Publications

Transcriptional programming of the innate immune response is pivotal for host protection. However, the transcriptional mechanisms that link pathogen sensing with innate activation remain poorly understood. During HIV-1 infection, human dendritic cells (DCs) can detect the virus through an innate sensing pathway, leading to antiviral interferon and DC maturation. Here, we develop an iterative experimental and computational approach to map the HIV-1 innate response circuitry in monocyte-derived DCs (MDDCs). By integrating genome-wide chromatin accessibility with expression kinetics, we infer a gene regulatory network that links 542 transcription factors with 21,862 target genes. We observe that an interferon response is required, yet insufficient, to drive MDDC maturation and identify PRDM1 and RARA as essential regulators of the interferon response and MDDC maturation, respectively. Our work provides a resource for interrogation of regulators of HIV replication and innate immunity, highlighting complexity and cooperativity in the regulatory circuit controlling the response to infection.

Transition metal complexes are ubiquitous in biology and chemical catalysis, yet they remain difficult to accurately describe with ab initio methods due to the presence of a large degree of dynamic electron correlation, and, in some cases, strong static correlation which results from a manifold of low-lying states. Progress has been hindered by a scarcity of high quality gas-phase experimental data, while exact ab initio predictions are usually computationally unaffordable due to the large size of the systems. In this work, we present a data set of 34 3d metal-containing complexes with gas-phase ligand-dissociation energies that have reported uncertainties of $\leq$ 2 kcal/mol. We perform all-electron phaseless auxiliary-field quantum Monte Carlo (ph-AFQMC) utilizing multi-determinant trial wavefunctions selected by a blackbox procedure. We compare the results with those from DFT with various functionals, and DLPNO-CCSD(T). We find MAE of 1.09 $\pm$ 0.28 kcal/mol for our best ph-AFQMC method, vs 2.89 kcal/mol for DLPNO-CCSD(T) and 1.57 - 3.87 kcal/mol for DFT. We find maximum errors of 2.96 $\pm$ 1.71 kcal/mol for our best ph-AFQMC method, vs 9.15 kcal/mol for DLPNO-CCSD(T) and 5.98 - 13.69 kcal/mol for DFT. The reasonable performance of several functionals is in stark contrast to the much poorer accuracy previously demonstrated for diatomics, suggesting a moderation in electron correlation due to ligand coordination. However, the unpredictably large errors for a small subset of cases with both DFT and DLPNO-CCSD(T) leave cause for concern, especially due to the unreliability of common multi-reference indicators. In contrast, the robust and, in principle, systematically improvable results of ph-AFQMC for these realistic complexes establish it as a useful tool for elucidating the electronic structure of transition metal-containing complexes and predicting their gas-phase properties.

The recently published GWTC-1 - a journal article summarizing the search for gravitational waves (GWs) from coalescing compact binaries in data produced by the LIGO-Virgo network of ground-based detectors during their first and second observing runs - quoted estimates for the rates of binary neutron star, neutron star black hole binary, and binary black hole mergers, as well as assigned probabilities of astrophysical origin for various significant and marginal GW candidate events. In this paper, we delineate the formalism used to compute these rates and probabilities, which assumes that triggers above a low ranking statistic threshold, whether of terrestrial or astrophysical origin, occur as independent Poisson processes. In particular, we include an arbitrary number of astrophysical categories by redistributing, via mass-based template weighting, the foreground probabilities of candidate events, across source classes. We evaluate this formalism on synthetic GW data, and demonstrate that this method works well for the kind of GW signals observed during the first and second observing runs.

The evaluation of partition functions is a central problem in statistical physics. For lattice systems and other discrete models the partition function may be expressed as the contraction of a tensor network. Unfortunately computing such contractions is difficult, and many methods to make this tractable require periodic or otherwise structured networks. Here I present a new algorithm for contracting unstructured tensor networks. This method makes no assumptions about the structure of the network and performs well in both structured and unstructured cases so long as the correlation structure is local.

Superconductivity in organic conductors is often tuned by the application of chemical or external pressure. With this type of tuning, orbital overlaps and electronic bandwidths are manipulated, whilst the properties of the molecular building blocks remain virtually unperturbed.Here, we show that the excitation of local molecular vibrations in the charge-transfer salt κ−(BEDT−TTF)2Cu[N(CN)2]Br induces a colossal increase in carrier mobility and the opening of a superconducting-like optical gap. Both features track the density of quasi-particles of the equilibrium metal, and can be achieved up to a characteristic coherence temperature T∗≊50K, far higher than the equilibrium transition temperature TC=12.5K. Notably, the large optical gap achieved by photo-excitation is not observed in the equilibrium superconductor, pointing to a light induced state that is different from that obtained by cooling. First-principle calculations and model Hamiltonian dynamics predict a transient state with long-range pairing correlations, providing a possible physical scenario for photo-molecular superconductivity.

Aiming to combine density functional theory (DFT) and wave-function theory, we study a mapping from the many-body interacting system to an effectively interacting Kohn-Sham system instead of a noninteracting Kohn-Sham system. Because a ground state of effectively interacting systems requires having a solution for the correlated many-body wave functions, this provides a natural framework to many-body wave-function theories such as the configuration interaction and the coupled-cluster method in the formal theoretical framework of DFT. Employing simple one-dimensional two-electron systems—namely, the one-dimensional helium atom, the hydrogen molecule, and the heteronuclear diatomic molecule—we investigate properties of many-body wave functions and exact exchange-correlation potentials of effectively interacting Kohn-Sham systems. As a result, we find that the asymptotic behavior of the exact exchange-correlation potential can be controlled by optimizing that of the effective interaction. Furthermore, the typical features of the exact noninteracting Kohn-Sham system, namely, a spiky feature and a step feature in the exchange-correlation potential for the molecular dissociation limit, can be suppressed by a proper choice of the effective interaction. These findings open a possibility to construct numerically robust and efficient exchange-correlation potentials and functionals based on the effectively interacting Kohn-Sham scheme.

M dwarfs have enormous potential for our understanding of structure and formation on both Galactic and exoplanetary scales through their properties and compositions. However, current atmosphere models have limited ability to reproduce spectral features in stars at the coolest temperatures (Teff<4200K) and to fully exploit the information content of current and upcoming large-scale spectroscopic surveys. Here we present a catalog of spectroscopic temperatures, metallicities, and spectral types for 5875 M dwarfs in the Apache Point Observatory Galactic Evolution Experiment (APOGEE) and Gaia DR2 surveys using The Cannon: a flexible, data-driven spectral-modeling and parameter-inference framework demonstrated to estimate stellar-parameter labels (Teff, logg, [Fe/H], and detailed abundances) to high precision. Using a training sample of 87 M dwarfs with optically derived labels spanning 2860

We show that in a model of a metal photoexcited by a transient pump pulse resonant with a phonon mode, the absolute dc conductivity may become negative, depending on the interplay between the electronic structure, the phonon frequency, and the pump intensity. The analysis includes the effects of inelastic scattering and thermal relaxation. Results for the time evolution of the negative conductivity state are presented; the associated nonequilibrium physics may persist for long times after the pulse. Our findings provide a theoretical justification for previously proposed phenomenology and indicate new routes to the generation and exploration of intrinsically nonequilibrium states.

The hemocyanin protein binds and transports molecular oxygen via two copper atoms at its core. The singlet state of the Cu2O2 core is thought to be stabilised by a superexchange pathway, but detailed in situ computational analysis is complicated by the multi-reference character of the electronic ground state. Here, electronic correlation effects in the functional site of hemocyanin are investigated using a novel approach, treating the localised copper 3d electrons with cluster dynamical mean field theory. This enables us to account for dynamical and multi-reference quantum mechanics, capturing valence and spin fluctuations of the 3d electrons. Our approach explains the stabilisation of the experimentally observed di-Cu singlet for the butterflied Cu2O2 core, with localised charge and incoherent scattering processes across the oxo-bridge that prevent long-lived charge excitations. This suggests that the magnetic structure of hemocyanin is largely influenced by the many-body corrections.

We theoretically study the low energy electromagnetic response of BCS type superconductors focusing on propagating collective modes that are accessible with THz near field optics. The interesting frequency and momentum range is ω<Δ and q<1/ξ where Δ is the gap and ξ is the coherence length. We show that it is possible to observe the superfluid plasmons, amplitude (Higgs) modes, Bardasis-Schrieffer modes and Carlson-Goldman modes using THz near field technique, although none of these modes couple linearly to far field radiation. Coupling of THz near field radiation to the amplitude mode requires particle-hole symmetry breaking while coupling to the Bardasis-Schrieffer mode does not and is typically stronger. The Carlson-Goldman mode appears in the near field reflection coefficient as a weak feature in the sub-THz frequency range. In a system of two superconducting layers with nanometer scale separation, an acoustic phase mode appears as the antisymmetric plasmon mode of the system. This mode leads to well defined resonance peaks in the near-field THz response and has strong anti crossings with the Bardasis-Schrieffer mode and amplitude mode, enhancing their response. In a slab of layered superconductor such as the high Tc compounds, which can be viewed as a natural optical cavity, many branches of propagating Josephson plasmon modes couple to the THz near field radiation.