Publications

First principle theoretical modeling of out-of-equilibrium processes observed in attosecond pump-probe transient absorption spectroscopy (TAS) triggering pure electron dynamics remains a challenging task, specially for heavy elements and/or core excitations containing fingerprints of scalar and spin-orbit relativistic effects. To address this, we formulate a methodology for simulating TAS within the relativistic real-time time-dependent density functional theory (RT-TDDFT) framework, for both the valence and core energy regime. Especially for TAS, full four-component (4c) RT simulations are feasible but computationally demanding. Therefore, in addition to the 4c approach, we also introduce the atomic mean-field exact two-component (amfX2C) Hamiltonian accounting for one- and two-electron picture-change corrections within RT-TDDFT. amfX2C preserves the accuracy of the parent 4c method at a fraction of its computational cost. Finally, we apply the methodology to study valence and near L

LaRh

To define the topology of driven systems, recent works have proposed synthetic dimensions as a way to uncover the underlying parameter space of topological invariants. Using time as a synthetic dimension, together with a momentum dimension, gives access to a synthetic 2D Chern number. It is, however, still unclear how the synthetic 2D Chern number is related to the Chern number that is defined from a parametric variable that evolves with time. Here we show that in periodically driven systems in the adiabatic limit, the synthetic 2D Chern number is a multiple of the Chern number defined from the parametric variable. The synthetic 2D Chern number can thus be engineered via how the parametric variable evolves in its own space. We justify our claims by investigating Thouless pumping in two 1D tight-binding models, a three-site chain model and a two-1D-sliding-chains model. The present findings could be extended to higher dimensions and other periodically driven configurations.

Using the truncated Wigner approximation (TWA) we study quench dynamics of two-dimensional lattice systems consisting of interacting spinless fermions with potential disorder. First, we demonstrate that the semiclassical dynamics generally relaxes faster than the full quantum dynamics. We obtain this result by comparing the semiclassical dynamics with exact diagonalization and Lanczos propagation of one-dimensional chains. Next, exploiting the TWA capabilities of simulating large lattices, we investigate how the relaxation rates depend on the dimensionality of the studied system. We show that strongly disordered one-dimensional and two-dimensional systems exhibit a transient, logarithmic-in-time relaxation, which was recently established for one-dimensional chains. Such relaxation corresponds to the infamous 1/f-noise at strong disorder.

We report on the strong field ionization of H2 by a corotating two-color laser field. We measure the electron momentum distribution in coincidence with the kinetic energy release (KER) of dissociating hydrogen molecules. In addition to a characteristic half-moon structure, we observe a low-energy structure in the electron momentum distribution at a KER of about 3.5 eV. We speculate that the outgoing electron interacts with the molecular ion, despite the absence of classical recollisions under these conditions. Time-dependent density functional theory simulations support our conclusions.

Recently the SP (Stochastic Polyak step size) method has emerged as a competitive adaptive method for setting the step sizes of SGD. SP can be interpreted as a method specialized to interpolated models, since it solves the interpolation equations. SP solves these equation by using local linearizations of the model. We take a step further and develop a method for solving the interpolation equations that uses the local second-order approximation of the model. Our resulting method SP2 uses Hessian-vector products to speed-up the convergence of SP. Furthermore, and rather uniquely among second-order methods, the design of SP2 in no way relies on positive definite Hessian matrices or convexity of the objective function. We show SP2 is competitive both in experiments and in theory.
We show SP2 is very competitive on matrix completion, non-convex test problems and logistic regression. We also provide a convergence theory on sums-of-quadratics.

Drosophila oogenesis is a powerful and tractable model for studies of cell and developmental biology due to the multitude of well-characterized events in both germline and somatic cells, the ease of genetic manipulation in fruit flies, and the large number of egg chambers produced by each fly. Recent improvements in live imaging and ex vivo culturing protocols have enabled researchers to conduct more detailed, longer-term studies of egg chamber development, enabling insights into fundamental biological processes. Here, we present a protocol for dissection, culturing, and imaging of late-stage egg chambers to study intercellular and directional cytoplasmic flow during “nurse cell dumping.” This critical developmental process towards the latter stages of oogenesis (stages 10b/11) results in rapid growth of the oocyte and shrinkage of the nurse cells and is accompanied by dynamic changes in cell shape.

This is a handbook of simple proofs of the convergence of gradient and stochastic gradient descent type methods. We consider functions that are Lipschitz, smooth, convex, strongly convex, and/or Polyak-Łojasiewicz functions. Our focus is on

Fluorescent protein biomaterials have important applications such as bioimaging in pharmacological studies. Self-assembly of proteins, especially into fibrils, is known to produce fluorescence in the blue band. Capable of self-assembly into nanofibers, we have shown we can modulate its aggregation into mesofibers by encapsulation of a small hydrophobic molecule. Conversely, azobenzenes are hydrophobic small molecules that are virtually non-fluorescent in solution due to their highly efficient photoisomerization. However, they demonstrate fluorogenic properties upon confinement in nanoscale assemblies by reducing the non-radiative photoisomerization. Here, we report the fluorescence of a hybrid protein-small molecule system in which azobenzene is confined in our protein assembly leading to fiber thickening and increased fluorescence. We show our engineered protein Q encapsulates AzoCholine, bearing a photoswitchable azobenzene moiety, in the hydrophobic pore to produce fluorescent mesofibers. This study further investigates the photocontrol of protein conformation as well as fluorescence of an azobenze-containing biomaterial.

The fluid–structure interactions between flexible fibres and viscous flows play an essential role in various biological phenomena, medical problems and industrial processes. Of particular interest is the case of particles transported freely in time-dependent flows. This work elucidates the dynamics and morphologies of actin filaments under oscillatory shear flows by combining microfluidic experiments, numerical simulations and theoretical modelling. Our work reveals that, in contrast to steady shear flows, in which small orientational fluctuations from a flow-aligned state initiate tumbling and deformations, the periodic flow reversal allows the filament to explore many different configurations at the beginning of each cycle. Investigation of filament motion during half time periods of oscillation highlights the critical role of the initial filament orientation on the emergent dynamics. This strong coupling between orientation and deformation results in new deformation regimes and novel higher-order buckling modes absent in steady shear flows. The primary outcome of our analysis is the possibility of suppression of buckling instabilities for certain combinations of the oscillation frequency and initial filament orientation, even in very strong flows. We explain this unusual behaviour through a weakly nonlinear Landau theory of buckling, in which we treat the filaments as inextensible Brownian Euler–Bernoulli rods whose hydrodynamics is described by local slender-body theory.