Transmission enhancement in loss-gain multilayers by resonant suppression of reflection

Using the transfer-matrix approach and solving time-domain differential equations, we analyze the loss compensation mechanism in multilayer systems composed of an absorbing transparent conductive oxide and dielectric doped with an active material. We reveal also another regime with the possibility of enhanced transmission with suppressed reflection originating from the resonant properties of the multilayers. For obliquely incident and evanescent waves, such enhanced transmission under suppressed reflection turns into the reflectionless regime, which is similar to that observed in the PT-symmetric structures, but does not require PT symmetry. We infer that the reflectionless transmission is due to the full loss compensation at the resonant wavelengths of the multilayers.Comment: 12 pages, 10 figure

Asymmetric transmission in planar chiral split-ring metamaterials: Microscopic Lorentz-theory approach

The electronic Lorentz theory is employed to explain the optical properties of planar split-ring metamaterials. Starting from the dynamics of individual free carriers, the electromagnetic response of an individual split-ring meta-atom is determined, and the effective permittivity tensor of the metamaterial is calculated for normal incidence of light. Whenever the split ring lacks in-plane mirror symmetry, the corresponding permittivity tensor has a crystallographic structure of an elliptically dichroic medium, and the metamaterial exhibits optical properties of planar chiral structures. Its transmission spectra are different for right-handed versus left-handed circular polarization of the incident wave, so the structure changes its transmittance when the direction of incidence is reversed. The magnitude of this change is shown to be related to the geometric parameters of the split ring. The proposed approach can be generalized to a wide variety of metal-dielectric metamaterial geometries

Trapped-mode excitation in all-dielectric metamaterials with loss and gain

Non-Hermitian photonics based on combining loss and gain media within a single optical system provides a number of approaches to control and generate the flow of light. In this paper, we show that by introducing non-Hermitian perturbation into the system with loss and gain constituents, the high-quality resonances known as trapped modes can be excited without the need to change the symmetry of the unit cell geometry. To demonstrate this idea, we consider a widely used all-dielectric planar metamaterial whose unit cell consists of a pair of rectangular nanoantennas made of ordinal (with loss) and doped (with gain) silicon. Since the quality factor of the trapped-mode resonance can be controlled by changing both spatial symmetry and non-Hermiticity, varying loss and gain allows us to compensate for the influence of asymmetry and restore the quality factor of the localized mode. The results obtained suggest new ways to achieve high-quality resonances in non-Hermitian metamaterials promising for many practical applications in nanophotonics.Comment: 7 pages, 6 figure

Linkage of Viral Sequences among HIV-Infected Village Residents in Botswana: Estimation of Linkage Rates in the Presence of Missing Data

Linkage analysis is useful in investigating disease transmission dynamics and the effect of interventions on them, but estimates of probabilities of linkage between infected people from observed data can be biased downward when missingness is informative. We investigate variation in the rates at which subjects' viral genotypes link across groups defined by viral load (low/high) and antiretroviral treatment (ART) status using blood samples from household surveys in the Northeast sector of Mochudi, Botswana. The probability of obtaining a sequence from a sample varies with viral load; samples with low viral load are harder to amplify. Pairwise genetic distances were estimated from aligned nucleotide sequences of HIV-1C env gp120. It is first shown that the probability that randomly selected sequences are linked can be estimated consistently from observed data. This is then used to develop estimates of the probability that a sequence from one group links to at least one sequence from another group under the assumption of independence across pairs. Furthermore, a resampling approach is developed that accounts for the presence of correlation across pairs, with diagnostics for assessing the reliability of the method. Sequences were obtained for 65% of subjects with high viral load (HVL, n = 117), 54% of subjects with low viral load but not on ART (LVL, n = 180), and 45% of subjects on ART (ART, n = 126). The probability of linkage between two individuals is highest if both have HVL, and lowest if one has LVL and the other has LVL or is on ART. Linkage across groups is high for HVL and lower for LVL and ART. Adjustment for missing data increases the group-wise linkage rates by 40–100%, and changes the relative rates between groups. Bias in inferences regarding HIV viral linkage that arise from differential ability to genotype samples can be reduced by appropriate methods for accommodating missing data

Viral Diversity and Diversification of Major Non-Structural Genes vif, vpr, vpu, tat exon 1 and rev exon 1 during Primary HIV-1 Subtype C Infection

To assess the level of intra-patient diversity and evolution of HIV-1C non-structural genes in primary infection, viral quasispecies obtained by single genome amplification (SGA) at multiple sampling timepoints up to 500 days post-seroconversion (p/s) were analyzed. The mean intra-patient diversity was 0.11% (95% CI; 0.02 to 0.20) for vif, 0.23% (95% CI; 0.08 to 0.38) for vpr, 0.35% (95% CI; −0.05 to 0.75) for vpu, 0.18% (95% CI; 0.01 to 0.35) for tat exon 1 and 0.30% (95% CI; 0.02 to 0.58) for rev exon 1 during the time period 0 to 90 days p/s. The intra-patient diversity increased gradually in all non-structural genes over the first year of HIV-1 infection, which was evident from the vif mean intra-patient diversity of 0.46% (95% CI; 0.28 to 0.64), vpr 0.44% (95% CI; 0.24 to 0.64), vpu 0.84% (95% CI; 0.55 to 1.13), tat exon 1 0.35% (95% CI; 0.14 to 0.56 ) and rev exon 1 0.42% (95% CI; 0.18 to 0.66) during the time period of 181 to 500 days p/s. There was a statistically significant increase in viral diversity for vif (p = 0.013) and vpu (p = 0.002). No associations between levels of viral diversity within the non-structural genes and HIV-1 RNA load during primary infection were found. The study details the dynamics of the non-structural viral genes during the early stages of HIV-1C infection

Elliptical dichroism: operating principle of planar chiral metamaterials

We employ a homogenization technique based on the Lorentz electronic theory to show that planar chiral structures (PCSs) can be described by an effective dielectric tensor similar to that of biaxial elliptically dichroic crystals. Such a crystal is shown to behave like a PCS insofar as it exhibits its characteristic optical properties, namely, co-rotating elliptical polarization eigenstates and asymmetric, direction-dependent transmission for left/right-handed incident wave polarization.Comment: 3 pages, version as accepted in Optics Letters but before final shortening

HIV-1 Subtype C Phylodynamics in the Global Epidemic

The diversity of HIV-1 and its propensity to generate escape mutants present fundamental challenges to control efforts, including HIV vaccine design. Intra-host diversification of HIV is determined by immune responses elicited by an HIV-infected individual over the course of the infection. Complex and dynamic patterns of transmission of HIV lead to an even more complex population viral diversity over time, thus presenting enormous challenges to vaccine development. To address inter-patient viral evolution over time, a set of 653 unique HIV-1 subtype C gag sequences were retrieved from the LANL HIV Database, grouped by sampling year as <2000, 2000, 2001-2002, 2003, and 2004-2006, and analyzed for the site-specific frequency of translated amino acid residues. Phylogenetic analysis revealed that a total of 289 out of 653 (44.3%) analyzed sequences were found within 16 clusters defined by aLRT of more than 0.90. Median (IQR) inter-sample diversity of analyzed gag sequences was 8.7% (7.7%; 9.8%). Despite the heterogeneous origins of analyzed sequences, the gamut and frequency of amino acid residues in wild-type Gag were remarkably stable over the last decade of the HIV-1 subtype C epidemic. The vast majority of amino acid residues demonstrated minor frequency fluctuation over time, consistent with the conservative nature of the HIV-1 Gag protein. Only 4.0% (20 out of 500; HXB2 numbering) amino acid residues across Gag displayed both statistically significant (p<0.05 by both a trend test and heterogeneity test) changes in amino acid frequency over time as well as a range of at least 10% in the frequency of the major amino acid. A total of 59.2% of amino acid residues with changing frequency of 10%+ were found within previously identified CTL epitopes. The time of the most recent common ancestor of the HIV-1 subtype C was dated to around 1950 (95% HPD from 1928 to 1962). This study provides evidence for the overall stability of HIV-1 subtype C Gag among viruses circulating in the epidemic over the last decade. However selected sites across HIV-1C Gag with changing amino acid frequency are likely to be under selection pressure at the population level