Imaging Carrier Transport Properties in Halide Perovskites using Time‐Resolved Optical Microscopy

Halide perovskites have remarkable properties for relatively crudely processed semiconductors, including large optical absorption coefficients and long charge carrier lifetimes. Thanks to such properties, these materials are now competing with established technologies for use in cost‐effective and efficient light‐harvesting and light‐emitting devices. Nevertheless, the fundamental understanding of the behavior of charge carriers in these materials—particularly on the nano‐ to microscale—has, on the whole, lagged behind empirical device performance. Such understanding is essential to control charge carriers, exploit new device structures, and push devices to their performance limits. Among other tools, optical microscopy and spectroscopic techniques have revealed rich information about charge carrier recombination and transport on important length scales. In this progress report, the contribution of time‐resolved optical microscopy techniques to the collective understanding of the photophysics of these materials is detailed. The ongoing technical developments in the field that are overcoming traditional experimental limitations in order to visualize transport properties over multiple time and length scales are discussed. Finally, strategies are proposed to combine optical microscopy with complementary techniques in order to obtain a holistic picture of local carrier photophysics in state‐of‐the‐art perovskite devices.     

The origin of optical asymmetry on earth.

The nature of optical isomerism, and the problem of the origin of optical asymmetry in relation to the origin of life are defined. Developments in particle physics, such as the discovery of parity non-conservation in weak interactions and more recently, of neutral currents, are described. Their significance is that there are a number of possible mechanisms whereby the fundamental asymmetry of matter could be reflected in a preference for one enantiomer over the other, and that, contrary to long-established views, optical isomers do not have identical energy contents: the difference, however, is estimated to be very small. Theories regarding the origin of optical asymmetry are classified in a two-dimensional matrix (origin by chance or due to already existing order; susceptible or not susceptible to experimental test). Recent experimental results and theoretical speculations are reviewed, and proposals are made for further experimental work.     

Optical and Nonlinear Optical Limiting Properties of AgNi Alloy Nanostructures

Silver-nickel alloy nanoparticles with varying size were synthesized by reducing the metal precursors chemically using a single-step solution-based synthesis route. The structural, optical, and nonlinear optical properties of the prepared samples were investigated. The synthesized samples having highly agglomerated, interconnected nature and found to exhibit dipole and multipole surface plasmon resonance related optical absorption bands. Nonlinear optical and optical limiting properties were investigated using a single beam open aperture z-scan technique with the use of 532 nm, 5-ns laser pulses. The nonlinearity observed was found to have contributions from saturable absorption (SA) and excited state absorption (ESA) related to free carriers. The effective nonlinear optical absorption was enhanced in AgNi alloy compared to pure Ag nanostructures.     

Structures of lipid-DNA complexes: supramolecular assembly and gene delivery

Recently, there has been a flurry of experimental work on understanding the supramolecular assemblies that are formed when cationic liposomes (CLs) are mixed with DNA. From a biomedical point of view, CLs (vesicles) are empirically known to be carriers of genes (sections of DNA) in nonviral gene delivery applications. Although viral-based carriers of DNA are presently the most common method of gene delivery, nonviral synthetic methods are rapidly emerging as alternative carriers, because of their ease of production and nonimmunogenicity (viral carriers very often evoke an undesirable and potentially lethal immune response). At the moment, cationic-lipid-based carriers have emerged as the most popular nonviral method to deliver genes in therapeutic applications, for example, CL carriers are used extensively in clinical trials worldwide. However, because the mechanism of transfection (the transfer of DNA into cells by CL carriers, followed by expression) of CL--DNA complexes remains largely unknown, the measured efficiencies are, at present, very low. The low transfection efficiencies of current nonviral gene delivery methods are the result of poorly understood transfection-related mechanisms at the molecular and self-assembled levels. Recently, work has been carried out on determining the supramolecular structures of CL--DNA complexes by the quantitative technique of synchrotron X-ray diffraction. When DNA is mixed with CLs (composed of mixtures of cationic DOTAP and neutral DOPC lipids), the resulting CL--DNA complex consists of a multilamellar structure (L(alpha)(C)) comprising DNA monolayers sandwiched between lipid bilayers. The existence of a different columnar inverted hexagonal (H(II)(C)) phase in CL--DNA complexes was also demonstrated using synchrotron X-ray diffraction. Ongoing functional studies and optical imaging of cells are expected to clarify the relationship between the supramolecular structures of CL--DNA complexes and transfection efficiency.     

Auxin Influx Carriers Control Vascular Patterning and Xylem Differentiation in Arabidopsis thaliana

Auxin is an essential hormone for plant growth and development. Auxin influx carriers AUX1/LAX transport auxin into the cell, while auxin efflux carriers PIN pump it out of the cell. It is well established that efflux carriers play an important role in the shoot vascular patterning, yet the contribution of influx carriers to the shoot vasculature remains unknown. Here, we combined theoretical and experimental approaches to decipher the role of auxin influx carriers in the patterning and differentiation of vascular tissues in the Arabidopsis inflorescence stem. Our theoretical analysis predicts that influx carriers facilitate periodic patterning and modulate the periodicity of auxin maxima. In agreement, we observed fewer and more spaced vascular bundles in quadruple mutants plants of the auxin influx carriers aux1lax1lax2lax3. Furthermore, we show AUX1/LAX carriers promote xylem differentiation in both the shoot and the root tissues. Influx carriers increase cytoplasmic auxin signaling, and thereby differentiation. In addition to this cytoplasmic role of auxin, our computational simulations propose a role for extracellular auxin as an inhibitor of xylem differentiation. Altogether, our study shows that auxin influx carriers AUX1/LAX regulate vascular patterning and differentiation in plants.     

Modeling Auxin Transport and Plant Development

The plant hormone auxin plays a critical role in plant development. Central to its function is its distribution in plant tissues, which is, in turn, largely shaped by intercellular polar transport processes. Auxin transport relies on diffusive uptake as well as carrier-mediated transport via influx and efflux carriers. Mathematical models have been used to both refine our theoretical understanding of these processes and to test new hypotheses regarding the localization of efflux carriers to understand auxin patterning at the tissue level. Here we review models for auxin transport and how they have been applied to patterning processes, including the elaboration of plant vasculature and primordium positioning. Second, we investigate the possible role of auxin influx carriers such as AUX1 in patterning auxin in the shoot meristem. We find that AUX1 and its relatives are likely to play a crucial role in maintaining high auxin levels in the meristem epidermis. We also show that auxin influx carriers may play an important role in stabilizing auxin distribution patterns generated by auxin-gradient type models for phyllotaxis.     

Plasmonic Optical Properties and Applications of Metal Nanostructures

In this review article, we provide an overview of recent research activities in the study of plasmonic optical properties of metal nanostructures with emphasis on understanding the relation between surface plasmon absorption and structure. Both experimental results and theoretical calculations have indicated that the plasmonic absorption strongly depends on the detailed structure of the nanomaterials. Examples discussed include spherical nanoparticles, nanorods, nanowires, hollow nanospheres, aggregates, and nanocages. Plasmon–phonon coupling measured from dynamic studies as a function of particle size, shape, and aggregation state is also reviewed. The fascinating optical properties of metal nanostructures find important applications in a number of technological areas including surface plasmon resonance, surface-enhanced Raman scattering, and photothermal imaging and therapy. Their novel optical properties and emerging applications are illustrated using specific examples from recent literature. The case of hollow nanosphere structures is highlighted to illustrate their unique features and advantages for some of these applications.     

Location of proline derivatives in conformational space. II. Theoretical optical activity

The coupling of theoretical optical calculations with experimental data provides a check of the validity of the theory or provides conformational information. The theory was validated by studies in which the approximate conformation was located independently. These studies have shown that a theory restricted to the two lowest energy transitions for each chromophore gives qualitative agreement with experiment. On the other hand, for some of the proline derivatives, the theoretical treatment allows detailed conformational assignments. Both successes and failures in correlating theory with experiment are discussed. The results presented provide a basis for assessing the prospects for relating protein and polypeptide optical activity to their conformations.     

Study of the optical properties of a pulse-periodic high-pressure cesium discharge

Results of theoretical and experimental studies of the optical spectrum of a pulse-periodic high-pressure cesium discharge are presented. The results of calculations are in good agreement with experimental data. The possibility of creating an efficient light source based on recombination emission from the discharge plasma is demonstrated. The formation mechanisms of the continuous spectrum of discharge radiation are considered.     

Near-Field Optical Experimental Investigation of Gold Nanohole Array

Gold nanohole arrays are fabricated with focused ion beam irradiating gold thin film supported on quartz substrate. The topography of the nanohole arrays is characterized using an atomic force microscope, and the near-field optical transmission properties of the nanohole array are investigated with a near-field scanning optical microscope. Our experimental results verify the near-optical transmission performance and further demonstrate that they are in agreement with the theoretical calculation results. The enhanced optical transmission of the nanohole arrays are expected to be used for a variety of applications in sensor and photonics devices.     

Competitive binding-based optical DNA mapping for fast identification of bacteria - multi-ligand transfer matrix theory and experimental applications on Escherichia coli

We demonstrate a single DNA molecule optical mapping assay able to resolve a specific Escherichia coli strain from other strains. The assay is based on competitive binding of the fluorescent dye YOYO-1 and the AT-specific antibiotic netropsin. The optical map is visualized by stretching the DNA molecules in nanofluidic channels. We optimize the experimental conditions to obtain reproducible barcodes containing as much information as possible. We implement a multi-ligand transfer matrix method for calculating theoretical barcodes from known DNA sequences. Our method extends previous theoretical approaches for competitive binding of two types of ligands to many types of ligands and introduces a recursive approach that allows long barcodes to be calculated with standard computer floating point formats. The identification of a specific E. coli strain (CCUG 10979) is based on mapping of 50–160 kilobasepair experimental DNA fragments onto the theoretical genome using the developed theory. Our identification protocol introduces two theoretical constructs: a P-value for a best experiment-theory match and an information score threshold. The developed methods provide a novel optical mapping toolbox for identification of bacterial species and strains. The protocol does not require cultivation of bacteria or DNA amplification, which allows for ultra-fast identification of bacterial pathogens.     

Practical Implementation of Accurate Finite-Element Calculations for Electromagnetic Scattering by Nanoparticles

Plasmonics - The finite-element method (FEM) is increasingly used as a numerical tool to support experimental and theoretical studies of the optical properties of nanoparticles, in contexts such as...     

Predicting Carriers of Ongoing Selective Sweeps without Knowledge of the Favored Allele

Methods for detecting the genomic signatures of natural selection have been heavily studied, and they have been successful in identifying many selective sweeps. For most of these sweeps, the favored allele remains unknown, making it difficult to distinguish carriers of the sweep from non-carriers. In an ongoing selective sweep, carriers of the favored allele are likely to contain a future most recent common ancestor. Therefore, identifying them may prove useful in predicting the evolutionary trajectory—for example, in contexts involving drug-resistant pathogen strains or cancer subclones. The main contribution of this paper is the development and analysis of a new statistic, the Haplotype Allele Frequency (HAF) score. The HAF score, assigned to individual haplotypes in a sample, naturally captures many of the properties shared by haplotypes carrying a favored allele. We provide a theoretical framework for computing expected HAF scores under different evolutionary scenarios, and we validate the theoretical predictions with simulations. As an application of HAF score computations, we develop an algorithm (PreCIOSS: Predicting Carriers of Ongoing Selective Sweeps) to identify carriers of the favored allele in selective sweeps, and we demonstrate its power on simulations of both hard and soft sweeps, as well as on data from well-known sweeps in human populations.     

Polarization and Filter Properties Investigation of Metal Gratings and Rings

We demonstrated the near-field optical transmission properties of nanogratings with spoke and rings structures through a near-field scanning optical microscope, and the far-field optical transmission properties with different polarization angles are investigated with an optical microscope. Our experimental results verified the polarization properties of the nanograting structures and further demonstrated the experimental results are supported by the finite difference time domain theoretical simulation. The optical microscope imaging of the spoke and ring structures also show that the grating structures can disperse visible light of different wavelengths.     

Mechanistic Insights into Ferredoxin-NADP(H) Reductase Catalysis Involving the Conserved Glutamate in the Active Site

Plant-type ferredoxin-NADP(H) reductases (FNRs) are flavoenzymes harboring one molecule of noncovalently bound flavin adenine dinucleotide that catalyze reversible reactions between obligatory one-electron carriers and obligatory two-electron carriers. A glutamate next to the C-terminus is strictly conserved in FNR and has been proposed to function as proton donor/acceptor during catalysis. However, experimental studies of this proposed function led to contradicting conclusions about the role of this glutamate in the catalytic mechanism. In the present work, we study the titration behavior of the glutamate in the active site of FNR using theoretical methods. Protonation probabilities for maize FNR were computed for the reaction intermediates of the catalytic cycle by Poisson-Boltzmann electrostatic calculations and Metropolis Monte Carlo titration. The titration behavior of the highly conserved glutamate was found to vary depending on the bound substrates NADP(H) and ferredoxin and also on the redox states of these substrates and the flavin adenine dinucleotide. Our results support the involvement of the glutamate in the FNR catalytic mechanism not only as a proton donor but also as a key residue for stabilizing and destabilizing reaction intermediates. On the basis of our findings, we propose a model rationalizing the function of the glutamate in the reaction cycle, which allows reinterpretation of previous experimental results.     

Submicroscopic malaria parasite carriage: how reproducible are polymerase chain reaction-based methods?

The polymerase chain reaction (PCR)-based methods for the diagnosis of malaria infection are expected to accurately identify submicroscopic parasite carriers. Although a significant number of PCR protocols have been described, few studies have addressed the performance of PCR amplification in cases of field samples with submicroscopic malaria infection. Here, the reproducibility of two well-established PCR protocols (nested-PCR and real-time PCR for the Plasmodium 18 small subunit rRNA gene) were evaluated in a panel of 34 blood field samples from individuals that are potential reservoirs of malaria infection, but were negative for malaria by optical microscopy. Regardless of the PCR protocol, a large variation between the PCR replicates was observed, leading to alternating positive and negative results in 38% (13 out of 34) of the samples. These findings were quite different from those obtained from the microscopy-positive patients or the unexposed individuals; the diagnosis of these individuals could be confirmed based on the high reproducibility and specificity of the PCR-based protocols. The limitation of PCR amplification was restricted to the field samples with very low levels of parasitaemia because titrations of the DNA templates were able to detect < 3 parasites/µL in the blood. In conclusion, conventional PCR protocols require careful interpretation in cases of submicroscopic malaria infection, as inconsistent and false-negative results can occur.     

Optical and conformational properties of the 7-(beta-D-ribofuranosyl) purines

The optical and conformational properties of certain 7-ribosyl purines have been studied using several experimental and theoretical methods. The CD, MCD, and absorption spectra of the 7-ribosyl purines and their cations have been determined experimentally with some solvent effects being noted. Theoretically we have used the SCF-CI and CNDO molecular orbital calculations to determine the optical properties of the bases; Simpson's bond exciton theory to determine the optical properties of the bases; Simpson's bond exciton theory to determine the optical properties of the ribose moiety; the optical activity was determined by the dipole coupling and electricmagnetic coupling equations; and the conformational energy calculations are included as a basis for excluding highly improbable conformations. On the basis of these calculations, we concluded that the oxy derivatives and the amino derivatives are predominately in the “extreme anti” conformation and “standard anti” conformation, respectively. However, the conclusions are tentative since at the present time the band assignments are not unequivocal. At least one n-π* transition has been identified in the spectra which is not notably sensitive to pH and solvent effects. Several implications of this observation are discussed.     

A model for oxygen supply in fixed bed reactors with immobilized hybridoma cells

In fixed bed reactors with animal cells immobilized in macroporous carriers sufficient oxygen supply is a critical parameter. For modelling of the oxygen consumption and the oxygen profile in a fixed bed oxygen gradients within the porous carriers and along the length of the fixed bed have to be considered. For the complex geometry of the fixed bed a model structure was assumed, that allows the calculation of the oxygen profile. The model for oxygen supply of the immobilized cells included the transport resistance from the bulk fluid into the carriers and diffusion within the carriers. The model was compared with experimental data obtained with a hybridoma cell line for production of monoclonal antibodies. Model calculations and experimental data agree rather well. The mean volume-specific oxygen uptake rate as an indicator for the cell activity increased with the superficial flow velocity of the bulk liquid flow, and did not depend on the length of the fixed bed in the range tested. This indicates, that the convective transport from the bulk liquid flow between the carriers to the outer surface of the carriers is a dominating transport resistance besides the diffusive oxygen supply within the carriers.