Improved all-optical OR logic gate based on combined Brillouin gain and loss in an optical fiber

Improved all-optical OR gates are proposed, using a novel fiber nonlinearity-based technique, based on the principles of combined Brillouin gain and loss in a polarization-maintaining fiber （PMF）. Switching contrasts are simulated to be between 82.4%-83.6%, for two respective configurations, and switching time is comparable to the phonon relaxation time in stimulated Brillouin scattering （SBS）.

General coupled-mode analysis of a geometrically symmetric waveguide array with nonuniform gain and loss

The exceptional point(EP)is one of the typical properties of parity–time-symmetric systems,arising from modes coupling with identical resonant frequencies or propagation constants in optics.Here we show that in addition to two different modes coupling,a nonuniform distribution of gain and loss leads to an offset from the original propagation constants,including both real and imaginary parts,resulting in the absence of EP.These behaviors are examined by the general coupled-mode theory from the first principle of the Maxwell equations,which yields results that are more accurate than those from the classical coupled-mode theory.Numerical verification via the finite element method is provided.In the end,we present an approach to achieve lossless propagation in a geometrically symmetric waveguide array.

Small signal gain and loss measurement of a CW Nd:YAG laser using an antiresonant ring interferometer

An antiresonant ring （ARR） interferometer configuration is introduced for the characterization of a continuous wave （CW） Nd：YAG laser output. The output of the ARR device is precisely characterized to determine the gain and loss of a laboratory CW Nd：YAG laser by using the Findlay-Clay approach. The ARR arm is then experimentally arranged inside the cavity of an arranged high power side-pumped CW Nd：YAG laser. A coated beam splitter with 50–50% re？ectivity at normal incidence is placed inside the cavity to provide a wide range of re？ectivity from 0 to 100%. This is performed by a rotatable stage and tilting the beam splitter by 10？ with the steps of 0.05. By changing the input electrical power of the laser pump the variation of the output laser power is monitored for 20 individual re？ectivity of ARR arm. Average pump threshold power of about 180 W is obtained. With the help of the derived equations and obtained threshold power, small signal gain and loss associated with the emerging beam is estimated. It is verified that the former is very dependent to the input parameters. Laser efficiency is also measures 5.6% which is quite comparable with the reported values.

Responses of Carbon Sink of Ecosystem Vegetation to Land Use Changes in Kunming City

[Objectives]To analyze the relationship between the land use pattern and the carbon sequestration level of the ecosystem vegetation in Kunming City,and to provide a certain reference for optimizing the land ecological use pattern and scientific carbon reduction and sequestration.[Methods]Based on remote sensing data,meteorological data,vegetation data and soil data,the Carnegie-Ames-Stanford Approach(CASA)was adopted to estimate the vegetation net primary productivity(NPP)in Kunming during 2005-2020,and then the vegetation carbon sink was calculated through the plant mortality model.Besides,it established the land use transfer matrix of Kunming City,and analyzed the change characteristics of the carbon sink of ecosystem vegetation in Kunming City under the influence of land use changes.[Results]During 2005-2020,the water area,construction land and unused land area in Kunming increased by 43.52,710.51 and 2.8 km 2,respectively;farmland,woodland and grassland decreased by 269.72,140.20 and 347.03 km 2,respectively;farmland,woodland,grassland,water area,construction land and unused land caused a total of 58212.72 t of vegetation net carbon sink loss in land conversion,accounting for 14.88%,25.23%,11.95%,10.58%,37.09%,and 0.26%,respectively.[Conclusions]This study is expected to help to improve the ecological carbon sequestration capacity of Kunming and promote the sustainable development of land resources.

Global parameter estimation of the Cochlodinium polykrikoides model using bioassay data

Cochlodinium polykrikoides is a notoriously harmful algal species that inflicts severe damage on the aquacultures of the coastal seas of Korea and Japan. Information on their expected movement tracks and boundaries of influence is very useful and important for the effective establishment of a reduction plan. In general, the information is supported by a red-tide（a.k.a algal bloom） model. The performance of the model is highly dependent on the accuracy of parameters, which are the coefficients of functions approximating the biological growth and loss patterns of the C. polykrikoides. These parameters have been estimated using the bioassay data composed of growth-limiting factor and net growth rate value pairs. In the case of the C. polykrikoides, the parameters are different from each other in accordance with the used data because the bioassay data are sufficient compared to the other algal species. The parameters estimated by one specific dataset can be viewed as locally-optimized because they are adjusted only by that dataset. In cases where the other one data set is used, the estimation error might be considerable. In this study, the parameters are estimated by all available data sets without the use of only one specific data set and thus can be considered globally optimized. The cost function for the optimization is defined as the integrated mean squared estimation error, i.e., the difference between the values of the experimental and estimated rates. Based on quantitative error analysis, the root-mean squared errors of the global parameters show smaller values, approximately 25%–50%, than the values of the local parameters. In addition, bias is removed completely in the case of the globally estimated parameters. The parameter sets can be used as the reference default values of a red-tide model because they are optimal and representative. However, additional tuning of the parameters using the in-situ monitoring data is highly required.As opposed to the bioassay data, it is necessary because the bioassay data have limitations in terms of the in-situ coastal conditions.

Genomic characterization and molecular dating of the novel bacterium Permianibacter aggregans HW001T,which originated from Permian ground water

The Permian Basin is a unique ecosystem located in the southwest of the USA.An unanswered question is whether the bacteria in the Permian Basin adapted to the changing paleomarine environment and survived in the remnants of Permian groundwater.In our previous study,a novel bacterial strain,Permianibacter aggregans HW001T,was isolated from micro-algae cultures incubated with Permian Basin waters,and was shown to originate from the Permian Ocean.In this study,strain HW001T was shown to be the representative strain of a novel family,classified as‘Permianibacteraceae’.The results of molecular dating suggested that the strain HW001T diverged~447 million years ago(mya),which is the early Permian period(~250 mya).Genome analysis was used to access its potential energy utilization and biosynthesis capacity.A large number of transporters,carbohydrate-active enzymes and protein-degradation related genes have been annotated in the genome of strain HW001T.In addition,a series of important metabolic pathways,such as peptidoglycan biosynthesis,osmotic stress response system and multifunctional quorum sensing were annotated,which may confer the ability to adapt to vari-ous unfavorable environmental conditions.Finally,the evolutionary history of strain HW001T was reconstructed and the horizontal transfer of genes was predicted,indicating that the adaptation of P.aggregans to a changing marine environment depends on the evolution of their metabolic capabilities,especially in signal transmission.In conclusion,the results of this study provide genomic information for revealing the adaptive mechanism of strain HW001T to the changing ancient oceans.

Structure-based Comparative Analysis and Prediction of N-linked Glycosylation Sites in Evolutionarily Distant Eukaryotes

The asparagine-X-serine/threonine （NXS/T） motif, where X is any amino acid except proline, is the consensus motif for N-linked glycosylation. Significant numbers of high-resolution crystal structures of glycosylated proteins allow us to carry out structural analysis of the N-linked glycosylation sites （NGS）. Our analysis shows that there is enough structural information from diverse glycoproteins to allow the development of rules which can be used to predict NGS. A Python-based tool was developed to investigate asparagines implicated in N-glycosylation in five species： Homo sapiens, Mus musculus, Drosophila melanogaster, Arabidopsis thaliana and Saccharo- myees cerevisiae. Our analysis shows that 78 % of all asparagines of NXS/T motif involved in N-gly- cosylation are localized in the loop/turn conformation in the human proteome. Similar distribution was revealed for all the other species examined. Comparative analysis of the occurrence of NXS/T motifs not known to be glycosylated and their reverse sequence （S/TXN） shows a similar distribu- tion across the secondary structural elements, indicating that the NXS/T motif in itself is not bio- logically relevant. Based on our analysis, we have defined rules to determine NGS. Using machine learning methods based on these rules we can predict with 93% accuracy if a particular site will be glycosylated. If structural information is not available the tool uses structural prediction results resulting in 74% accuracy. The tool was used to identify glycosylation sites in 108 human proteins with structures and 2247 proteins without structures that have acquired NXS/T site/s due to non-synonymous variation. The tool, Structure Feature Analysis Tool （SFAT）, is freely available to the public at http：//hive.biochemistry.gwu.edu/tools/sfat.