Unified Gas-kinetic Wave-Particle Methods III: Multiscale Photon Transport

In this paper, we extend the unified gas-kinetic wave-particle (UGKWP) method to the multiscale photon transport. In this method, the photon free streaming and scattering processes are treated in an un-splitting way. The duality descriptions, namely the simulation particle and distribution function, are utilized to describe the photon. By accurately recovering the governing equations of the unified gas-kinetic scheme (UGKS), the UGKWP preserves the multiscale dynamics of photon transport from optically thin to optically thick regime. In the optically thin regime, the UGKWP becomes a Monte Carlo type particle tracking method, while in the optically thick regime, the UGKWP becomes a diffusion equation solver. The local photon dynamics of the UGKWP, as well as the proportion of wave-described and particle-described photons are automatically adapted according to the numerical resolution and transport regime. Compared to the $S_n$ -type UGKS, the UGKWP requires less memory cost and does not suffer ray effect. Compared to the implicit Monte Carlo (IMC) method, the statistical noise of UGKWP is greatly reduced and computational efficiency is significantly improved in the optically thick regime. Several numerical examples covering all transport regimes from the optically thin to optically thick are computed to validate the accuracy and efficiency of the UGKWP method. In comparison to the $S_n$ -type UGKS and IMC method, the UGKWP method may have several-order-of-magnitude reduction in computational cost and memory requirement in solving some multsicale transport problems.Comment: 27 pages, 15 figures. arXiv admin note: text overlap with arXiv:1810.0598

Spore photoproduct within DNA is a surprisingly poor substrate for its designated repair enzyme—The spore photoproduct lyase

DNA repair enzymes typically recognize their substrate lesions with high affinity to ensure efficient lesion repair. In UV irradiated endospores, a special thymine dimer, 5-thyminyl-5,6-dihydrothymine, termed the spore photoproduct (SP), is the dominant DNA photolesion, which is rapidly repaired during spore outgrowth mainly by spore photoproduct lyase (SPL) using an unprecedented protein-harbored radical transfer process. Surprisingly, our in vitro studies using SP-containing short oligonucleotides, pUC 18 plasmid DNA, and E. coli genomic DNA found that they are all poor substrates for SPL in general, exhibiting turnover numbers of 0.01–0.2 min−1. The faster turnover numbers are reached under single turnover conditions, and SPL activity is low with oligonucleotide substrates at higher concentrations. Moreover, SP-containing oligonucleotides do not go past one turnover. In contrast, the dinucleotide SP TpT exhibits a turnover number of 0.3–0.4 min−1, and the reaction may reach up to 10 turnovers. These observations distinguish SPL from other specialized DNA repair enzymes. To the best of our knowledge, SPL represents an unprecedented example of a major DNA repair enzyme that cannot effectively repair its substrate lesion within the normal DNA conformation adopted in growing cells. Factors such as other DNA binding proteins, helicases or an altered DNA conformation may cooperate with SPL to enable efficient SP repair in germinating spores. Therefore, both SP formation and SP repair are likely to be tightly controlled by the unique cellular environment in dormant and outgrowing spore-forming bacteria, and thus SP repair may be extremely slow in non-spore-forming organisms

EPR Study of UV-irradiated Thymidine Microcrystals Supports Radical Intermediates in Spore Photoproduct Formation

Spore photoproduct is a thymidine dimer formed when bacterial endospore DNA is exposed to ultraviolet (UV) radiation. The mechanism of formation of this thymidine dimer has been proposed to proceed through a radical-pair intermediate. The intermediate forms when a methyl-group hydrogen atom of one thymidine nucleobase is transferred to the C6 position of an adjacent thymidine nucleobase, forming two species, the TCH2 and TH radicals, respectively. Using a series of thymidine isotopologues and electron paramagnetic resonance (EPR) spectroscopy, we show that microcrystals of thymidine exposed to UV radiation produce these two radical species. We observe three sources that donate the additional hydrogen at the C6 position of the TH radical. One of the three sources is the methyl group of another thymidine molecule in a significant fraction of the TH species. This lends support to the radical-pair intermediate proposed in the formation of spore photoproduct

Probing Triple-W Production and Anomalous WWWW Coupling at the CERN LHC and future 100TeV proton-proton collider

Triple gauge boson production at the LHC can be used to test the robustness of the Standard Model and provide useful information for VBF di-boson scattering measurement. Especially, any derivations from SM prediction will indicate possible new physics. In this paper we present a detailed Monte Carlo study on measuring WWW production in pure leptonic and semileptonic decays, and probing anomalous quartic gauge WWWW couplings at the CERN LHC and future hadron collider, with parton shower and detector simulation effects taken into account. Apart from cut-based method, multivariate boosted decision tree method has been exploited for possible improvement. For the leptonic decay channel, our results show that at the sqrt{s}=8(14)[100] TeV pp collider with integrated luminosity of 20(100)[3000] fb-1, one can reach a significance of 0.4(1.2)[10]sigma to observe the SM WWW production. For the semileptonic decay channel, one can have 0.5(2)[14]sigma to observe the SM WWW production. We also give constraints on relevant Dim-8 anomalous WWWW coupling parameters.Comment: Accepted version by JHE

Diatom and silicoflagellate assemblages in modern surface sediments associated with human activity: A case study in Sishili Bay, China

The spatial distribution of diatom and silicoflagellate fossils deposited in modern surface sediments was studied in inshore and offshore zones of Sishili Bay, China, to explore the impact of human activity on the coastal ecosystem. The sediments from 28 sites representing a gradient in intensity of human activity from inshore to offshore were sampled. Although the nutrient parameters inshore showed far higher concentrations than the offshore area, due to sewage discharge and waste dumping in the bay, the average fossil abundance did not differ significantly between the two areas. The diatom fossil Paralia sulcata, supposed to be a eutrophic indicator dominated most sediment samples and displayed a significant and positive correlation with dissolved inorganic nitrogen and phosphorus in the upper water column, but did not show a significant difference in abundance between inshore area and offshore area. Factors such as sediment disturbance (e.g., shipping), grazing pressure (e.g., shellfish aquaculture farm) and sediment characteristics (e.g., grain size) can affect the preservation of fossil debris in the sediment and lower the precision with which human activities can be associated with the fossil abundance.The spatial distribution of diatom and silicoflagellate fossils deposited in modern surface sediments was studied in inshore and offshore zones of Sishili Bay, China, to explore the impact of human activity on the coastal ecosystem. The sediments from 28 sites representing a gradient in intensity of human activity from inshore to offshore were sampled. Although the nutrient parameters inshore showed far higher concentrations than the offshore area, due to sewage discharge and waste dumping in the bay, the average fossil abundance did not differ significantly between the two areas. The diatom fossil Paralia sulcata, supposed to be a eutrophic indicator dominated most sediment samples and displayed a significant and positive correlation with dissolved inorganic nitrogen and phosphorus in the upper water column, but did not show a significant difference in abundance between inshore area and offshore area. Factors such as sediment disturbance (e.g., shipping), grazing pressure (e.g., shellfish aquaculture farm) and sediment characteristics (e.g., grain size) can affect the preservation of fossil debris in the sediment and lower the precision with which human activities can be associated with the fossil abundance. (C) 2012 Elsevier Ltd. All rights reserved