Fast optoelectronic charge state conversion of silicon vacancies in diamond.

Group IV vacancy color centers in diamond are promising spin-photon interfaces with strong potential for applications in photonic quantum technologies. Reliable methods for controlling and stabilizing their charge state are urgently needed for scaling to multiqubit devices. Here, we manipulate the charge state of silicon vacancy (SiV) ensembles by combining luminescence and photocurrent spectroscopy. We controllably convert the charge state between the optically active SiV- and dark SiV2- with megahertz rates and >90% contrast by judiciously choosing the local potential applied to in-plane surface electrodes and the laser excitation wavelength. We observe intense SiV- photoluminescence under hole capture, measure the intrinsic conversion time from the dark SiV2- to the bright SiV- to be 36.4(67) ms, and demonstrate how it can be enhanced by a factor of 105 via optical pumping. Moreover, we obtain previously unknown information on the defects that contribute to photoconductivity, indicating the presence of substitutional nitrogen and divacancies.

Three-Photon Excitation of InGaN Quantum Dots.

We demonstrate that semiconductor quantum dots can be excited efficiently in a resonant three-photon process, while resonant two-photon excitation is highly suppressed. Time-dependent Floquet theory is used to quantify the strength of the multiphoton processes and model the experimental results. The efficiency of these transitions can be drawn directly from parity considerations in the electron and hole wave functions in semiconductor quantum dots. Finally, we exploit this technique to probe intrinsic properties of InGaN quantum dots. In contrast to nonresonant excitation, slow relaxation of charge carriers is avoided, which allows us to measure directly the radiative lifetime of the lowest energy exciton states. Since the emission energy is detuned far from the resonant driving laser field, polarization filtering is not required and emission with a greater degree of linear polarization is observed compared to nonresonant excitation.

Nearest-Neighbor dsDNA Stability Analysis Using Alchemical Free-Energy Simulations.

The thermodynamic stability of double-stranded (ds)DNA depends on its sequence. It is influenced by the base pairing and stacking with neighboring bases along DNA molecules. Semiempirical schemes are available that allow us to predict the thermodynamic stability of DNA sequences based on empirically derived nearest-neighbor contributions of base pairs formed in the context of all possible nearest-neighbor base pairs. Current molecular dynamics (MD) simulations allow one to simulate the dynamics of DNA molecules in good agreement with experimentally obtained structures and available data on conformational flexibility. However, the suitability of current force field methods to reproduce dsDNA stability and its sequence dependence has been much less well tested. We have employed alchemical free-energy simulations of whole base pair transversions in dsDNA and in unbound single-stranded partner molecules. Such transversions change the sequence context but not the nucleotide content or base pairing in dsDNA and allow a direct comparison with the empirical nearest-neighbor dsDNA stability model. For the alchemical free-energy changes in the unbound single-stranded (ss)DNA partner molecules, we tested different setups assuming either complete unstacking or unrestrained simulations with partial stacking in the unbound ssDNA. The free-energy simulations predicted nearest-neighbor effects of similar magnitude, as observed experimentally but showed overall limited correlation with experimental data. An inaccurate description of stacking interactions and other possible reasons such as the neglect of electronic polarization effects are discussed. The results indicate the need to improve the realistic description of stacking interactions in current molecular mechanic force fields.

CHARMM-GUI supports the Amber force fields.

As part of our ongoing efforts to support diverse force fields and simulation programs in CHARMM-GUI, this work presents the development of FF-Converter to prepare Amber simulation inputs with various Amber force fields within the current CHARMM-GUI workflow. The currently supported Amber force fields are ff14SB/ff19SB (protein), Bsc1 (DNA), OL3 (RNA), GLYCAM06 (carbohydrate), Lipid17 (lipid), GAFF/GAFF2 (small molecule), TIP3P/TIP4P-EW/OPC (water), and 12-6-4 ions, and more will be added if necessary. The robustness and usefulness of this new CHARMM-GUI extension are demonstrated by two exemplary systems: a protein/N-glycan/ligand/membrane system and a protein/DNA/RNA system. Currently, CHARMM-GUI supports the Amber force fields only for the Amber program, but we will expand the FF-Converter functionality to support other simulation programs that support the Amber force fields.