Formulation of transition dipole gradients for non-adiabatic dynamics with polaritonic states.

A general formulation of the strong coupling between photons confined in a cavity and molecular electronic states is developed for the state-interaction state-average spin-restricted ensemble-referenced Kohn-Sham method. The light-matter interaction is included in the Jaynes-Cummings model, which requires the derivation and implementation of the analytical derivatives of the transition dipole moments between the molecular electronic states. The developed formalism is tested in the simulations of the nonadiabatic dynamics in the polaritonic states resulting from the strong coupling between the cavity photon mode and the ground and excited states of the penta-2,4-dieniminium cation, also known as PSB3. Comparison with the field-free simulations of the excited-state decay dynamics in PSB3 reveals that the light-matter coupling can considerably alter the decay dynamics by increasing the excited state lifetime and hindering photochemically induced torsion about the C=C double bonds of PSB3. The necessity of obtaining analytical transition dipole gradients for the accurate propagation of the dynamics is underlined.

Rapid Detection of a Downy Mildew Pathogen, Peronospora destructor, in Infected Onion Tissues and Soils by Loop-Mediated Isothermal Amplification.

Downy mildew of onion caused by a soil-inhabiting water mold, Peronospora destructor, is one of the most devastating diseases that can destroy entire onion fields in a matter of days. In this study, we developed a loop-mediated isothermal amplification (LAMP) assay that allows for rapid detection of P. destructor by visual inspection. The internal transcribed spacer 2 region of P. destructor was used to design primer sets for LAMP reactions. The optimal temperature and incubation time were determined for the most efficient primer set. In the optimized condition, the LAMP assay exhibited at least 100 times more sensitivity than conventional PCR, detecting femtogram levels of P. destructor genomic DNA (gDNA). Detection of the pathogen from a small number of spores without gDNA extraction further confirmed the high sensitivity of the assay. For specificity, the LAMP assay was negative for gDNA of other fungal pathogens that cause various diseases on onion and oomycetes, whereas the assay was positive for gDNA extracted from onion tissues showing the typical downy mildew symptoms. Finally, we examined the efficacy of the LAMP assay in detection of P. destructor in soils. Soils collected from onion fields that had been contaminated with P. destructor were solarized for 60 days. Whereas the LAMP assay was negative for the solarized soils, we were able to detect P. destructor that oversummers in fields. The LAMP assay developed in this study enables rapid detection and diagnosis of downy mildew of onion in infected tissues and in soil.

Origamic metal-organic framework toward mechanical metamaterial.

Origami, known as paper folding has become a fascinating research topic recently. Origami-inspired materials often establish mechanical properties that are difficult to achieve in conventional materials. However, the materials based on origami tessellation at the molecular level have been significantly underexplored. Herein, we report a two-dimensional (2D) porphyrinic metal-organic framework (MOF), self-assembled from Zn nodes and flexible porphyrin linkers, displaying folding motions based on origami tessellation. A combined experimental and theoretical investigation demonstrated the origami mechanism of the 2D porphyrinic MOF, whereby the flexible linker acts as a pivoting point. The discovery of the 2D tessellation hidden in the 2D MOF unveils origami mechanics at the molecular level.

Reconstruction of Range-Doppler Map Corrupted by FMCW Radar Asynchronization.

Frequency-modulated continuous wave (FMCW) radar system synchronization using external clock signals can cause repeated Range-Doppler (R-D) map corruption when clock signal asynchronization problems occur between the transmitter and receiver. In this paper, we propose a signal processing method for the reconstruction of the corrupted R-D map owing to the FMCW radar's asynchronization. After calculating the image entropy for each R-D map, the corrupted ones are extracted and reconstructed using the normal R-D maps acquired before and after the individual maps. To verify the effectiveness of the proposed method, three target detection experiments were conducted: a human target detection in an indoor environment and a wide place and a moving bike-rider target detection in an outdoor environment. The corrupted R-D map sequence of observed targets in each case was reconstructed properly and showed the validity by comparing the map-by-map range and speed changes in the detected target with the ground-truth information of the target.

Calculation of exciton couplings based on density functional tight-binding coupled to state-interaction state-averaged ensemble-referenced Kohn-Sham approach.

We introduce the combination of the density functional tight binding (DFTB) approach, including onsite correction (OC) and long-range corrected (LC) functional and the state-interaction state-averaged spin-restricted ensemble-referenced Kohn-Sham (SI-SA-REKS or SSR) method with extended active space involving four electrons and four orbitals [LC-OC-DFTB/SSR(4,4)], to investigate exciton couplings in multichromophoric systems, such as organic crystals and molecular aggregates. We employ the LC-OC-DFTB/SSR(4,4) method to calculate the excitonic coupling in anthracene and tetracene. As a result, the LC-OC-DFTB/SSR(4,4) method provides a reliable description of the locally excited (LE) state in a single chromophore and the excitonic couplings between chromophores with reasonable accuracy compared to the experiment and the conventional SSR(4,4) method. In addition, the thermal fluctuation of excitonic couplings from dynamic nuclear motion in an anthracene crystal with LC-OC-DFTB/SSR(4,4) shows a similar fluctuation of excitonic coupling and spectral density with those of first-principle calculations. We conclude that LC-OC-DFTB/SSR(4,4) is capable of providing reasonable features related to LE states, such as Frenkel exciton with efficient computational cost.

Singlet Oxygen Generation from Polyaminoglycerol by Spin-Flip-Based Electron Transfer.

Reactive oxygen species have drawn attention owing to their strong oxidation ability. In particular, the singlet oxygen (1O2) produced by energy transfer is the predominant species for controlling oxidation reactions efficiently. However, conventional 1O2 generators, which rely on enhanced energy transfer, frequently suffer from poor solubility, low stability, and low biocompatibility. Herein, we introduce a hyperbranched aliphatic polyaminoglycerol (hPAG) as a 1O2 generator, which relies on spin-flip-based electron transfer. The coexistence of a lone pair electron on the nitrogen atom and a hydrogen-bonding donor (the protonated form of nitrogen and hydroxyl group) affords proximity between hPAG and O2. Subsequent direct electron transfer after photo-irradiation induces hPAG•+-O2 •- formation, and the following spin-flip process generates 1O2. The spin-flip-based electron transfer pathway is analyzed by a series of photophysical, electrochemical, and computational studies. The 1O2 generator, hPAG, is successfully employed in photodynamic therapy and as an antimicrobial reagent.

Generalized Formulation of the Density Functional Tight Binding-Based Restricted Ensemble Kohn-Sham Method with Onsite Correction to Long-Range Correction.

We present a generalized formulation for the combination of the density functional tight binding (DFTB) approach and the state-interaction state-average spin-restricted ensemble-referenced Kohn-Sham (SI-SA-REKS or SSR) method by considering onsite correction (OC) as well as the long-range corrected (LC) functional. The OC contribution provides more accurate energies and analytic gradients for individual microstates, while the multireference character of the SSR provides the correct description for conical intersections. We benchmark the LC-OC-DFTB/SSR method against various DFTB calculation methods for excitation energies and conical intersection structures with π/π* or n/π* characters. Furthermore, we perform excited-state molecular dynamics simulations with a molecular rotary motor with variations of LC-OC-DFTB/SSR approaches. We show that the OC contribution to the LC functional is crucial to obtain the correct geometry of conical intersections.

Vital Signal Detection Using Multi-Radar for Reductions in Body Movement Effects.

Vital signal detection using multiple radars is proposed to reduce the signal degradation from a subject's body movement. The phase variation in the transceiving signals of continuous-wave radar due to respiration and heartbeat is generated by the body surface movement of the organs monitored in the line-of-sight (LOS) of the radar. The body movement signals obtained by two adjacent radars can be assumed to be the same over a certain distance. However, the vital signals are different in each radar, and each radar has a different LOS because of the asymmetric movement of lungs and heart. The proposed method uses two adjacent radars with different LOS to obtain correlated signals that reinforce the difference in the asymmetrical movement of the organs. The correlated signals can improve the signal-to-noise ratio in vital signal detection because of a reduction in the body movement effect. Two radars at different frequencies in the 5.8 GHz band are implemented to reduce direct signal coupling. Measurement results using the radars arranged at angles of 30°, 45°, and 60° showed that the proposed method can detect the vital signals with a mean accuracy of 97.8% for the subject moving at a maximum velocity of 53.4 mm/s.

Detrending Technique for Denoising in CW Radar.

A detrending technique is proposed for continuous-wave (CW) radar to remove the effects of direct current (DC) offset, including DC drift, which is a very slow noise that appears near DC. DC drift is mainly caused by unwanted vibrations (generated by the radar itself, target objects, or surroundings) or characteristic changes in components in the radar owing to internal heating. It reduces the accuracy of the circle fitting method required for I/Q imbalance calibration and DC offset removal. The proposed technique effectively removes DC drift from the time-domain waveform of the baseband signals obtained for a certain time using polynomial fitting. The accuracy improvement in the circle fitting by the proposed technique using a 5.8 GHz CW radar decreases the error in the displacement measurement and increases the signal-to-noise ratio (SNR) in vital signal detection. The measurement results using a 5.8 GHz radar show that the proposed technique using a fifth-order polynomial fitting decreased the displacement error from 1.34 mm to 0.62 mm on average when the target was at a distance of 1 m. For a subject at a distance of 0.8 m, the measured SNR improved by 7.2 dB for respiration and 6.6 dB for heartbeat.

PyUNIxMD: A Python-based excited state molecular dynamics package.

Theoretical/computational description of excited state molecular dynamics is nowadays a crucial tool for understanding light-matter interactions in many materials. Here we present an open-source Python-based nonadiabatic molecular dynamics program package, namely PyUNIxMD, to deal with mixed quantum-classical dynamics for correlated electron-nuclear propagation. The PyUNIxMD provides many interfaces for quantum chemical calculation methods with commercial and noncommercial ab initio and semiempirical quantum chemistry programs. In addition, the PyUNIxMD offers many nonadiabatic molecular dynamics algorithms such as fewest-switch surface hopping and its derivatives as well as decoherence-induced surface hopping based on the exact factorization (DISH-XF) and coupled-trajectory mixed quantum-classical dynamics (CTMQC) for general purposes. Detailed structures and flows of PyUNIxMD are explained for the further implementations by developers. We perform a nonadiabatic molecular dynamics simulation for a molecular motor system as a simple demonstration.

Self-Assembly of Mitochondria-Targeted Photosensitizer to Increase Photostability and Photodynamic Therapeutic Efficacy in Hypoxia.

The development of photosensitizers for cancer photodynamic therapy has been challenging due to their low photostability and therapeutic inefficacy in hypoxic tumor microenvironments. To overcome these issues, we have developed a mitochondria-targeted photosensitizer consisting of an indocyanine moiety with triphenylphosphonium arms, which can self-assemble into spherical micelles directed to mitochondria. Self-assembly of the photosensitizer resulted in a higher photostability by preventing free rotation of the indoline ring of the indocyanine moiety. The mitochondria targeting capability of the photosensitizer allowed it to utilize intramitochondrial oxygen. We found that the mitochondria-targeted photosensitizer localized to mitochondria and induced apoptosis of cancer cells both normoxic and hypoxic conditions through generation of ROS. The micellar self-assemblies of the photosensitizer were further confirmed to selectively localize to tumor tissues in a xenograft tumor mouse model through passive targeting and showed efficient tumor growth inhibition.

Metal-organic framework based on hinged cube tessellation as transformable mechanical metamaterial.

Mechanical metamaterials exhibit unusual properties, such as negative Poisson's ratio, which are difficult to achieve in conventional materials. Rational design of mechanical metamaterials at the microscale is becoming popular partly because of the advance in three-dimensional printing technologies. However, incorporating movable building blocks inside solids, thereby enabling us to manipulate mechanical movement at the molecular scale, has been a difficult task. Here, we report a metal-organic framework, self-assembled from a porphyrin linker and a new type of Zn-based secondary building unit, serving as a joint in a hinged cube tessellation. Detailed structural analysis and theoretical calculation show that this material is a mechanical metamaterial exhibiting auxetic behavior. This work demonstrates that the topology of the framework and flexible hinges inside the structure are intimately related to the mechanical properties of the material, providing a guideline for the rational design of mechanically responsive metal-organic frameworks.

Formulation and Implementation of the Spin-Restricted Ensemble-Referenced Kohn-Sham Method in the Context of the Density Functional Tight Binding Approach.

The spin-restricted ensemble-referenced Kohn-Sham (REKS) method and its state-interaction state-averaged variant (SI-SA-REKS, or SSR) provide computational platform for seamless inclusion of multireference effects into the density functional calculations. The SSR method enables an accurate calculation of the vertical excitation energies for the molecules with multireference ground states and describes conical intersections between the ground and excited states with the accuracy matching the most sophisticated ab initio multireference wave function methods. In this work, the SSR method is formulated and implemented in the context of the long-range corrected density functional tight binding (LC-DFTB) approach. The new LC-DFTB/SSR method enables calculation of the excited electronic states and the S1/S0 conical intersections of very large molecules. The LC-DFTB/SSR method is benchmarked against vertical excitation energies and conical intersection energies and geometries of several organic molecules with π/π* and n/π* transitions. It is demonstrated that the LC-DFTB/SSR method describes these molecules with reasonable accuracy, which can be considerably improved by a slight modification of the LC-DFTB spin polarization parameters.

Surface Hopping Dynamics beyond Nonadiabatic Couplings for Quantum Coherence.

Description of correct electron-nuclear couplings is crucial in modeling of nonadiabatic dynamics. Within traditional semiclassical or mixed quantum-classical dynamics, the coupling between quantum electronic states and classical nuclear trajectories is governed by nonadiabatic coupling vectors coupled to classical nuclear momenta. This enables us to develop a very powerful nonadiabatic dynamics algorithm, namely, surface hopping dynamics, which can describe the splitting of nuclear wave packets and detailed balance. Despite its efficiency and practicality, it suffers from the lack of quantum decoherence due to incorrect accounts for the electron-nuclear coupling. Here we present a new surface hopping algorithm based on the exact electron-nuclear correlation from the exact factorization of molecular wave functions. This algorithm demands comparable computational costs to existing surface hopping methods. Numerical simulations with two-state models and a multidimensional multistate realistic molecule show that the electron-nuclear coupling beyond the nonadiabatic coupling terms can describe the quantum coherence properly.