Publications

Many-body theories such as dynamical mean field theory (DMFT) have enabled the description of the electron exchange-correlation interactions that are missing in current density functional theory (DFT) calculations. However, there has been relatively little focus on the wavefunctions from these theories. We present the methodology of the newly developed Elk-TRIQS interface and how to calculate the DFT with DMFT (DFT+DMFT) wavefunctions, which can be used to calculate DFT+DMFT wavefunction dependent quantities. We illustrate this by calculating the electron localized function (ELF) in monolayer SrVO

The three-dimensional structure of human chromosomes is tied to gene regulation and replication timing, but there is still a lack of consensus on the computational and biological definitions for chromosomal substructures such as topologically associating domains (TADs). TADs are described and identified by various computational properties leading to different TAD sets with varying compatibility with biological properties such as boundary occupancy of structural proteins. We unify many of these computational and biological targets into one algorithmic framework that jointly maximizes several computational TAD definitions and optimizes TAD selection for a quantifiable biological property. Using this framework, we explore the variability of TAD sets optimized for six different desirable properties of TAD sets: high occupancy of CTCF, RAD21, and H3K36me3 at boundaries, reproducibility between replicates, high intra- vs inter-TAD difference in contact frequencies, and many CTCF binding sites at boundaries. The compatibility of these biological targets varies by cell type, and our results suggest that these properties are better reflected as subpopulations or families of TADs rather than a singular TAD set fitting all TAD definitions and properties. We explore the properties that produce similar TAD sets (reproducibility and inter- vs intra-TAD difference, for example) and those that lead to very different TADs (such as CTCF binding sites and inter- vs intra-TAD contact frequency difference).

Living matter moves, deforms, and organizes itself. In cells this is made possible by networks of polymer filaments and crosslinking molecules that connect filaments to each other and that act as motors to do mechanical work on the network. For the case of highly cross-linked filament networks, we discuss how the material properties of assemblies emerge from the forces exerted by microscopic agents. First, we introduce a phenomenological model that characterizes the forces that crosslink populations exert between filaments. Second, we derive a theory that predicts the material properties of highly crosslinked filament networks, given the crosslinks present. Third, we discuss which properties of crosslinks set the material properties and behavior of highly crosslinked cytoskeletal networks. The work presented here, will enable the better understanding of cytoskeletal mechanics and its molecular underpinnings. This theory is also a first step toward a theory of how molecular perturbations impact cytoskeletal organization, and provides a framework for designing cytoskeletal networks with desirable properties in the lab.

Commonly prescribed antidepressants, such as selective serotonin reuptake inhibitors (SSRIs) take weeks to achieve therapeutic benefits1, 2. The underlying mechanisms of why antidepressants take weeks or months to reverse depressed mood are not understood. Using a single cell sequencing approach, we analyzed gene expression changes in mice subjected to stress-induced depression and determined their temporal response to antidepressant treatment in the cerebral cortex. We discovered that both glial and neuronal cell populations elicit gene expression changes in response to stress, and that these changes are reversed upon treatment with fluoxetine (Prozac), a widely prescribed selective serotonin reuptake inhibitor (SSRI). Upon reproducing the molecular signaling events regulated by fluoxetine3 in a cortical culture system, we found that these transcriptional changes are serotonin-dependent, require reciprocal neuron-glia communication, and involve temporally-specified sequences of autoregulation and cross-regulation between FGF2 and BDNF signaling pathways. Briefly, stimulation of Fgf2 synthesis and signaling directly regulates Bdnf synthesis and secretion cell-non-autonomously requiring neuron-glia interactions, which then activates neuronal BDNF-TrkB signaling to drive longer-term neuronal adaptations4–6 leading to improved mood. Our studies highlight temporal and cell type specific mechanisms promoting the onset of the antidepressant response, that we propose could offer novel avenues for mitigating delayed onset of antidepressant therapies.

We present a general methodology that enables the disentanglement of the electronic and lattice contributions to the metal-insulator transition by building an energy landscape from numerical solutions of the equation of state. The methodology works with any electronic structure method that provides electronic expectation values at given atomic positions. Applying the theory to rare-earth perovskite nickelates (RNiO

https://arxiv.org/abs/2103.10831

In moiré heterostructures, gate-tunable insulating phases driven by electronic correlations have been recently discovered. Here, we use transport measurements to characterize the gate-driven metal-insulator transitions and the metallic phase in twisted WSe

Natural hyperbolic materials with dielectric permittivities of opposite sign along different principal axes can confine long-wavelength electromagnetic waves down to the nanoscale, well below the diffraction limit. This has been demonstrated using hyperbolic phonon polaritons (HPP) in hexagonal boron nitride (hBN) and -MoO3, among other materials. However, HPP dissipation at ambient conditions is substantial and its fundamental limits remain unexplored1,2. Here, we exploit cryogenic nano-infrared imaging to investigate propagating HPP in isotopically pure hBN and naturally abundant -MoO3 crystals. Close to liquid-nitrogen temperatures, the losses for HPP in isotopic hBN drop significantly, resulting in propagation lengths in excess of 25 micrometers, with lifetimes exceeding 5 picoseconds, thereby surpassing prior reports on such highly-confined polaritonic modes. Our nanoscale, temperature-dependent imaging reveals the relevance of acoustic phonons in hyperbolic polariton damping and will be instrumental in mitigating such losses for miniaturized middle infrared technologies operating at the liquid-nitrogen temperatures.

We consider non-Fermi liquids in which the inelastic scattering rate has an intrinsic particle-hole asymmetry and obeys ω/T scaling. We show that, in contrast to Fermi liquids, this asymmetry influences the low-temperature behaviour of the thermopower even in the presence of impurity scattering. Implications for the unconventional sign and temperature dependence of the thermopower in cuprates in the strange metal (Planckian) regime are emphasized.

The physics of the triangular lattice Hubbard model exhibits a rich phenomenology, ranging from a metal-insulator transition, intriguing thermodynamic behavior, and a putative spin liquid phase at intermediate coupling, ultimately becoming a magnetic insulator at strong coupling. In this multi-method study, we combine a finite-temperature tensor network method, minimally entangled thermal typical states (METTS), with two Green function-based methods, connected-determinant diagrammatic Monte Carlo (DiagMC) and cellular dynamical mean-field theory (CDMFT), to establish several aspects of this model. We elucidate the evolution from the metallic to the insulating regime from the complementary perspectives brought by these different methods. We compute the full thermodynamics of the model on a width-4 cylinder using METTS in the intermediate to strong coupling regime. We find that the insulating state hosts a large entropy at intermediate temperatures, which increases with the strength of the coupling. Correspondingly, and consistently with a thermodynamic Maxwell relation, the double occupancy has a minimum as a function of temperature which is the manifestation of the Pomeranchuk effect of increased localisation upon heating. The intermediate coupling regime is found to exhibit both pronounced chiral as well as stripy antiferromagnetic spin correlations. We propose a scenario in which time-reversal symmetry broken states compete with nematic, lattice rotational symmetry breaking orders at lowest temperatures.