We propose a concept of terahertz waveguide plasmon amplifier based on a metal groove with active graphene. It is shown that the power amplification factor of the longitudinal-section magnetic (LSM) waveguide plasmon  near the cut-off frequency of this mode can exceed the amplification factor of the transverse magnetic (TM) plasmon in a layered graphene structure by more than four orders of magnitude for the same frequency. This is caused by the increase of the LSM plasmon wavelength near the cut-off frequency, smaller energy velocity of the LSM mode, and greater energy release from graphene for the LSM plasmon due to stronger lateral confinement of the LSM waveguide plasmon as compared to the TM plasmon in a layered graphene structure. We show that the enhancement of the LSM plasmon amplification factor near the cut-off frequency is a stronger effect than that due to screening of graphene. Creation of the inverse population of free charge carriers in graphene at THz frequencies3 as well as the development of tools for excitation of highly confined graphene plasmons1 resulted in possibility of compensation losses and amplification of THz electromagnetic field in active graphene structures giving rise to various concepts of THz graphene lasers5 and plasmonic amplifiers8. It is known that efficiency of the optical pumping of graphene is rather low because graphene absorbs less than 2.3% of the incident optical pump power9. A concept of the diffusion pumping of graphene allows for creating the free carrier population inversion in graphene with greater efficiency8. The diffusion pumping of graphene through a narrow-gap black-As substrate can prevent heating of graphene11. Creation of the population inversion in graphene via the electron and hole injection in graphene was studied in12. It was shown that electron–hole injection in graphene can substantially reduce the pumping threshold13. The possibility of plasmon amplification and necessary conditions for the plasmon lasing regime in graphene pumped by the electron–hole injection was discussed in14.Graphene is an atom thick monolayer of graphite possessing unique properties such as high mobility, linear energy spectrum of free charge carriers and zero energy band-gap15. The influence of embedded graphene layer on the guided modes of optical layered waveguides was investigated in16. Dispersion characteristics and damping of waveguide modes17, and the magnetoplasmon-polariton excitations18 in the layered structures with gated two-dimensional electron systems and graphene were studied theoretically.Propagation of THz plasmons in layered structures and metal waveguides with two-dimensional electron systems, particularly with graphene, has been actively studied theoretically and experimentally throughout the last decade. The effect of a graphene monolayer on the propagation of transverse electric modes in a rectangular metal waveguide was theoretically studied in6 and diffusion8 pumping was theoretically discussed. Amplification of THz plasmons in a pair of parallel active graphene layers was theoretically studied in19. We will show below in this paper that the amplification of plasmons in a waveguide with active graphene could be more efficient than that in the layered graphene structures due to strong transverse confinement of the plasmon field in a waveguide.Active guiding of THz surface plasmons in layered structure with inversely populated graphene with optical21 and experimentally realized22. The transition region between bound and leaky mode ranges in a metal groove waveguide was explored in23. Amplification of plasmons in waveguide structures with inversely populated graphene has not been studied so far.Open plasmonic waveguides are promising for transferring the electromagnetic signals in THz plasmonic integrated circuits. Waveguide plasmons are at an advantage because the field of such plasmons is fully confined in the plane transverse to the direction of the plasmon propagation. Propagation of the channel plasmons and their field structure in rectangular and triangular metal grooves were theoretically discussedd, placed in the bottom of a rectangular metal groove of width L and infinite depth. As a matter of fact, we assume that above graphene there is a hollow  graphene, schematically shown in Fig. 24 unlike the case of layered structures or hollow metal waveguides with transverse magnetic (TM) and transverse electric (TE) modes. We focus on the longitudinal-section magnetic (LSM) plasmon with the ac electric and magnetic fields 1, 2, and 3 corresponding to three different groove widths L = 1 μm, 2 μm, and 5 μm, respectively. Curve 4 in Fig. 18. Dispersion of the TM plasmon in a layered graphene structure and its increment were calculated using dispersion equation presented in25. One can see t hat, for large metal groove width, the LSM plasmon dispersion curve merges with the TM plasmon dispersion curve at high THz frequencies. This occurs because at high THz frequencies the influence of the side metal walls of the groove becomes negligible and the wavevector component transverse to the plasmon propagation direction becomes much smaller as compared to the longitudinal one: In a metal waveguide partially filled with dielectric, the eigenmodes of the waveguide split into the longitudinal-section magnetic (LSM) modes and the longitudinal-section electric (LSE) modesL as in Fig. In Fig. entclass1pt{minimaentclass1pt{minimaL as in Figs. Let us discuss the physical origins of significant increase of the LSM plasmon power amplification factor. First, the longitudinal component of the LSM plasmon wavevector entclass1pt{minima19, where 26We wonder which factors influence the increment of the modes. According to the energy conservation law, the spatial growths of the plasmon energy flux defined asAs can be seen from Eq. , the powL as in the previous figures in comparison with the energy velocity of the TM plasmon. One can see that the energy velocity of the TM plasmon monotonically increases with decreasing the plasmon frequency. The energy velocity of the LSM plasmon is smaller than the energy velocity of the TM plasmon and markedly decreases near the cut-off frequencies. Also note that the energy velocity of the LSM plasmon becomes smaller for smaller width of the groove. At the cut-off frequency, the plane wave oscillates strictly across the side walls of the groove waveguide being homogeneous  along the waveguide. As a result, the wave does not transfer the energy along the waveguide so that the energy velocity becomes zero in this case. In general, the cut-off frequency of a specific metallic waveguide mode is determined by the transverse wavevector of this mode24 which in turn depends on the width of the metal groove in our case.We calculated the energy velocities of the LSM plasmon presented in Fig. The ratio 25. Comparison the effect of vertical and lateral plasmon field confinement on the power increment of the LSM and TM plasmon modes is shown in Fig. d = 10 μm (curve 1) near its cut-off frequency is greater than the power increment of the TM plasmon in the layered graphene structure with a much closer metal screen placed at distance d = 0.01 μm from graphene (curve 3). It means that the enhancement of the LSM plasmon power increment near its cut-off frequency is a stronger effect as compared to that due to screening of graphene.It is known that graphene screening by a nearby metal plate (gate) enhances the amplification of THz plasmons as compared to the case of unscreened plasmons due to stronger vertical confinement of the screened plasmon field near graphene26. However, the effect of losses (gain) increases near the cut-off frequencies since the imaginary part of the wavevector become equal and can even exceed its real part (the latter tends to zero at the cut-off frequency). As a result, the group velocity loses definite physical meaning and senselessly differs from the energy velocity in this case. That is why we use only the energy velocity quantity in our paper.Note that the energy velocity introduced in our paper well coincides with the group velocity in the systems with small losses z axis) and y and z axes, where the first superscript indicates the direction along the y axis, the second index does for the z axis). We use the following boundary conditions. The components of the electric field tangential to the metal surfaces are set to zero at the walls and bottom of the groove waveguide: z axis) wavevector component , ε0 is the electric constant, 6:e is the elementary charge, T are the mean free time and temperature of the charge carriers in graphene, respectively, F and –EF for electrons and holes, respectively), τ. The remaining terms in Eq.  near the cut-off frequency of this mode can exceed that of the TM plasmon in a layered graphene structure by more than four orders of magnitude for the same frequency. This is caused by the increase of the LSM plasmon wavelength (up to tens of micrometer) and stronger interaction of the LSM plasmon with active graphene as compared to the TM plasmon due to smaller energy velocity of the LSM mode and greater energy release from graphene for the LSM plasmon near its cut-off frequency. The plasmon energy velocity exceeds 10


LINE-1 or L1) comprises about 17% of the human genome. L1 retrotransposition is known to cause genomic instability and related disorders, and resveratrol suppresses this retrotransposition; however, the underlying mechanism is still not elucidated. Recent observations showed that low-molecular-weight compounds might induce L1 retrotransposition through unknown mechanisms. This study aimed to determine polyphenol resveratrol (RV)’s effect on L1-RTP (retrotransposition) in somatic cells. Surprisingly, RV completely blocked L1-RTP. Experiments using the PPARα inhibitor GW6471 or siRNA-mediated PPARα depletion showed that RV-mediated L1-RTP’s inhibition depended on peroxisome proliferator-activated receptor α (PPARα). We demonstrated that RV inhibits p38 and cAMP response element binding protein phosphorylation, which are involved in MAPK signaling, and the L1-ORF1 protein’s chromatin recruitment. Furthermore, RV increased the expression of sirtuin-6 (SIRT6), which inhibited the activation of L1. The sirtuins family, SIRT1, SIRT6, and SIRT7, but not SIRT3, are involved in RV-mediated inhibition of L1-RTP. Overall, our findings suggest that RV directly modulates PPARα-mediated L1-RTP in somatic cells and that MAPK signaling interacts with SIRT6 closely and may play a role in preventing human diseases such as cancer.The retroelement long interspersed element-1 ( LINE-1 or L1), a highly active autonomous and non-long terminal repeat retrotransposon, is the most abundant endogenous retroelement in humans and accounts for approximately 17% of the human genome3. L1 can retrotranspose to new genomic loci via a “copy and paste” mechanism. Notably, the L1 element can retrotranspose itself as well as other retroelements, such as Alu and SVA (SINE-VNTR-Alu: short interspersed element-variable number tandem repeat-Alu). A single human cell contains more than 5 × 105 copies of L1, most of which are functionally inactive. However, 80–100 copies are capable of active retrotransposition. By analyzing the blood coagulation factor VIII gene in hemophilia A, it was found to be potentially capable of retrotransposistion in human genome4. Moreover, genetic mutation by L1 insertion has been reported, and a relationship with disease development is known. L1 insertions were reported in various human tumors, especially in cancer-related genes such as c-myc and APC in breast and colon carcinomas, respectively6. Recently, genome instability was a contributing factor to many age-related diseases. L1 drives IFN in senescent cells and developed age-related diseases7. L1-RTP is induced by disease development and environmental pollutants such as benzo[a]pyrene (B[a]P).Long interspersed element-1 (9. ORF2 is a multidomain protein with endonuclease and reverse transcriptase functions11. ORF1 and ORF2 perform L1-RTP (retrotransposition), which proceeds via three steps: transcription, reverse transcription, and insertion of the newly synthesized L1 DNA into the host genome via target-site primed reverse transcription13.The L1 genomic sequence is ~ 6 kb in length and contains two open reading frames (ORF1 and ORF2), with molecular masses of ~ 40 and 150 kDa, respectively. ORF1 is a basic protein with a nucleic acid chaperone activity and is present within cytoplasmic ribonucleoprotein complexes or stress granules in the cytoplasm14. We also found that L1-RTP is induced by 2-amino-1-methyl-6-phenylimidazopyridine (PhIP) and 2-amino-3,8-dimethyl-imidazoquinoxaline (MeIQx), heterocyclic amines (HCAs) formed during the cooking of red meat as food-borne carcinogens, as well as benzo[a]pyrene (B[a]P), environmental pollutants16. Moreover, we reported that L1-RTP was induced during two-stage skin carcinogenesis initiated by 7,12-dimethylbenz[a]anthracene (DMBA) and 12-O-tetradecanoylphorbol-13-acetate17 and abused drugs including methamphetamine, cocaine, morphine, and fentanyl citrate19. We suggested that many carcinogenic and substance abuse drugs induced L1-RTP and genome instability, but we did not identify any compounds that inhibited L1-RTP.We recently reported that 6-formylindolocarbazole (FICZ), a tryptophan photoproduct, acts as a potent inducer of L1-RTP20. Several studies have shown pleiotropic health benefits of RV, suggesting that it may prevent the progression of various age-related diseases23.Conversely, this study focuses on resveratrol (RV) , a polyphenolic phytoalexin abundant in several plants and is also found in grapes, pine, and red wine+-dependent deacylases that play a crucial role in transcription and L1 resistant factor24. It has been reported that the expression of SIRT6 is increased when cells are exposed to RV. SIRT6 knockout mice drive inflammation and show strong L1 activation, and cells display excess genomic instability25. Moreover, SIRT7 mediated chromatin form regulation, Lamin A/C, and repression of L1 element transcription level26. Collectively, we took particular note of the sirtuins family and assessed the mechanism of L1-RTP inhibition by RV. We investigated if L1-RTP inhibition involves PPARa and SIRT6, which interact with SNF2H, a component of the SWI chromatin remodeling complex. SNF2H is a member of the SWI/SNF chromatin remodeling complex family known to regulate target genes’ transcription by altering chromatin structure. SIRT6 and SNF2H are chromatin remodeling factors involved in repair during DNA damage, suggesting that they are also involved in the aging process.Our focus in this study was on peroxisome proliferator-activated receptor α (PPARα) as a ligand for RV, and sirtuins (SIRT) 6 are NADL1 retrotransposition also occurs in somatic cells28, in which deregulation of the process may trigger various disease states owing to gene deletions. RV has been reported to inhibit L1 methylation and RTP, but the mechanism of this is unclear29. Therefore, we analyzed the L1 repressive mechanism of RV using the L1-RTP inducers we have previously reported. Elucidating the mechanisms that inhibit L1 function in RV could contribute to the aging process and the extension of a healthy life span.These observations suggest that human somatic cells are susceptible to genome instability by L1-RTP, but it is unclear whether L1-RTP inhibits cellular activity by altering genomic stability or if external stimuli mechanistically induce it. However, other studies have provided evidence that 14. Briefly, HeLa cells were transfected with pCEP4/L1 mneol/ColE1  and selected for 2 days with hygromycin. RV for additional 2 days, cells were grown on neomycin for 3–4 weeks  colonies. As shown in Fig. L1-RTP was detected by a colony formation assay, as described15. We next examined the effect of RV on L1-RTP that is induced by these compounds. As shown in Fig. 30. The p38 pathway and a transcription factor, cAMP response element binding protein (CREB), are present downstream of MAPK31. We have previously reported that FICZ, MeIQx, and PhIP induce L1-RTP by phosphorylating the p38 pathway and CREB. Therefore, we analyzed whether the phosphorylation of the p38 pathway and CREB by FICZ, MeIQx, and PhIP was inhibited by RV. To confirm this, we performed western blotting (WB) analysis, showing that RV markedly inhibited the phosphorylation of p38 and CREB by FICZ, MeIQx and PhIP  gene family30. SIRT1 and SIRT7 exist in the nucleus and nucleolus, respectively, while SIRT3 exists in the mitochondria. To further demonstrate SIRT1, SIRT3, SIRT6, and SIRT7 dependency, we described that two different siRNAs sequences . DSBs formation is associated with its chromatin incorporation regulated by SIRT6 and SNF2H. To examine whether SNF2H is involved in RV inhibited L1-RTP, and to further demonstrate this SNF2H dependency, we found that two F2H Fig. b. These F2H Fig. c. SIRT6 F2H Fig. d. RV-indF2H Fig. e. These 34. To confirm this, we performed L1-RTP analysis after treatment with RV or N-acetyl cysteine (NAC), an antioxidant compound serving as a positive control, which was found to have a minimal effect on L1-RTP  a protein encoded by human immunodeficiency virus type-1 (HIV-1)41. We searched among the compounds that regulate L1-RTP but were unable to find compounds that inhibit L1-RTP. This study found that RV inhibited L1-RTP in HeLa cells and HuH-7 cells and investigated the molecular mechanism involved. We discovered that RV, a polyphenol with antioxidant properties, inhibited L1-RTP at concentrations ranging from 5 to 20 μM, which is one-half of the vasodilator effect of RV (30–40 μM)42. Under physiological conditions, RV is described as being present at the order of a few μM, so RV-based inhibition of L1-RTP could occur within an in vivo range.Recent studies have shown that the insertion of human L1 into genes occurs in the germline during early development, and in somatic cells such as cancer cells17. As these compounds exist within our surroundings, we are frequently exposed to them. RV can reportedly regulate L1 methylation29, whereas the mechanism by which RV regulates the metastatic potential of L1 remains elusive. Therefore, we investigated whether RV inhibits compounds that induce L1-RTP and clarified the analysis of the mechanism. We found that RV inhibited FICZ-, MeIQx-, and PhIP-induced L1-RTP in HeLa cells and HuH-7 cells. RV inhibited the phosphorylation of p38 and CREB by FICZ and HCA. Moreover, FICZ- or HCA-induced chromatin recruitment of ORF1 was blocked by RV. Taken together, our data suggested that RV inhibited L1-RTP by inhibiting p38 and CREB phosphorylation as well as by blocking the chromatin recruitment of the L1-ORF1 protein. Recently it was reported that L1 activity dependent on and integrated with cellular phosphorylation regulatory cascades significantly increased our understanding of interactions between L1 and the host44. We suggested that L1-RTP required MAPK phosphorylation and its downstream transcription factor in previous articles. Several articles reported that RV is a MAPK inhibitor; thus, RV inhibits the L1-RTP inducer. Collectively, L1-RTP required phosphorylation of ORF1 protein and downstream cascade factor or environmental transcription factor in host cells.We previously showed that environmental carcinogens, tryptophan photoproducts, and HCAs, originating from the cooking of red meat, induced L1-RTP45; thus, we suggested that RV first interacts with and binds to PPARα to initiate the L1-RTP inhibition step. PPARα inhibitors reportedly induce L1 activation37, suggesting that PPARα is involved in the pathway that induces L1-RTP.To determine the molecular mechanism of RV-mediated L1-RTP inhibition, we examined whether RV-based inhibition of L1-RTP depended on its antioxidant effect. The effect of RV was compared to that of NAC, which was found not to inhibit L1-RTP; thus, RV acts independently of its antioxidant effect. We further tested this using an inhibitor and siRNA-based depletion of the PPARα, the first target factor identified for RV. Interestingly, biochemical analysis revealed that RV inhibited L1-RTP in a PPARα-dependent manner. The 4’-hydroxyl group of resveratrol is critical for the direct activation of PPARα33. SIRT6 was found to repress L1 activity by ribosylating Kruppel-associated box (KRAB)-associated protein 1 (KAP1) of transcription inhibition factor. SIRT6 binds to the 5ʹ-UTR of the L1 promoter and ribosylates KAP125. The SIRT6-mediated KAP1 mono-ADP-ribosylation (MARylation) promotes the interaction between KAP1 and SIRT6, thereby promoting the recruitment to the L1 5ʹ-UTR24. L1-RTP is facilitated by the chemical modification of the Poly (ADP-ribose) Polymerase 2 recruitment of replication protein A to other DNA repair proteins. Moreover, RV was shown to increase SIRT genes’ expression. Here, we confirmed that RV increased SIRT6 protein expression. Combined with the finding that SIRT6 interacts with L1, this strongly suggests that it mediates inhibition of L1-RTP. The cell signal is PPARα as target factor and involves the regulatory function of SIRT6 and L1. SNF2H is involved in RV-mediated inhibition of L1-RTP, but SNF2H did not interact with ORF1 by IP-WB. We confirmed that expression of SIRT6 increased by RV is inhibited by PPARα and SNF2H siRNA.Many studies have recently identified potential restriction factors for L146. We suggested that RV inhibiting L1-RTP by two cell signaling pathways. First, RV directly modulated the PPARα receptor and SNF2H upregulated SIRT6 expression inhibited L1; second, ORF1 interacted with SIRT6 and PPARα blocked MAPK signaling , compounds that induce autoimmune diseases and cancer development. The effect of RV is essential from the perspective of preventive medicine—we are exposed to ultraviolet light and carcinogens in the environment regularly. We reported previously that the picomolar levels of FICZ (3 pM) could induce L1-RTP14; notably, about 8 pM FICZ is generated after 24-h exposure of tissue-culture medium to ordinary laboratory light47. Moreover, picomolar levels of HCAs induced L1-RTP, comparable to the PhIP concentration detected in human breast milk48. These data suggest that somatic cells are exposed to factors that promote genome instability in the typical life environment. As people age, genetic instability is stimulated by exposure to environmental and intrinsic factors. Activation of transposable elements occurs due to environmental factors and can extend to loss of neuronal function50.In our current study, we showed that RV directly modulates the PPARα receptor to inhibit L1-RTP. Furthermore, we suggest a new signaling pathway in which SIRT6 interacts with p38 in MAPK signaling, with RV inhibiting L1-RTP via suppression of MAPK signaling. Cea et al. reported that SIRT6 binds DNA damage sites and recruits and blocks MAPK signalinging Fig. . SIRT1 aing Fig. . These f51. RV can reverse this process in a SIRT1 dependent manner. SIRT7 mediated H3K18 deacetylation regulates the L1 expression and promotes L1 association with elements of the nuclear lamina26. As SIRT6 plays a crucial role in silencing L1 activity, SIRT6 activator as RV may prove effective at counteracting the age-related loss of L1 silencing. Our results demonstrate that SIRT1, SIRT6, and SIRT7 were associated with the L1 element and PPARα, so RV inhibited genome instability, including L1. RV appears to promote genomic stability, limiting the occurrence of genetic mutations.Sirtuins protect against many of the various aging-associated conditions, including skin damaged by UV radiation of SIRT1 in human keratinocytesIn this study, RV-mediated inhibition of L1-RTP depended on PPARα, SIRT1, 6, 7, and SNF2H. RV inhibits p38 and CREB phosphorylation, which are involved in MAPK signaling, and chromatin recruitment of the L1-ORF1 protein. Furthermore, RV increased the expression of SIRT6, which inhibited L1 activation. We suggest that RV directly modulates PPARα-mediated L1-RTP in somatic cells and that MAPK signaling closely interacts with SIRT6 preventing human diseases, such as cancer and sporadic cases of inborn errors.N-acetylcysteine (NAC) were procured from Wako Pure Chemical Industries, Ltd . Acetoxy-forms of HCAs  were synthesized . FICZ is a tryptophan photoproduct . GW6471 PPARα inhibitor was purchased from Wako . Neomycin (Wako) and hygromycin  were used after checking the cytotoxic effects in each cell line. Antibodies against PPARα , sirtuin 1 (SIRT1), sirtuin 3 (SIRT3), sirtuin 6 (SIRT6), sirtuin 7 (SIRT7), p38, phosphorylated p38, CREB, phosphorylated CREB, and SNF2H , H2AX (Millipore), enhanced green fluorescent protein , Anti-FLAG Tag M2 antibody , and glyceraldehyde 3-phosphate dehydrogenase (GAPDH)  were used as primary antibodies. A rabbit polyclonal antibody against human ORF1 was generated using the peptide MGKKQNRKTGNSKTQSAC as an immunogen 14. Anti-mouse and anti-rabbit secondary IgG conjugated to horseradish peroxidase were obtained from DAKO Japan .Protease and phosphatase inhibitors were purchased from Roche Diagnostics . Resveratrol and L1 retrotransposition was assayed as described previously53 using reporter vectors based on pCEP4/L1 mneoI/ColE1 (pL1-NeoR). The construct contained all components of human L1 in a single transcriptional unit, with a neomycin-resistance gene in the reverse orientation. When L1 retrotransposes, the intron within the neomycin  resistance gene is spliced out, resulting in a neomycin-resistant cell. Constructs were transfected into ~ 2.0 × 106 cells using Lipofectamine 2000 (Life Technologies), with selection for 3 days on 25 μg/mL hygromycin. Transformants were then transferred to 100-mm plates at ~ 1 × 105 per six plates, treated for an additional 2 days with the indicated amounts of chemicals, and finally grown on 300 (HeLa cell) or 250 (HuH-7 cell) μg/mL neomycin to select for cells in which retrotransposition occurred. After 2–3 weeks, colonies were stained with methylene blue and counted. Plating efficiency was examined to exclude cytotoxic effects of RV and observed that uM of RV. HeLa cells were treated for 2 days with RV at doses ranging from 200 to 1.25 μM, and 500 cells of each test group were plated onto 6-cm plates. After additional 7 days, cells were fixed and stained with methylene blue.19. Cells were washed with phosphate-buffered saline and resuspended in 50 mM Tris–HCl pH 7.6, 150 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.5% deoxycholic acid, 1% NP-40, and protease inhibitors. Cells were ultrasonicated for 12.5 min  at medium power (250 W) at 4 °C with a Bioruptor , and soluble cellular extracts were recovered after centrifugation for 10 min at 16,000×g. Protein concentration was determined using the BCA Protein Assay Reagent Kit , and extracts were analyzed by WB. Blots were probed with primary antibodies, labeled with secondary antibodies conjugated to horseradish peroxidase, and visualized using Pierce Western Blotting Substrate Plus (Thermo Scientific). The original data obtained using WB and the result of adjusting the brightness using Photoshop are shown in the supplementary information.WB was analyzed as described previously15. We transfected 10 nM of siRNA using Lipofectamine RNAiMAX in HeLa cells and HuH-7 in 2.0 × 106 cells. The nucleotide sequences of each siRNA are shown in Table R to evaluate the inhibitory effects of the siRNAs on L1-RTP induction. Two days later, the cells were replated, incubated for 2 days with RV, and analyzed. As a control, Silencer Negative Control siRNAs  were used.Two small interfering RNAs (siRNAs) were prepared (Thermo Scientific), and their functions were evaluated by transfection into cells followed by WB analysis15, which encodes a chimeric protein of ORF1 protein A and the calmodulin-binding protein. On day 2, after transfection of pORF1-TAP into HeLa cells, FICZ or HCAs was added to the culture medium before RV, and cell extracts were prepared on the following day. The chromatin-enriched fraction (chromatin fraction) was isolated using the Subcellular Protein Fractionation Kit (Thermo Fisher Scientific) with micrococcal nuclease as described previously15. Detection of ORF1-TAP was performed by probing with a horseradish peroxidase-conjugated α-rabbit IgG antibody. H2AX served as a positive control for the chromatin fraction. Fractionation and detection of H2AX were evaluated using previously described methods15. A subcellular fractionation analysis revealed ORF1 after transfection of expression vectors encoding a chimeric ORF1-TAP protein.We used the pORF1-TAP (tandem affinity purification) construct15. HEK293T cells were transfected with each plasmid by Lipofectamine 2000. To express ORF1-EGFP, flag-tagged SIRT6 flag-tagged ovalbumin (OVA), and ST (streptavidin-tagged)-EGFP, we constructed pORF1-EGPF, pFlag-SIRT6, pFlag-OVA, and pST-EGFP. Cells were suspended in IP buffer composed of 20 mM Tris–HCl (pH 7.6), 5 mM EDTA, 150 mM NaCl, 0.5% NP-40, 10% glycerol. 500 μg of cell extract were reacted with 4 μg of αFlag or EGFP or αPPARα and then recovered with Dynabeads protein G beads (Thermo scientific). About one-tenth of each extract subjected to IP was loaded onto SDS-PAGE and simultaneously analyzed as an input sample. The immunohistochemical analysis was done by the reported method15. We used the TrueBlot  secondary antibody, which masks the detection of the heavy and light IgG chains, and thus, it displayed them as thin or undetectable bands.Immunoprecipitation (IP) assay was carried out, according to the reported methodU-test, with an n value of more than four. P-values of less than 0.05 were considered statistically significant.Statistical significance was evaluated using the Mann–Whitney Supplementary Figures.


A high-performance electro-optic Mach–Zehnder modulator (MZM) with outstanding characteristics is proposed. The MZM is in a push-pull configuration that is constructed using an ITO/graphene-based silicon waveguide. A novel idea for engineering of the plasma dispersion effect in an ITO/graphene-based waveguide is proposed so that the modulation characteristics of the MZM are highly improved. Plasma dispersion effects of ITO and graphene layers are tailored in such a way that a large difference between real parts of guided mode effective index of the two arms is achieved while their corresponding imaginary parts are equal. As a result, a very low  Optical modulators have already been investigated by many research groups20. The demand for high speed, low power consumption, high modulation depth and compact optical modulators still continues to support rapidly growing data in integrated optical systems.Optical modulators are the key components of photonic communication networks and processing systems. The input information of the modulators can be transferred to the amplitude, phase or polarization of the optical carrier through electro-optic22. However, pure silicon optical modulators are mainly based on the weak plasma dispersion effect, which hinders the realization of compact and integrated interconnections7. As a result, new materials and structures have already been explored to mitigate the drawbacks of silicon optical modulators. One of the outstanding materials that could revolutionize silicon photonics is graphene.Silicon photonics is a promising technology that has received tremendous interest for realizing efficient integrated optical devices such as modulators23. The superb optical characteristics of graphene have made it an amazing choice for various applications such as photodetectors25, logic gates27, polarizers28, plasmonic tweezers29, isolators30, mode-locked lasers32, switches and modulators37. The complementary metal-oxide-semiconductor (CMOS) compatibility and great tenability of graphene are of exceptional importance for optical modulators. In addition, high carrier mobility of more than 19. The modulator was performed by applying an external voltage across the graphene layers and changing the Fermi levels so that the absorption mechanisms were tuned. However, the modulation bandwidth was limited to 1 GHz. In 2016, a broadband graphene-based optical modulator was proposed where a modulation depth of 2 dB and insertion loss of 0.9 dB at a very high bandwidth of 35 GHz were reported38. However, the high bandwidth was achieved at the cost of high drive voltage of 25 V. It should be emphasized that most of the previously proposed graphene modulators have been based on the EA effects while the electro-refractive effect in graphene may also lead to high-performance modulators and phase shifters40.Graphene is a two-dimensional (2D) sheet of carbon atoms arranged in a honeycomb lattice that exhibits unique electrical, mechanical, thermal and optical properties43. The ITO-based EA modulators work within the α-dominant region of ITO permittivity where the optical loss is changed by modulating voltage. In contrast, the n-dominant region of ITO permittivity is of interest for phase shifters and electro-refractive modulators. However, according to Kramers–Kronig relations44, the real part variations of ITO refractive index is inevitably accompanied by the variations of optical loss α. Therefore, it is important to design electro-refractive modulators with low required voltage and simultaneously low insertion loss. In recent years, different kinds of electro-refractive modulators based on ITO have been studied. In 2018, an ITO-based Mach–Zehnder modulator (MZM) was proposed where a half-wave voltage and active device length product of 45. However, the switching speed was undesirably limited to 1 kHz. In 2018, another research group presented a lower 46. However, such a 47. It was experimentally shown that the 48.Indium tin oxide (ITO) as a transparent conductive oxide (TCO) is another material for next-generation optical modulators. The carrier concentration in ITO can be several orders of magnitude higher than silicon which leads to significant index modulation. Furthermore, the permittivity of ITO can be effectively tuned through an external bias voltage so that its real part can cross the zero point known as epsilon-near zero (ENZ). Various EA optical modulators using the ENZ behavior of ITO have been investigatedIn this paper, a very high performance ITO/graphene-based electro-optic MZM is proposed. The modulator is made of an engineered silicon waveguide based on two graphene sheets and two ITO layers as active materials whose characteristics are modified by an external voltage. The free-carrier dispersion effects in ITO and graphene are engineered so that large real part variations of guided mode effective indices in the two arms are obtained while their imaginary parts are the same. As a result, a 49. A graphene sheet is transferred to the hBN and an ITO layer is subsequently grown that are spaced by The perspective view of the proposed MZM is schematically shown in Fig. D) of aSi is firstly assumed to be 100 nm but it will be optimized in the following section. It should be emphasized that in practice graphene sheets cannot be laminated on sharp corners and on 90° waveguide edges practically. However, we first assume an ideal waveguide with rectangular cross section. The practical aspects of the modulator including the waveguide with trapezoidal cross section is investigated at the end of the paper.The total width and height of the ridge are respectively taken as As it is shown in Fig. In order to gain a better insight into the operation of the proposed waveguide, the effects of graphene sheets and ITOs on the guided mode should be investigated, separately. Hence, the stacks of the waveguide are theoretically separated to form the hypothetical waveguides shown in Fig. 50 and theoretical52 works where chemical potentials of 0.7 eV to 1 eV have been reported. However, our proposed modulator can also operate with lower voltages and chemical potentials. Furthermore, assuming 53, a breakdown voltage of 6.5 V is obtained for the In order to calculate the guided mode effective index of the waveguide shown in Fig. entclass1pt{minimaAs it is shown in Fig. According to Fig. As a general rule, a large real part change of the effective index is of interest for an electro-refractive modulator while the imaginary parts at the two states of modulator should be nearly equal. Therefore, as it is shown in Fig. The effective index for the guided mode of the structure shown in Fig. As it is shown in Fig. According to Fig. mentclass2pt{minimAs it is shown in Fig. d as Eq.  (see “Med as Eq. ”. When tAs it is shown in Fig. entclass1pt{minimaIn order to find the optimum The characteristics of the guided mode at the optimum initial doping and as a function of the applied voltage is plotted in Fig. D in Fig. D are calculated and shown in Fig. D leads to more confinement of guided mode and as a result higher light-matter interaction so that a larger phase shift is acquired. On the other side, as it is expected, the IL of the modulator increases from 2 dB at One of the geometrical parameters that can affect the modulator characteristics is the thickness of aSi (Another phenomenon that should be noticed is the electrostatic effect of the upper graphene sheet on the carrier concentration of the lower ITO layer as a consequence of thin aSi. As it is shown in Fig. The important point that should be taken into account is that it is not practically possible to place the stack of layers on the Si ridge with vertical side walls. Therefore, a trapezius with the side wall angle of It is instructive to investigate the effect of electrodes on the device operation. The metal electrodes are located at the two sides of the waveguide to apply the required external voltages. Such metal electrodes can possibly increase the IL of the device. The electrodes are assumed to be 1200 nm away from each other in our simulations. The guided modes of the proposed waveguide in the presence of the electrodes and without electrodes are calculated and respectively shown in Fig. Now, the operation of the modulator with the designed waveguide is investigated. The transmission spectra of the MZM in the on and off states are shown in Fig. For the sake of completeness, the effect of applied voltage errors on the performance of the modulator is studied. In this regard, the transmission spectra of the modulator in the off state for various pull voltage errors at Finally, other electrical characteristics of the proposed modulator are calculated. One of the most important parameters is the bandwidth of the modulator which is limited by the RC time constant of the modulator. The total capacitance of the proposed waveguide is the parallel combination of the two oxide capacitances (g to Eq.  (see “Meg to Eq. ”, the qu55, and a graphene-contact resistance of 56, the total ohmic resistance is obtained as The total resistance of the waveguide is also obtained by adding the graphene sheet resistance to the graphene- and ITO-contact resistances. Assuming a sheet resistance of mentclass2pt{minim61:62e is the electron charge, 61 and The simulation results in “63. Here, 43:The dielectric constant of ITO is calculated from the Drude model where the ITO carrier concentration is required. The induced carrier concentration in ITO is calculated according to:Then, the calculated chemical potential is applied to Eq.  and finaRegarding the analysis of the MZM, the transfer matrices of input Y-junction, the arms and output Y-junction are respectively expressed as:The output power of the MZM can be obtained by:In summary, we proposed a very high-performance electro-optic ITO/graphene-based MZM. According to the presented analysis, the contributions of the plasma dispersion effects in graphene and ITO layers are engineered so that a large difference between


Moreover, dimethylated arsenicals did not adsorb to BC at all, and in the case of FeBC, qm values of dimethylarsinic acid (DMA(V)), dimethylmonothioarsinic acid (DMMTA(V)), and dimethyldithioarsinic acid (DMDTA(V)) were calculated to be 7.08, 0.43, and 0.28 mg/g, respectively. This was due to the formation of iron oxide  on the surface of BC. Linear combination fitting using As K-edge X-ray absorption near edge structure spectra confirmed that all chemical forms of dimethylated arsenicals adsorbed on the two-line ferrihydrite were DMA(V). Thus, FeBC could retain highly mobile and toxic arsenicals such as DMMTA(V) and DMDTA(V)) in the environment, and transform them into DMA(V) with relatively low toxicity.In this study, the adsorption characteristics of dimethylated arsenicals to rice husk biochar (BC) and Fe/biochar composite (FeBC) were assessed through isothermal adsorption experiments and X-ray absorption spectroscopy analysis. The maximal adsorption capacities (q Daphnia magna were 9.5, <30, 1.7, and 6.5 mg/L, respectively  was 58 mg [Yoon et al.  studied as 58 mg , whilst An X-ray absorption near edge structure (XANES) analysis was performed to evaluate the chemical forms of dimethylated arsenicals adsorbed onto FeBC. As the main cause of the adsorption of dimethylated arsenicals onto FeBC was presumed to be the two-line ferrihydrite formed on the FeBC surface, the adsorption characteristics of dimethylated arsenicals on FeBC were studied by using the As K-edge XANES spectra of two-line ferrihydrite samples adsorbed with DMA(V), DMMTA(V), and DMDTA(V). In contrast, except for the two-line ferrihydrite adsorbed with As(V), the absorption energy of all samples adsorbed with DMA(V), DMMTA(V), and DMDTA(V) were the same as that of the reference compound . Daphnia magna was reported to be 9.5, <30, 1.7, and 6.5 mg/L, respectively [DMMTA(V) has been shown to exhibit high human- and eco-toxicity compared to DMA(V) and DMDTA(V). Cytotoxicity levels (IC50) of As(III), DMA(V), DMMTA(V), and DMDTA(V) in bladder cancer EJ-1 cells was reported to be 75 μM, ≥1 mM, 17 μM, and ≥1 mM, respectively , whilst ectively . In thisIn this study, the adsorption characteristics of As(V) and dimethylated arsenicals (DMA(V), DMMTA(V), and DMDTA(V)) on BC and FeBC were assessed. As BC was modified with two-line ferrihydrite, the maximum adsorption capacity of As(V) increased approximately 5-fold, from 1.28 to 6.32 mg/g. This may have been due to the Fe oxide modification, thereby increasing adsorption sites on the FeBC surface and decreasing the electrostatic repulsion. Dimethylated arsenicals did not adsorb onto BC, whereas on FeBC, DMA(V), DMMTA(V), and DMDTA(V) showed maximum adsorption capacities at 7.08, 0.43, and 0.28 mg/g, respectively. As such, dimethylated arsenicals were adsorbed through the reaction with two-line ferrihydrite presented on the surface of FeBC. Similar to observations in previous studies, adsorption inhibition was observed with an increase in thiol-group content. The XANES-LCF analysis confirmed that the main form of dimethylated arsenicals adsorbed to two-line ferrihydrite was DMA(V). This indicated that FeBC could be utilized to lower the mobility of dimethylated arsenicals in the environment and to transform them into less hazardous forms.


The scattering of gases on solid surfaces plays a vital role in many advanced technologies. In this study, the scattering behavior of helium on graphene surfaces was investigated, including the thermal accommodation coefficient (TAC), outgoing zenith angle of helium, bounce number, and interaction time. First, we performed molecular dynamics simulations to describe the incident angle-resolved behaviors, and showed that the scattering is highly dependent on the zenith angle of incident helium but insensitive to the azimuthal angle. The contribution of the normal velocity component of the incident helium dominated the energy transfer. The nonlinear relationship of the parameters to the zenith angle of the incident helium could be suppressed by increasing the graphene temperature or decreasing the speed of the incident helium. Subsequently, the scattering performance considering all gas molecules in the hemispherical space was evaluated using the Monte Carlo method with angle-resolved results. The result showed that the TAC, its nominal components, and the zenith angle of the scattered helium increased with higher speeds of incident helium and lower temperatures of graphene. This study should provide a fundamental understanding of energy transfer between gas and two-dimensional materials and guidelines to tune the scattering behavior between them. The scattering dynamics of gas-phase molecules on the surface of solids ,2,3 play2 were found to be independent of the gas pressure and temperature  with a cutoff of 12.0 Å, where ε takes 1.6228 meV, and σ is 3.053 Å. Those values come from the OPLS-AA force field [A vacuum layer of 50 Å was added on each side of the graphene to avoid interaction between real helium atoms and the imaged carbon atoms of the graphene. The helium atom was initially placed at a plane 40 Å higher than the top surface of the graphene. The atomistic interactions of graphene were described using the modified AIREBO force field , which hce field  accordinBk is the Boltzmann constant, T is the thermodynamic temperature, and m is the mass of the helium atom. The incident zenith angle (polar angle) and azimuthal angle of helium were specified to evaluate the effect of the incident angle of the molecular beam. It is worth noting that samples with a polar angle of 90° correspond to the cases where the normal velocity component is zero. The helium atom could be attracted to the graphene surface purely by the van der Waals interactions. During the scattering of helium on graphene, helium gained kinetic energy from the graphene and eventually escaped from the attraction of the graphene surface. The simulation ceased when the outgoing helium was 15.0 Å from the graphene surface. The velocity and coordinates of the helium atom were recorded during the scattering process for further analysis.All molecular dynamics simulations were conducted with the LAMMPS code . A heliuE, v, m, and T denote the kinetic energy, speed, mass, and thermodynamic temperature of the helium atom, respectively. sT and gT indicate the temperature of the solid surface and the incident helium gas. Bk is the Boltzmann constant. The subscripts “in” and “o” indicate the incident and scattered helium, respectively.The Maxwell model has been widely applied for calculation of the thermal accommodation coefficient . This model indicates that the α fraction of gas molecules has diffuse scattering on the solid surface, and the remaining fraction has specular scattering. In this way, TAC is described asnα) and nominal tangential thermal accommodation coefficient  byin,xyv and in,zv denote the in-plane and normal components of the speed of the helium atom, respectively.To identify the contributions of the in-plane and out-of-plane components of the energy transfer, we decomposed the thermal energy accommodation into the nominal normal thermal accommodation coefficient  and real tangential thermal accommodation coefficient  may also be evaluated using the following definition, given the zenith angle inθ of the incident helium:According to the definition of TAC, the real normal thermal accommodation coefficient fi–(9), respectively. In this way, the relative frequencies in the various ranges of the incident angles can be obtained. Subsequently, the angle-resolved TAC was recalculated by replacing the denominator of Then, the Monte Carlo method was used to sample the velocity components of the helium gas. In detail, the Box–Muller transform method with the acceptance–rejection method was used, such that zv, of incident helium was zero, such that the helium atom was adsorbed onto the graphene surface by the van der Waals interactions. As shown in zv decreased from zero to the negative maximum, where the negative sign indicates helium moving towards the graphene surface. During this process, helium atoms initially moved slowly downward and then accelerated. Afterward, the interaction between helium and graphene changed from attraction to repulsion, and the normal velocity component of helium declined. When helium arrived at the first minimum position above the graphene surface, zv became zero. After that, the helium atom bounced back from the graphene surface due to the repulsion forces between helium and graphene. The zv of helium atom increased quickly to the local maximum, where the attraction and repulsion between helium and graphene were balanced. Then, zv decreased as the attraction of graphene became weaker, dominating the graphene–helium interaction as helium moved away from the graphene. There were several different following behaviors. As shown in sample 1, the helium was far away enough from the graphene surface and had enough kinetic energy to escape from attraction by the graphene, leading to a scattering process with a single bounce. Another case is that the kinetic energy stored in the graphene might not be large enough for the first bounce-back process, and the helium atom would be attracted to the graphene surface again until it obtained enough kinetic energy to escape from attraction by the graphene. This is illustrated by sample 2, in which there were five bounces of helium until it flew away from the interaction region. In this study, we did not find any cases where the helium atom was trapped on the graphene surface within the simulation time.The scattering process of gas molecules on solid surfaces can be composed of the adsorption, trapping, and escaping stages. One of the latter two stages may not show up during the scattering. The scattering behavior shown above varies randomly depending on the initial status of the graphene and the helium atom, such as the initial location, incident velocity, and incident angle of the helium atom. As shown in inθ) ranged from 0° to 90° with an increment of 10°, while the azimuthal angle (inφ) was specified at 0°, 30°, 60°, and 90°, respectively, as shown in φin, TAC values increased significantly with larger values of inθ. Furthermore, TAC was insensitive to the inφ with the given inθ. For instance, TAC was 0.127 for a inθ of 0° and 0.319 for a inθ of 90°, which was 2.525 times that of the former value. For inθ of 0°, the incident velocity of the helium atom was normal to the graphene surface, and it was parallel to the surface for inθ of 90°. To evaluate the contribution of the normal and in-plane velocity components, we decomposed the TAC into nominal normal thermal accommodation (NNTAC) and nominal tangential thermal accommodation coefficients (NTTAC) in Equations (2) and (3). inθ was greater than 60°, which means that in-plane kinetic energy was transferred from the helium to the graphene. As a result, we found that the kinetic energy component of the normal velocity contributed to a higher TAC and higher energy transfer along with a larger zenith angle. According to the definition in the Maxwell model, the real normal thermal accommodation coefficient  and real tangential thermal accommodation coefficient  were calculated by Equations (5) and (6), respectively. Bk·sT) was 0.086 eV, and the kinetic energy of the incident helium atom at 500 K was 0.0646 eV, which was 75.1% of the former. When the zenith angle was smaller than 30°, the normal kinetic energy transferred by ideal diffusive scattering was a small value, which is the denominator. The case was the same when the zenith angle was larger than 70°. Interestingly, the variance in RNTAC at a small inθ was larger than that of RTTAC at a high value of inθ, which also demonstrates the importance of the normal velocity of the incident helium and the large contribution of the normal kinetic energy transfer during the scattering process.Systems of monolayer graphene and a helium atom were simulated to elucidate the zenith-angle effect of the incident helium on the scattering process. The zenith angle  were set as the threshold planes of the scattering. Those curves showed that, similarly to the bounce number, the interaction time had a correlation with the zenith angle of the incident helium except for the special cases of a inθ of 90°. The interaction time gradually increased from 1.839 ps to 4.968 ps for a inθ from 0° to 80°. The TAC averaged by the interaction time changed slightly. For inθ of 90°, the value rose sharply to 16.681 ps. To evaluate the influence of the normal velocity of the incident helium, we evaluated the interaction time by setting the threshold planes as 7 Å above the graphene surfaces. The dashed curves represent the results in inθ of 90°, which decreased the efficiency of the heat energy transfer.The interaction time between helium atoms and the graphene surface provides another angle to understand the scattering process of helium on the surface, as shown in To understand why the zenith angle of incident helium significantly affected the TAC and scattering behaviors, we plotted the contour of the potential energy for the helium–graphene system. The potential energy was calculated by averaging the potential energy of the system in a dynamic run. First, a helium atom was introduced above the well-equilibrated monolayer graphene. Then, the potential energy was sampled by placing the helium atom in the x–z plane shown by an inlet with a resolution of 0.1Å. The reference potential energy was set when the helium atom was 20 Å above the graphene surface. Then, the system ran 1000 steps in the NVE ensemble with a timestep of 1.0 fs between each sample of the potential energy. In this way, the system was sampled 1000 times, and the averaged potential energies were plotted in the x–z plane in inθ of 0°. inθ of 10° and 90°, respectively. Those results confirm that the energy transfer of helium on graphene was insensitive to the azimuthal angle. inθ of 10°, the NNTAC values ranged from 0.043 to 0.079, while the NTTAC values fluctuated from 0.061 to 0.067. We found that the relative variance in the normal kinetic energy transfer was larger than that in the in-plane counterpart. The absolute values of NTTAC were comparable to those of the NNTAC. In the case of a θin of 90°, the NNTAC values ranged from 0.304 to 0.353, while the NTTAC values fluctuated from −0.023 to −0.0006. It is notable that the in-plane energy transfers from helium to graphene and the change in NNTAC were much larger than those in NTTAC in absolute values. In terms of RNTAC and RTTAC, the red curve of RNTAC and blue cure of RTTAC show larger fluctuations in inθ of 10° and inθ of 90°, respectively. The reasons are the same as described above. On the other hand, we found that the variation in RNTAC with a inθ of 90˚ and RTTAC with a inθ of 10˚ was much lower than their counterparts, and the absolute values of those curves were much larger. We can conclude that energy transfer between helium and graphene is insensitive to the azimuth.oθ), average bounce number of helium, and interaction time of helium with graphene (t) were plotted with the various azimuthal angles in oθ for a inθ of 10° ranged between 21.056° and 21.932°, while the range of oθ for a inθ of 90° was from 57.463° to 59.042°. The variance in both cases was less than 4% and was much smaller than the change in TAC.The zenith angle of scattered helium  shown in inθ was larger than 30°, the zenith angle oθ became smaller with higher graphene temperatures. This change increased as inθ increased. In addition, the change in oθ with graphene temperature was much lower than that in TAC and TAC components, and changes at a high inθ were larger than those at a low inθ. In the cases of the three temperatures, the inθ of specular reflection was between 30° and 40° and became smaller with higher graphene temperatures. The linear region of inθ was between 30° and 60°, and the slope became smaller with higher graphene temperatures.The zenith angle of the scattered helium , the zenith angle of scattered helium, the bounce number, and the interaction time of helium with graphene. Performance was insensitive to the azimuthal angle of the incident helium but highly dependent on the zenith angle. Moreover, the nominal normal thermal accommodation coefficient (NNTAC) and nominal tangential thermal accommodation coefficient (NTTAC) were defined by decomposing the kinetic energy transfer into the in-plane and normal velocity components of helium. We found that TAC and NNTAC increased nonlinearly with larger zenith angles in the cases of incident helium at 500 K and graphene at 1000 K. In contrast, the NTTAC decreased with increasing zenith angle. However, NNTAC outweighed NTTAC, and kinetic energy transfer via the normal velocity of helium dominated the energy transfer between helium and graphene. The real normal thermal accommodation coefficient (RNTAC) and real tangential thermal accommodation coefficient (RTTAC) defined by the Maxwell Model were consistent with the NNTAC and NTTAC, respectively, except for larger fluctuations in RNTAC at a low zenith angle and RTTAC at a large zenith angle. The zenith angle of the scattered helium nonlinearly increased with a larger zenith angle of incident helium. The zenith angle of the scattered helium was linearly correlated with the zenith angle of the incident helium in the middle range from 30° to 60°. However, it deviated from a linear correlation significantly at either low or high zenith angles of incident helium. The scattered helium had the same zenith angle, approximately 44°, as the incident helium. The bounce number increased with higher zenith angles of incident helium. In the case of a constant incident helium speed and graphene temperature, it was consistent with our hypothesis that a higher bounce number corresponded to greater energy transfer between the gas and the solid surface. Helium took more time to interact with the graphene when the zenith angle of incident helium was larger. In particular, an extremely long flight time was required when the incident helium speed was parallel to the graphene surface. The effect of the zenith angle of the incident helium atom stemmed from a heterogeneous distribution of potential energy between helium and graphene, and the dynamic vibration of the graphene atoms mitigated the differences in the potential energy of the system given various in-plane locations of helium.When the incident helium speed was fixed and the graphene temperature was enhanced, the nonlinear behavior of the angle-resolved parameters of the TAC, NNTAC, NTTAC, RNTAC, and RTTAC, the zenith angle of the scattered helium, and the bounce number of helium were suppressed. The dependence of these parameters on the zenith angle of incident helium was different at low and high zenith angles of incident helium. For instance, TAC, NNTAC, and RNTAC increased with higher graphene temperatures at low zenith angles of incident helium, but decreased at higher zenith angles of incident helium. However, the NTTAC and RTTAC had opposite trends. The reduction in the zenith angle of scattered helium and the bounce number at higher graphene temperatures was much more severe at a higher zenith angle of the incident helium. The interaction time of helium decreased slightly with a higher graphene temperature. Relative potential analysis of the system showed a bigger potential-energy change at higher graphene temperatures due to a larger vibration among carbon atoms in the graphene, which resulted in a change in the scattering performance.When the graphene temperature was fixed and the incident helium speed was changed, the nonlinear behavior of the angle-resolved parameters of the TAC, NNTAC, NTTAC, RNTAC, and RTTAC, the zenith angle of the scattered helium, and the bounce number of helium could be suppressed by reducing the incident helium speed. The phenomena observed when increasing the graphene temperature regarding TAC, NNTAC, TTAC, RNTAC, RTTAC, bounce number and interaction time could also be achieved by decreasing the incident helium speed. Significantly, the TAC, NTAC, NNTAC, RNTAC, and RTTAC were insensitive to the zenith angle of incident helium at 100 K. In this section, we found that a large bounce number of helium and longer interaction time between helium and graphene could not guarantee a higher TAC and higher energy transfer.Integrated scattering performance was obtained through weighting the values of the parameters with various zenith angles of the incident helium via the relative frequencies of the zenith angles by Monte Carlo simulation, and showed the scattering performance of helium on graphene considering all molecules in the hemispherical space. The Monte Carlo simulations considered the fast atom effect of helium atoms. The result showed that the zenith angle of incident helium followed a normal distribution with an expected value of 45.55°. The integrated TAC, NNTAC, NTTAC, and bounce number of helium increased with higher incident helium speeds and decreased with higher graphene temperatures. Significantly, the NNTAC accounted for more than 90% of the TAC. The integrated bounce number of helium was consistent with the interaction time of helium with graphene. The intuition that larger bounce numbers and longer interaction times correspond to higher transfers of energy is only valid when disregarding the change in incident helium speed. As the incident helium speed changes, larger bounce numbers and longer interaction times could show lower TAC values. In this study, we provided a clear description of the scattering performance of helium on high-temperature graphene surfaces in both angle-resolved and integrated aspects. These findings can provide a better fundamental understanding and a new way, such as through incident angles, to tune the scattering behavior of gas molecules on 2D materials.


Assessments, in particular high stakes assessments, impact the nature of teaching and learning. Given this, the goal of citizenship if seen as important needs to feature within high stakes school exit assessments rather than only as part of curriculum and assessment policy rhetoric. South Africa’s Mathematical Literacy (ML) curriculum foregrounds critical democratic citizenship. We analyse the ML Grade 12 exit assessments from their start in 2008 to 2020 to understand the emphasis placed on critical citizenship and how this emphasis has shifted over time. The literature base links critical citizenship orientations with reasoning and reflecting questions, so we focused on examination questions in this category. Our findings show shifts away from critical citizenship related agendas towards foregrounding a life preparation orientation for the self-managing person. Linked with this shift, we note a move away from general societal contexts towards more personal/individual contexts and moves from almost entirely national contexts to inclusion of global contexts. We noted movement from more open-phrased questions towards closed ‘check figure calculated is valid’-type questions. Assessment memoranda suggest assessors view these questions as reasoning items, eroding the critical citizenship agenda. While increasing numbers of students are taking ML rather than Mathematics, average performance stands at around 40%. This points to limited and diminishing access to mathematical reasoning and reflecting for critical democratic citizenship. The paper highlights ways in which analysis of examinations over time can provide a window into the presence or absence of the citizenship agenda in mathematics education. Mathematical Literacy (ML) and within it the goal of preparing secondary learners for post school citizenship roles appears in various forms across a range of international curricula. In some countries it is implemented across curricular learning areas, while in others it is included within various mathematics offerings. South Africa has a relatively unique offering in that ML is a distinct subject from Mathematics in the upper secondary grades (Grades 10–12). ML is compulsory for, and only available to, students not taking Mathematics. While there are many differences in interpretations of the notion of Mathematical Literacy across countries, many, including South Africa, align closely with the PISA conceptualisation as needing to assist learners “to recognise the role that mathematics plays in the world and to make the well-founded judgments and decisions needed by constructive, engaged and reflective citizens.” OECD, , p.75.In this article, based on the notion that assessment is an ‘essential circuit’ of education Ball,  and, as We begin with a brief description of the particularities of the post-apartheid South African context that guides our conceptualisation of mathematics education for citizenship. Our context differs somewhat to countries that have integrated a mathematics for critical democratic citizenship approach in that South African democracy is relatively new. Education system transformation occurred in parallel with democratic transformation in 1994. In the aftermath of apartheid, the education system in general and mathematics education in particular were mandated to develop participating citizens who would contribute to building an equitable non-racist democratic society. These citizens would critically analyse the mathematics of societal, environmental, economic and political issues through understanding the formatting power of mathematics and challenging injustices. The curriculum introduction stated: “In the past the curriculum has perpetuated race, class, gender and ethnic divisions and has emphasised separateness, rather than common citizenship and nationhood. It is therefore imperative that the curriculum be restructured to reflect the values and principles of our new democratic society” DoE, .Mathematics was mandated to prepare learners for critical democratic citizenship. In Grades 0–9 the subject named Mathematics was replaced with the subject named ‘Mathematics, Mathematical Literacy and Mathematical Sciences’ (MLMMS) whose rationale emphasised empowering learners to “understand the contested nature of mathematical knowledge” preparing learners for participation in society in a democratic, non-racist and non-sexist manner DoE, , p. 1 anA similar trajectory of change followed in Grades 10–12 but differed in that this phase introduced two pathways for students: the option of taking Mathematics or taking Mathematical Literacy (ML). These were examined in Grade 12 for the first time in 2008. In the 2008 examinations, 47% of learners enrolled for the grade 12 examinations took ML. Over the years since 2008, with some fluctuations, increasing proportions of learners took ML. By 2020, 59% of all students enrolled for Grade12 examinations were taking ML. The curriculum description states ML: “provides learners with an awareness and understanding of the role that mathematics plays in the modern world. Mathematical Literacy is a subject driven by life-related applications of mathematics. It enables learners to develop the ability and confidence to think numerically and spatially in order to interpret and critically analyse everyday situations and to solve problems” DOE, , p. 9.Early analysis of the ML curriculum statement indicated an emphasis on critical democratic citizenship and practical relevance and applications in contrast to Mathematics which had less integration with contexts and included emphasis on preparing students for further mathematics related studies  engaging thoughtfully with local, national and global issues. However, the ML curriculum was also organised by mathematical content areas and the assessment specifications included mathematical skills , mathematical skills in context  alongside those framed by the notion of a self-managing person and by critical attention to societal issues. In the detail of the curriculum content the notion of ML for critical democratic citizenship was less foregrounded than in the introductory sections. This tension between the overall aims and conceptualisation of ML as a subject and the detailed specification of what was to be taught and assessed has been alluded to in relation to specific topic areas Gal, , the conBetween 2008 and 2013, the Grade 12 exit assessments were based on this initial ML curriculum. However, ongoing critiques of the complexity of the South African curriculum documents alongside the continued weak performance of South African students in standardized tests led to the appointment of a ministerial panel in mid 2009 to investigate implementation difficulties. A key panel recommendation was that a single Curriculum and Assessment Policy document for each subject in a phase be prepared to “help address the complexities and confusion created by curriculum and assessment policy vagueness and lack of specification, document proliferation and misinterpretation”  for the examination analysis of the critical citizenship agenda. Our perspective draws on the works of Skovsmose , 2021 onMany mathematics education researchers have drawn on critical perspectives for conceptualising mathematics teaching and learning, highlighting the importance of understanding the formatting power of mathematics across sociopolitical  or as individuals (either as self-managing persons or future workers). Both these positions are noted in the initial and revised ML curriculum. Thus, in wanting to understand the changes in the citizenship agenda over time, we sought to answer questions about the nature of the reasoning in the ML examinations, the nature of the contexts included and positioning of the student. The methodology section below explains our choice of sample and our coding system for questions addressing reasoning and reflecting along with the indicators used to assign codes.As our sample set is informed by the ML assessment taxonomy and policy guidelines for assessment we begin with a brief description of these.Level 1: Knowing (30%)Level 2: Applying routine procedures in familiar contexts (30%)Level 3: Applying multi-step procedures in a variety of contexts (20%)Level 4: Reasoning and reflecting (20%)The assessment guidelines DoE, , p. 8 acRR1: pose and identify questions about what mathematics they require to solve a problemRR2: interpret the solution they determine to a problem in the context of the problem and where necessary to adjust the mathematical solution to make sense in the contextRR3: critique solutions to problems and statements about situations made by othersRR4 generalise patterns observed in situations, make predictions based on these patterns and or other evidence and determine conditions that will lead to desired outcomesWith the literature pointing to reasoning and reflecting (RR) as key to critical citizenship orientations, we looked at the delineation of Level 4 in this document more closely. Level 4 was described with four sub-levels:RRa: “Questions that require a decision, opinion or prediction about a particular scenario based on calculations in a previous question or on given information” (p. 115)RRb: “Questions that require learners to pose and answer questions about which mathematics they require to solve a problem, select and use the mathematical content, recognise the limitations of using mathematics to solve the problem, and consider other non-mathematical techniques and factors that may define or determine a solution to the problem” (p. 116)The taxonomy of levels of cognitive demand was retained in the revised ML curriculum assessment specification, with ongoing allocation of 20% of the marks to the Reasoning and Reflecting level. However, the revised assessment guidelines  suggested only two sub-levels, rather than the four above:selection of a problem-solving approach was a background precursor to the marks allocated to the problem-solving process itself. RR2 and RR4 (RRa in the revised guidelines) both involved interpretation of calculated answers or patterns in presented information. We therefore found it useful to collect these sub-categories under the heading of Reasoning & Reflecting: Interpretation (RRI). This left the RR3 sub-category focus on the idea of critique—Reasoning & Reflecting: Critique (RRC).To analyse the presence of critical democratic citizenship in the ML Grade 12 exit assessments we looked to Level 4 as this was the level involving the reasoning and reflecting required for engaged citizenship. However, our analysis of the ML examinations (below) noted that no questions addressed the RR1/RRb sub-categories requiring learners to pose their own questions. Instead, much as in the mathematical problem-solving taxonomies of writers such as Polya , the selRRa’s emphasis on interpreting calculations points to a predominant focus in our RRI category, but the inclusion of the word ‘opinion’ suggested some openings for critique and therefore some RRC. RRb similarly has some connection with our Critique category (RRC) in its noting of recognising limitations to mathematics used and consideration of extra-mathematical issues—although the “critique” aspect is less explicitly stated. However, as our analysis later indicates, what we saw in the examination papers was an increasing prevalence of questions asking students to check/verify the correctness of a calculation. These were categorised by examiners as being Level 4 Reasoning and Reflecting items. This necessitated the inclusion of a ‘Check Calculation’ category in our analysis. Thus, aspects of RRa  fell into our RRI and RRC categories identified above while other aspects pointed to the Check Calculation category (based mostly on given information).The assessment guidelines for the initial and the revised ML curricula stipulate two exams at the end of grade 12. Exam 1 focuses on levels 1 and 2 of the cognitive demand taxonomy and Exam 2 on levels 3 and 4. This informed our decision to focus on Exam 2 in our analysis. Greater specificity of content and contexts in the revised ML curriculum followed through into the revised Grade 12 examinations structure with Exam 1 limited to familiar contexts and Exam 2 to both familiar and unfamiliar contexts.https://www.education.gov.za/Curriculum/NationalSeniorCertificate(NSC)Examinations.aspx) from the start of assessments in 2008 up to 2020. The 2021 exams were unavailable on the website at the time of writing. Furthermore, since the 2021 examinations were affected by the 2021 pandemic-related revisions made to the examination guidelines we excluded them from our data set. [By the time of the pandemic lockdowns in South Africa the 2020 examinations were already set.]We sourced all the Grade 12 ML Exam 2 s from the Department of Basic Education (DBE) website . Subsequent questions asked learners to calculate percentages spent on different categories of beneficiaries etc. This led to inclusion of attention to both the nature of the context, and specifically whether societal or individual contexts were foregrounded, and whether these involved national or global issues. A corollary aspect we noted was whether the issue raised positioned the learner more as a self-managing individual or a participating citizen. For example, we coded developing reasoning and reflecting in a range of possible work contexts as linked to being a self-managing person who would look to find employment.To summarise the data in a table we grouped the examinations into four phases corresponding with distinguishable periods of curriculum implementation. Phase 1 involved the first three years (2008–10) and marked a period where examiners and teachers were making sense of the new subject and aligning curriculum intentions with assessments. Phase 2 marked the revised curriculum coming into play. It began in 2011, when the revised ML document was released (with shifting emphasis on citizenship) for implementation in 2012 with Grade 10 s. While the first examination of this revised curriculum occurred in 2014, proposed shifts and discussions underway about focusing on learners as self-managing persons would have likely exerted influence from 2011. Phase 3 includes the examinations in the first three years of examination of the revised curriculum and Phase 4 focuses on the three most recent years (excluding 2021 as explained above). These four phases are shown in Table In analysing the exams, we each first (open) looked at Exams 1&2 of the first (2008) and last (2020) assessment to generate some possible questions to guide qualitative content and orientation analysis. We asked: Which questions require reasoning and reflecting? What is the nature of these questions? What subclasses of reasoning and reflecting are there? What is the nature of the context? Is the context national or global? How is the learner positioned: Citizen-in-Society (PC- participating citizen) or Individual (SMP-self-managing person). We then developed a spreadsheet and placed all Level 4 Reasoning and Reflecting questions from all assessments into it. We checked agreement that we had captured all of these and not included those of lower levels of the taxonomy. Then two authors coded all the exams, guided by the above questions, cross checking each other’s codes and finalising codes based on agreement. There was general agreement across codes even while several questions were considered to border across categories. The following codes . Most RRI and RRC sub-questions were 2- or 3-mark questions with a few marks allocated to calculation or knowledge within these. In contrast, the Level 4 sub-questions of the CheckCalc type , reflected by marks allocated, feature in the examinations over time. This increases somewhat from 7.4% in the first phase to just over 15% in the latter three phases. However, looking across the sub-types of Level 4 questions we see that reasoning and reflecting (RRC and RRI jointly) remains under 10% of total assessment marks throughout all four phases. In contrast, the CheckCalc type questions that hardly featured in the first phase (under 1%) increase steadily over time making up 12.1% of total assessment marks in the most recent phase.Questions classified as RRC are of particular importance in answering the question about the extent to which critical democratic citizenship is foregrounded in our assessments. Across all phases the percentage of RRC questions as a total of Level 4 questions is low, but substantially higher in the first phase of examinations (24%) and negligible in the latter two phases. This absence is even more stark across the total marks across Exams 1 and 2 where the small percentage of marks awarded to critical reasoning and reflecting in the first two phases (1.8% and 1.5%) almost entirely disappears in the latter two phases (0% and 0.4%).The shift away from some critical reasoning and reflection questions is also visible in the nature of the scenarios and contexts that the reasoning and reflecting questions are linked to as seen in Table Table In our initial reading of both Exams 1 and 2 we noted a recent increase in questions that were set in international contexts. For example, information on the cost of studying nursing in England, or of holidaying in Australia, comparing Uber to other transport options in the USA, tourism in Scotland and so forth. Such foreign contexts were almost entirely absent in the first two phases of examinations (0% in Phase 1 and 5% in Phase 2) yet make up over a quarter of the marks in Phases 3 (41%) and 4 (26%). While analysis of the nature of these questions is beyond the scope of this article, we noted many of these contexts were likely to be of greater relevance to a wealthier minority of South African learners despite the majority (2/3) of ML learners coming from non-fee-paying schools in poor areas. We are not saying that global contexts per se are of more relevance to wealthier learners as issues such as global warming, pandemics, conflicts, environmental catastrophes, oil prices etc. are of relevance to all. However, holidaying to Australia, uber in the USA, etc. are somewhat different to these.We begin with two brief exemplar questions from the first and last phases respectively to illustrate subtle but noteworthy shifts in the aspect of engaging critically with presented manipulated graphical information. Thereafter we provide a fuller question with sub-parts from the most recent phase of examinations to illuminate the nature of shift in style of Level 4 questions from open towards closed phrasing in which all possibilities for correctness can be clearly stated in the memorandum removing the need for marker discretion on validity of the students’ arguments Fig. .In 1.2.3 it is explicitly stated that the purpose of the graphs was for the salesman to support his claim (to convince the viewer of his argument). The word ‘misleading’ is used in the latter part and students are asked to identify the misleading graph and to explain how it has been manipulated to mislead. This contrasts with the 2019 question in Fig. In the appendix we provide a set of Level 4 sub-questions that are part of a single question (Q2) that deals with South African Revenue Service (SARS) information, salaries and salary deductions of foreign earnings. This is an example of the way in which questioning style became increasingly closed – with the answer to calculations often being given, and interpretive and critical reasoning removed—though examiners consider reasoning and reflecting addressed by the terms ‘verify’ if ‘correct’ and ‘valid’. These terms are repeated in sub-questions. Only one mark in each sub-question is allocated to the yes-valid or no-invalid conclusion based on the answer of calculations. The coding of these questions is: 2.1.1  (Soc-Nat-PC) 2.3.2  (Soc-Nat-SMP) 2.4.3 b  (Soc-Glob-SMP).The marking memorandum shows these questions along with their full mark allocation counted as Level 4 – yet in each case only one mark is allocated to the interpretation of what the calculation means for evaluating the validity of the statement. An example of the marking schedule for one of these sub questions 2.4.3 is given in Fig. We see through this analysis of ML examinations since their start that the broad post-apartheid ML specific policy orientations to education for equity and critical citizenship, while somewhat visible in the first few years of examinations decreased substantially over time, giving way to a focus on performativity as a self-managing person. We have noted the broader political currents that fed into ML curriculum reform, with assessment shifts reflecting these changes in currents in a range of ways. In substantive terms, this was evident in the diminishing number of questions requiring critical reasoning and reflecting questions over time to a complete absence of such questions since the revised curriculum was examined in 2015. At a more technical level, and underlining the complexity of policy trajectories that Ball  describeOur analysis points to diminishing attention to critical democratic citizenship across the four phases of ML examinations (2008–2020). Within this diminishing attention, there were changes in the style of questions deemed to involve reasoning and reflecting, with an increasing proportion of marks allocated to working through a calculation rather than requiring the interpretation, judgement or critique that the research highlights as necessary for active citizenship from a mathematically literate perspective. The prevalence of items positioning the student as a self-managing person increased substantially over time, with a concomitant decrease in positioning relating to participant citizenship. Alongside and aligned with this shift, was an increase in individual-oriented contexts and a decrease in societal issues. Taken together, and linking back to the essential circuits, these shifts mirror what we noted at the level of ML curriculum specification: diminishing focus on critical citizenship and an increased emphasis on the self-managing person as marked in the introduction of revised ML curriculum.Our findings therefore suggest marked changes in the orientation of ML exit assessments over time, with increasing conflations of reasoning and reflecting on contextual and societal issues replaced with showing the relevant steps of a calculation and checking given answers. Check Calculation type questions have become the dominant type of ‘reasoning and reflecting’ question in examinations since the revised curriculum was first examined in 2014. While we do not consider such questions to involve reasoning and reflecting in any substantive way it is clear from the memoranda that examiners include such questions for their target of 20% reasoning and reflecting questions. This points to ML assessments receding from the initial aspirations for the subject in which goals of simultaneously developing individuals as self-managing persons and participating citizens in a young democracy were sought. Since it is widely acknowledged that assessment  drive teaching the absence of questions requiring critical engagement with broader societal issues in exit examinations is cause for concern to the citizenship agenda.Exacerbating this diminishing focus on critical democratic citizenship in the ML examinations, while also bringing this focus into sharp relief, are the broader patterns of participation and performance in ML over time. The proportion of Grade 12 students writing ML versus Mathematics increased from 47 to 59% over the period of our review. Government figures show that across the years less than 13% of students in schools situated in the bottom three quintiles (based on the socio-economic status of the communities in which they are situated), score above 60% on the ML exit examinations. In the wealthiest quintile of schools, this percentage has dropped from around 50% initially to 40%. The national average remained low across this period at around 40%. This suggests that competences at even the more basic levels of the ML taxonomy are not being successfully engendered for the vast majority, with higher prevalence of low performance, and more limited access to reasoning and reflecting for the poor than for the wealthy.Gal  has noteWhile we have focused on ML in our country, our findings suggest value in analysing exit assessments across other mathematics curricula to gauge the extent to which critical citizenship agendas feature currently and over time across different contexts. The COVID-19 pandemic brought massive changes to our world and placed a spotlight on (and in some cases exacerbated) existing problems and inequities   have pointed to the increased need for the development of critical mathematics education for supporting democratic citizenship. Yet Covid-19 disruptions to schooling in our own and we expect in many other contexts has seemed to push the focus of educational policy towards ‘catch-up’ involving a focus on ‘basics’ and ‘key skills and content’. Here concern for developing critical thinkers is increasingly backgrounded. Readers will judge the extent to which the findings in this paper that point to little (and reducing) attention to citizenship in mathematics examinations and broader education policy applies to their contexts. If, as many have argued, high stakes examinations drive teaching and learning then educators promoting mathematics for development of critically reflective and socially responsible citizens need to ask: How do we ensure quality opportunities for demonstrating mathematics for critical citizenship in examination contexts?