Publications

Cryo-electron microscopy (cryo-EM) has recently become a leading method for obtaining high-resolution structures of biological macromolecules. However, cryo-EM is limited to biomolecular samples with low conformational heterogeneity, where most conformations can be well-sampled at various projection angles. While cryo-EM provides single-molecule data for heterogeneous molecules, most existing reconstruction tools cannot retrieve the ensemble distribution of possible molecular conformations from these data. To overcome these limitations, we build on a previous Bayesian approach and develop an ensemble refinement framework that estimates the ensemble density from a set of cryo-EM particle images by reweighting a prior conformational ensemble, e.g., from molecular dynamics simulations or structure prediction tools. Our work provides a general approach to recovering the equilibrium probability density of the biomolecule directly in conformational space from single-molecule data. To validate the framework, we study the extraction of state populations and free energies for a simple toy model and from synthetic cryo-EM particle images of a simulated protein that explores multiple folded and unfolded conformations.

During eukaryotic cell division, microtubules connect to chromosomes by attaching to the kinetochore via the NDC80 complex (NDC80c). The regulation of kinetochore microtubule (KMT) detachment is crucial for correcting mitotic errors. Here, we investigate the mechanism of KMT detachment by combining photoconversion measurements of KMT detachment rate, FLIM-FRET measurements of NCD80c/KMT binding, and mathematical modeling. Our results support a dual detachment mechanism in which KMTs detach from kinetochores when either 1) all NDC80c spontaneously unbind from the KMT or 2) following KMT catastrophe. We identify kinetochore components that selectively impact these two mechanisms and show that the affinity of NDC80c for KMTs is reduced at low-tension, non-bioriented kinetochores due to centromere-localized Aurora B phosphorylating the NDC80c, resulting in an elevated detachment rate for the associated KMTs. Taken together, this work leads to a biophysical model for the molecular basis of KMT detachments and their regulation during mitotic error correction.

The 3D pose estimation problem – aligning pairs of noisy 3D point clouds – is a problem with a wide variety of real- world applications. Here we focus on the use of quaternion- based neural network approaches to this problem and ap- parent anomalies that have arisen in previous efforts to re- solve them. In addressing these anomalies, we draw heav- ily from the extensive literature on closed-form methods to solve this problem. We suggest that the major concerns that have been put forward could be resolved using a sim- ple multi-valued training target derived from rigorous theo- retical properties of the rotation-to-quaternion map of Bar- Itzhack. This multi-valued training target is then demon- strated to have good performance for both simulated and ModelNet targets. We provide a comprehensive theoretical context, using the quaternion adjugate, to confirm and es- tablish the necessity of replacing single-valued quaternion functions by quaternions treated in the extended domain of multiple-charted manifolds.

Evidence is accumulating for the crucial role of a solid's free electrons in the dynamics of solid-liquid interfaces. Liquids induce electronic polarization and drive electric currents as they flow; electronic excitations, in turn, participate in hydrodynamic friction. Yet, the underlying solid-liquid interactions have been lacking a direct experimental probe. Here, we study the energy transfer across liquid-graphene interfaces using ultrafast spectroscopy. The graphene electrons are heated up quasi-instantaneously by a visible excitation pulse, and the time evolution of the electronic temperature is then monitored with a terahertz pulse. We observe that water accelerates the cooling of the graphene electrons, whereas other polar liquids leave the cooling dynamics largely unaffected. A quantum theory of solid-liquid heat transfer accounts for the water-specific cooling enhancement through a resonance between the graphene surface plasmon mode and the so-called hydrons -- water charge fluctuations --, particularly the water libration modes, that allows for efficient energy transfer. Our results provide direct experimental evidence of a solid-liquid interaction mediated by collective modes and support the theoretically proposed mechanism for quantum friction. They further reveal a particularly large thermal boundary conductance for the water-graphene interface and suggest strategies for enhancing the thermal conductivity in graphene-based nanostructures.

Several recent works have introduced highly compact representations of single-particle Green's functions in the imaginary time and Matsubara frequency domains, as well as efficient interpolation grids used to recover the representations. In particular, the intermediate representation with sparse sampling and the discrete Lehmann representation (DLR) make use of low-rank compression techniques to obtain optimal approximations with controllable accuracy. We consider the use of the DLR in dynamical mean-field theory (DMFT) calculations, and in particular, show that the standard full Matsubara frequency grid can be replaced by the compact grid of DLR Matsubara frequency nodes. We test the performance of the method for a DMFT calculation of Sr

We introduce trilayer and multilayer moiré heterostructures that cannot be viewed from the ``moiré-of-moiré" perspective of helically-twisted trilayer graphene. These ``intrinsically trilayer" moiré systems feature periodic modulation of a local quasicrystalline structure. They open the door to realizing moiré heterostructures with vastly more material constituents because they do not constrain the lattice constants of the layers. In this manuscript, we define intrinsically multilayer patterns, provide a recipe for their construction, derive their local configuration space, and connect the visual patterns to physical observables in material systems.

Molecular magnets have received significant attention because of their potential applications in quantum information and quantum computing. A delicate balance of electron correlation, spin-orbit coupling (SOC), ligand field splitting, and other effects produces a persistent magnetic moment within each molecular magnet unit. The discovery and design of molecular magnets with improved functionalities would be greatly aided by accurate computations. However, the competition among the different effects poses a challenge for theoretical treatments. Electron correlation plays a central role, since d-, or f-element ions, which provide the magnetic states in molecular magnets, often require explicit many-body treatments. SOC, which expands the dimensionality of the Hilbert space, can also lead to non-perturbative effects in the presence of strong interaction. Furthermore, molecular magnets are large, with tens of atoms in even the smallest systems. We show how an

The simulation of strongly correlated quantum impurity models is a significant challenge in modern condensed matter physics that has multiple important applications. Thus far, the most successful methods for approaching this challenge involve Monte Carlo techniques that accurately and reliably sample perturbative expansions to any order. However, the cost of obtaining high precision through these methods is high. Recently, tensor train decomposition techniques have been developed as an alternative to Monte Carlo integration. In this study, we apply these techniques to the single-impurity Anderson model at equilibrium by calculating the systematic expansion in power of the hybridization of the impurity with the bath. We demonstrate the performance of the method in a paradigmatic application, examining the first-order phase transition on the infinite dimensional Bethe lattice, which can be mapped to an impurity model through dynamical mean field theory. Our results indicate that using tensor train decomposition schemes allows the calculation of finite-temperature Green's functions and thermodynamic observables with unprecedented accuracy. The methodology holds promise for future applications to frustrated multi-orbital systems, using a combination of partially summed series with other techniques pioneered in diagrammatic and continuous-time quantum Monte Carlo.

By applying auxiliary-field quantum Monte Carlo, we calculate the equation of state (EOS) and B1-B2 phase transition of magnesium oxide (MgO) up to 1 TPa. The results agree with available experimental data at low pressures and are used to benchmark the performance of various exchange-correlation functionals in density functional theory calculations. We determine PBEsol is an optimal choice for the exchange-correlation functional and perform extensive phonon and quantum molecular-dynamics calculations to obtain the thermal EOS. Our results provide a preliminary reference for the EOS and B1-B2 phase boundary of MgO from zero up to 10,500 K.

The effect of spin-orbit (and Darwin) interaction on a 2D electron gas subject to a radial symmetric, inhomogeneous 1/r-magnetic field is discussed analytically in a perturbative and non-perturbative manner. For this purpose, we investigate the radial Hall conductivity that emerges from an additional homogeneous electric field perturbation perpendicular to the 2D electron gas, which solely interacts via spin-orbit coupling. Numerical calculations of the absorptive spin-orbit spectra show for an ideal InSb electron gas a behaviour that is dominated by the localized (atomic) part of the distorted Landau levels. In contrast, however, we also find analytically that a (non-local) divergent static response emerges for Fermi energies close to the ionization energy in the thermodynamic limit. The divergent linear response implies that the external electric field is entirely absorbed outside the 2D electron gas by induced radial spin-orbit currents, as it would be the case inside a perfect conductor. This spin-orbit induced polarization mechanism depends on the effective g