Ultrafast Transient Infrared Spectroscopy of Photoreceptors with Polarizable QM/MM Dynamics

Ultrafast transient infrared (TRIR) spectroscopy is widely used to measure the excitation-induced structural changes of protein-bound chromophores. Here, we design a novel and general strategy to compute TRIR spectra of photoreceptors by combining μs-long MM molecular dynamics with ps-long QM/AMOEBA Born-Oppenheimer molecular dynamics (BOMD) trajectories for both ground and excited electronic states. As a proof of concept, the strategy is here applied to AppA, a blue-light-utilizing flavin (BLUF) protein, found in bacteria. We first analyzed the short-time evolution of the embedded flavin upon excitation revealing that its dynamic Stokes shift is ultrafast and mainly driven by the internal reorganization of the chromophore. A different normal-mode representation was needed to describe ground- and excited-state IR spectra. In this way, we could assign all of the bands observed in the measured transient spectrum. In particular, we could characterize the flavin isoalloxazine-ring region of the spectrum, for which a full and clear description was missing

Coupling of Electronic and Motional Dynamics in a Cold Atom Optical Lattice

We study the coupling of internal electronic excitations to vibrational modes of the external motion of ultracold atoms in an optical lattice. For different ground and excited state potentials the on-site coupling of excitations and vibrations term renormalizes the effective electronic transition energy, which appears e.g. in clock transitions. In addition in the Mott state with filling factor one, the dipole-dipole coupling between neighbouring sites includes emission and absorption of vibrational quanta. Such processes create a significant mechanism for excitation of vibrations leading to motional heating of the lattice atoms by resonant light interaction. We calculate estimates of the corresponding parameters from a perturbation expansion in small atomic displacements.Comment: 4 pages, 5 figure

DataProVe: Fully Automated Conformance Verification Between Data Protection Policies and System Architectures

Privacy and data protection by design are relevant parts of the General Data Protection Regulation (GDPR), in which businesses and organisations are encouraged to implement measures at an early stage of the system design phase to fulfil data protection requirements. This paper addresses the policy and system architecture design and propose two variants of privacy policy language and architecture description language, respectively, for specifying and verifying data protection and privacy requirements. In addition, we develop a fully automated algorithm based on logic, for verifying three types of conformance relations (privacy, data protection, and functional conformance) between a policy and an architecture specified in our languages’ variants. Compared to related works, this approach supports a more systematic and fine-grained analysis of the privacy, data protection, and functional properties of a system. Our theoretical methods are then implemented as a software tool called DataProVe and its feasibility is demonstrated based on the centralised and decentralised approaches of COVID-19 contact tracing applications

Collective Light Emission of a Finite Size Atomic Chain

Radiative properties of collective electronic states in a one dimensional atomic chain are investigated. Radiative corrections are included with emphasize put on the effect of the chain size through the dependence on both the number of atoms and the lattice constant. The damping rates of collective states are calculated in considering radiative effects for different values of the lattice constant relative to the atomic transition wave length. Especially the symmetric state damping rate as a function of the number of the atoms is derived. The emission pattern off a finite linear chain is also presented. The results can be adopted for any chain of active material, e.g., a chain of semiconductor quantum dots or organic molecules on a linear matrix.Comment: 10 pages, 20 figure

Collective Electronic Excitation Coupling between Planar Optical Lattices using Ewald's Method

Using Ewald's summation method we investigate collective electronic excitations (excitons) of ultracold atoms in parallel planar optical lattices including long range interactions. The exciton dispersion relation can then be suitably rewritten and efficiently calculated for long range resonance dipole-dipole interactions. Such in-plane excitons resonantly couple for two identical optical lattices, with an energy transfer strength decreasing exponentially with the distance between the lattices. This allows a restriction of the transfer to neighboring planes and gives rise to excitons delocalized between the lattices. In general equivalent results will hold for any planar system containing lattice layers of optically active and dipolar materials.Comment: 6 pages, and 7 figure

Efficient Fluoride Removal from Aqueous Solution Using Zirconium-Based Composite Nanofiber Membranes

Herein, composite nanofiber membranes (CNMs) derived from UiO-66 and UiO-66-NH2 Zr-metal-organic frameworks (MOFs) were successfully prepared, and they exhibited high performance in adsorptive fluoride removal from aqueous media. The resultant CNMs were confirmed using different techniques, such as X-ray diffraction (XRD), field emission scanning electron microscopy (FE-SEM), and Brunauer–Emmett–Teller (BET) in addition to Fourier-transform infrared spectroscopy (FTIR). The parameters that govern the fluoride adsorption were evaluated, including adsorbent dose, contact time, and pH value, in addition to initial concentration. The crystalline structures of CNMs exhibited high hydrothermal stability and remained intact after fluoride adsorption. It could also be observed that the adsorbent dose has a significant effect on fluoride removal at high alkaline values. The results show that UiO-66-NH2 CNM exhibited high fluoride removal due to electrostatic interactions that strongly existed between F− and metal sites in MOF in addition to hydrogen bonds formed with MOF amino groups. The fluoride removal efficiency reached 95% under optimal conditions of 20 mg L−1, pH of 8, and 40% adsorbent dose at 60 min. The results revealed that UiO-66-NH2 CNM possesses a high maximum adsorption capacity (95 mg L−1) over UiO-66 CNM (75 mg L−1), which exhibited better fitting with the pseudo-second-order model. Moreover, when the initial fluoride concentration increased from 20 to 100 mg/L, fluoride adsorption decreased by 57% (UiO-66 CNM) and 30% (UiO-66-NH2 CNM) after 60 min. After three cycles, CNM revealed the regeneration ability, demonstrating that UiO-66-NH2 CNMs are auspicious adsorbents for fluoride from an aqueous medium

Endophytic Bacteria Improve Plant Growth, Symbiotic Performance of Chickpea (Cicer arietinum L.) and Induce Suppression of Root Rot Caused by Fusarium solani under Salt Stress

Salinity causes disturbance in symbiotic performance of plants, and increases susceptibility of plants to soil-borne pathogens. Endophytic bacteria are an essential determinant of cross-tolerance to biotic and abiotic stresses in plants. The aim of this study was to isolate non–rhizobial endophytic bacteria from the root nodules of chickpea (Cicer arietinum L.), and to assess their ability to improve plant growth and symbiotic performance, and to control root rot in chickpea under saline soil conditions. A total of 40 bacterial isolates from internal root tissues of chickpea grown in salinated soil were isolated. Four bacterial isolates, namely Bacillus cereus NUU1, Achromobacter xylosoxidans NUU2, Bacillus thuringiensis NUU3, and Bacillus subtilis NUU4 colonizing root tissue demonstrated plant beneficial traits and/or antagonistic activity against F. solani and thus were characterized in more detail. The strain B. subtilis NUU4 proved significant plant growth promotion capabilities, improved symbiotic performance of host plant with rhizobia, and promoted yield under saline soil as compared to untreated control plants under field conditions. A combined inoculation of chickpea with M. ciceri IC53 and B. subtilis NUU4 decreased H2O2 concentrations and increased proline contents compared to the un-inoculated plants indicating an alleviation of adverse effects of salt stress. Furthermore, the bacterial isolate was capable to reduce the infection rate of root rot in chickpea caused by F. solani. This is the first report of F. solani causing root rot of chickpea in a salinated soil of Uzbekistan. Our findings demonstrated that the endophytic B. subtilis strain NUU4 provides high potentials as a stimulator for plant growth and as biological control agent of chickpea root rot under saline soil conditions. These multiple relationships could provide promising practical approaches to increase the productivity of legumes under salt stress

Channel equalization for indoor lighting communications networks

We consider indoors communications networks using modulated LEDs to transmit the information packets. A generic indoor channel equalization formulation is proposed assuming the existence of both line of sight and diffuse emitters. The proposed approach is of relevance to emergent indoors distributed sensing modalities for which various lighting based network communications protocols are considered

Excitons and cavity polaritons for ultracold atoms in an optical lattice

We study the resonant electronic excitation dynamics for ultracold atoms trapped in a deep optical lattice prepared in a Mott insulator state. Excitons in these artificial crystals are similar to Frenkel excitons in Noble atom or molecular crystals. They appear when the atomic excited state line width is smaller than the exciton band width generated by dipole-dipole coupling. When the atoms are placed within a cavity the electronic excitations and the quantized cavity mode get coupled. In the collective strong coupling regime excitations form two branches of cavity polaritons with Rabi splitting larger than the atomic and the cavity line width. To demonstrate their properties we calculate the transmission, reflection, and absorption spectra for an incident weak probe field, which show resonances at the polariton frequencies.Comment: 9 pages, 9 figure