Publications
KIM application programmming interface as a standard for molecular simulations
Mean-field analysis of intra-unit-cell order in the Emery model of the CuO2 plane
Motivated by recent experiments on high-Tc cuprate superconductors pointing toward intra-unit-cell (IUC) order in the pseudogap phase, we investigate three distinct intra-unit-cell-ordering possibilities: nematic, nematic-spin-nematic, and current-loop order. The first two are Fermi-surface instabilities involving a spontaneous charge and magnetization imbalance between the two oxygen sites in the unit cell, respectively, while the third describes circulating currents within the unit cell.
ATP-induced helicase slippage reveals highly coordinated subunits
Helicases are vital enzymes that carry out strand separation of duplex nucleic acids during replication, repair and recombination 1,2. Bacteriophage T7 gene product 4 is a model hexameric helicase that has been observed to use dTTP, but not ATP, to unwind double-stranded (ds)DNA as it translocates from 5′ to 3′ along single-stranded (ss)DNA 2-6. Whether and how different subunits of the helicase coordinate their chemo-mechanical activities and DNA binding during translocation is still under debate 1,7.
Can radiation damage to protein crystals be reduced using small-molecule compounds?
Recent studies have defined a data-collection protocol and a metric that provide a robust measure of global radiation damage to protein crystals. Using this protocol and metric, 19 small-molecule compounds (introduced either by cocrystalliz-ation or soaking) were evaluated for their ability to protect lysozyme crystals from radiation damage. The compounds were selected based upon their ability to interact with radiolytic products (e.g.
Preface
Joint time-dependent density-functional theory for excited states of electronic systems in solution
We present a joint time-dependent density-functional theory for the description of solute-solvent systems in time-dependent external potentials. Starting with the exact quantum-mechanical action functional for both electrons and nuclei, we systematically eliminate solvent degrees of freedom and thus arrive at coarse-grained action functionals that retain the highly accurate ab initio description for the solute and are, in principle, exact. This procedure allows us to examine approximations underlying popular embedding theories for excited states.
Time-resolved optical writing on a photosensitive and fluorescent polymer film
Recently a melt-processed blend of 1,4-bis(α-cyano-4- octadecyloxystyryl)-2,5-dimethoxybenzene (C18-RG) dye and polyethylene terephthalate glycol (PETG) has been demonstrated as a promising 3-dimentional optical data storage (ODS) medium 1. ODS in this novel system relies on the laser-induced switching of the aggregation state of the excimerforming fluorescent dye in the inert host polymer. Here we investigate the mechanism and the time scales involved in the writing process.
Imaging the microscopic structure of shear thinning and thickening colloidal suspensions
The viscosity of colloidal suspensions varies with shear rate, an important effect encountered in many natural and industrial processes. Although this non-Newtonian behavior is believed to arise from the arrangement of suspended particles and their mutual interactions, microscopic particle dynamics are difficult to measure. By combining fast confocal microscopy with simultaneous force measurements, we systematically investigate a suspension's structure as it transitions through regimes of different flow signatures.
Single-shot correlations and two-qubit gate of solid-state spins
Measurement of coupled quantum systems plays a central role in quantum information processing. We have realized independent single-shot read-out of two electron spins in a double quantum dot. The read-out method is all-electrical, cross-talk between the two measurements is negligible, and read-out fidelities are ∼86% on average. This allows us to directly probe the anticorrelations between two spins prepared in a singlet state and to demonstrate the operation of the two-qubit exchange gate on a complete set of basis states.
Dark progression reveals slow timescales for radiation damage between T = 180 and 240 K
Can radiation damage to protein crystals be outrun by collecting a structural data set before damage is manifested? Recent experiments using ultra-intense pulses from a free-electron laser show that the answer is yes. Here, evidence is presented that significant reductions in global damage at temperatures above 200 K may be possible using conventional X-ray sources and current or soon-to-be available detectors.