (but small) low-pass image. We test this model on a dataset of face images, which are highly non-stationary and contain large-scale geometric structures.
Remarkably, denoising, super-resolution, and image synthesis results all demonstrate that these structures can be captured with significantly smaller conditioning neighborhoods than required by a Markov model implemented in the pixel domain. Our results show that score estimation for large complex images can be reduced to low-dimensional Markov conditional models across scales, alleviating the curse of dimensionality.

The accurate computation of forces and other energy derivatives has been a long-standing challenge for quantum Monte Carlo methods. A number of technical obstacles contribute to this challenge. We discuss how these obstacles can be removed with the auxiliary-field quantum Monte Carlo (AFQMC) approach. AFQMC is a general, high-accuracy, many-body total-energy method for molecules and solids. The implementation of back-propagation for pure estimators allows direct calculation of gradients of the energy via the Hellmann-Feynman theorem. A planewave basis with norm-conserving pseudopotentials is used for the study of periodic bulk materials. Completeness of the planewave basis minimizes the effect of so-called Pulay terms. The ionic pseudopotentials, which can be incorporated in AFQMC in exactly the same manner as in standard independent-electron methods, regulate the force and stress estimators and eliminate any potential divergence of the Monte Carlo variances. The resulting approach allows applications of full geometry optimizations in bulk materials. It also paves the way for many-body computations of the phonon spectrum in solids.

Using a density-functional theory plus dynamical mean-field theory methodology, we compute the many-body electronic structure and optical conductivity of NdNiO

Understanding carrier trapping in solids has proven key to semiconductor technologies but observations thus far have relied on ensembles of point defects, where the impact of neighboring traps or carrier screening is often important. Here, we investigate the capture of photo-generated holes by an individual negatively-charged nitrogen-vacancy (NV) center in diamond at room temperature. Using an externally gated potential to minimize space-charge effects, we find the capture probability under electric fields of variable sign and amplitude shows an asymmetric-bell-shaped response with maximum at zero voltage. To interpret these observations, we run semi-classical Monte Carlo simulations modeling carrier trapping through a cascade process of phonon emission, and obtain electric-field-dependent capture probabilities in good agreement with experiment. Since the mechanisms at play are insensitive to the trap characteristics, the capture cross sections we observe - largely exceeding those derived from ensemble measurements - should also be present in materials platforms other than diamond.

Electromagnetic fields can be confined in the presence of metal nanostructures. Recently, subnanometer scale confinement has been demonstrated to occur at atomic protrusions on plasmonic nanostructures. Such an extreme field may dominate atomic-scale light--matter interactions in

The microscopic mechanism of the light-matter interactions that induce orbital angular momentum (OAM) in electromagnetic fields is not thoroughly understood. In this work, we employ Archimedean spiral vortex generators in time-resolved numerical simulations using the Octopus code to observe the behind-the-scenes of OAM generation. We send a perfect circularly-polarized plane-wave light onto plasmonic optical vortex generators and observe the resulting twisted light formation with complete spatio-temporal information. In agreement with previous works, we find that emission from the plasmonic spiral branches shapes the vortex-like structure and governs the OAM generation in the outgoing electromagnetic field. To characterize the generated beam further, we emulate the emission from vortex generators with current emitters preserving the spiral geometry. We subject a point-particle system to the generated field and record the orbital angular momentum transfer between the electromagnetic field and the point particle. Finally, we probe the OAM density locally by studying the induced classical trajectory of point particles, which provides further insight into the spatio-temporal features of the induced OAM.