The mechanism of caesium intercalation of graphene

Properties of many layered materials, including copper- and iron-based superconductors, topological insulators, graphite and epitaxial graphene can be manipulated by inclusion of different atomic and molecular species between the layers via a process known as intercalation. For example, intercalation in graphite can lead to superconductivity and is crucial in the working cycle of modern batteries and supercapacitors. Intercalation involves complex diffusion processes along and across the layers, but the microscopic mechanisms and dynamics of these processes are not well understood. Here we report on a novel mechanism for intercalation and entrapment of alkali-atoms under epitaxial graphene. We find that the intercalation is adjusted by the van der Waals interaction, with the dynamics governed by defects anchored to graphene wrinkles. Our findings are relevant for the future design and application of graphene-based nano-structures. Similar mechanisms can also play a role for intercalation of layered materials.Comment: 8 pages, 7 figures in published form, supplementary information availabl

Uncertainty quantification of growth rates of thermoacoustic instability by an adjoint Helmholtz solver

Thermoacoustic instabilities are often calculated with Helmholtz solvers combined with a low-order model for the flame dynamics. Typically, such a formulation leads to an eigenvalue problem in which the eigenvalue appears under nonlinear terms, such as exponentials related to the time delays that result from the flame model. The objective of the present paper is to quantify uncertainties in thermoacoustic stability analysis with a Helmholtz solver and its adjoint. This approach is applied to the model of a combustion test rig with a premixed swirl burner. The nonlinear eigenvalue problem and its adjoint are solved by an in-house adjoint Helmholtz solver, based on an axisymmetric finite-volume discretization. In addition to first-order correction terms of the adjoint formulation, as they are often used in the literature, second-order terms are also taken into account. It is found that one particular second-order term has significant impact on the accuracy of the predictions. Finally, the probability density function (PDF) of the growth rate in the presence of uncertainties in the input parameters is calculated with a Monte Carlo approach. The uncertainties considered concern the gain and phase of the flame response, the outlet acoustic reflection coefficient, and the plenum geometry. It is found that the second-order adjoint method gives quantitative agreement with results based on the full nonlinear eigenvalue problem, while requiring much fewer computations.Technological foundations for the design of thermally and mechanically highly loaded components of future space transportation systems (SFB TR40), Royal Academy of Engineering Research Fellowships Schem

Uncertainty quantification of growth rates of thermoacoustic instability by an adjoint Helmholtz solver

Thermoacoustic instabilities are often calculated with Helmholtz solvers combined with a low-order model for the flame dynamics. Typically, such a formulation leads to an eigenvalue problem in which the eigenvalue appears under nonlinear terms, such as exponentials related to the time delays that result from the flame model. The objective of the present paper is to quantify uncertainties in thermoacoustic stability analysis with a Helmholtz solver and its adjoint. This approach is applied to the model of a combustion test rig with a premixed swirl burner. The nonlinear eigenvalue problem and its adjoint are solved by an in-house adjoint Helmholtz solver, based on an axisymmetric finite-volume discretization. In addition to first-order correction terms of the adjoint formulation, as they are often used in the literature, second-order terms are also taken into account. It is found that one particular second-order term has significant impact on the accuracy of the predictions. Finally, the probability density function (PDF) of the growth rate in the presence of uncertainties in the input parameters is calculated with a Monte Carlo approach. The uncertainties considered concern the gain and phase of the flame response, the outlet acoustic reflection coefficient, and the plenum geometry. It is found that the second-order adjoint method gives quantitative agreement with results based on the full nonlinear eigenvalue problem, while requiring much fewer computations.Technological foundations for the design of thermally and mechanically highly loaded components of future space transportation systems (SFB TR40), Royal Academy of Engineering Research Fellowships Schem

Intrinsic and extrinsic corrugation of monolayer graphene deposited on SiO2

Using scanning tunneling microscopy (STM) in ultra high vacuum and atomic force microscopy, we investigate the corrugation of graphene flakes deposited by exfoliation on a Si/SiO2 (300 nm) surface. While the corrugation on SiO2 is long-range with a correlation length of about 25 nm, some of the graphene monolayers exhibit an additional corrugation with a preferential wave length of about 15 nm. A detailed analysis shows that the long range corrugation of the substrate is also visible on graphene, but with a reduced amplitude, leading to the conclusion that the graphene is partly freely suspended between hills of the substrate. Thus, the intrinsic rippling observed previously on artificially suspended graphene can exist as well, if graphene is deposited on SiO2.Comment: 10 pages, 11 figures, including supplementary materia

Characterization of cis- and trans-acting elements in the imprinted human SNURF-SNRPN locus

The imprinted SNRPN locus is a complex transcriptional unit that encodes the SNURF and SmN polypeptides as well as multiple non-coding RNAs. SNRPN is located within the Prader-Willi and Angelman syndrome (PWS/AS) region that contains multiple imprinted genes, which are coordinately regulated by a bipartite imprinting center (IC). The SNRPN 5′ region co-localizes with the PWS-IC and contains two DNase I hypersensitive sites, DHS1 at the SNRPN promoter, and DHS2 within intron 1, exclusively on the paternally inherited chromosome. We have examined DHS1 and DHS2 to identify cis- and trans-acting regulatory elements within the endogenous SNRPN 5′ region. Analysis of DHS1 by in vivo footprinting and chromatin immunoprecipitation identified allele-specific interaction with multiple regulatory proteins, including NRF-1, which regulates genes involved in mitochondrial and metabolic functions. DHS2 acted as an enhancer of the SNRPN promoter and contained a highly conserved region that showed allele-specific interaction with unphosphorylated RNA polymerase II, YY1, Sp1 and NRF-1, further suggesting a key role for NRF-1 in regulation of the SNRPN locus. We propose that one or more of the regulatory elements identified in this study may also contribute to PWS-IC function

An Unexpected Function of the Prader-Willi Syndrome Imprinting Center in Maternal Imprinting in Mice

Genomic imprinting is a phenomenon that some genes are expressed differentially according to the parent of origin. Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are neurobehavioral disorders caused by deficiency of imprinted gene expression from paternal and maternal chromosome 15q11–q13, respectively. Imprinted genes at the PWS/AS domain are regulated through a bipartite imprinting center, the PWS-IC and AS-IC. The PWS-IC activates paternal-specific gene expression and is responsible for the paternal imprint, whereas the AS-IC functions in the maternal imprint by allele-specific repression of the PWS-IC to prevent the paternal imprinting program. Although mouse chromosome 7C has a conserved PWS/AS imprinted domain, the mouse equivalent of the human AS-IC element has not yet been identified. Here, we suggest another dimension that the PWS-IC also functions in maternal imprinting by negatively regulating the paternally expressed imprinted genes in mice, in contrast to its known function as a positive regulator for paternal-specific gene expression. Using a mouse model carrying a 4.8-kb deletion at the PWS-IC, we demonstrated that maternal transmission of the PWS-IC deletion resulted in a maternal imprinting defect with activation of the paternally expressed imprinted genes and decreased expression of the maternally expressed imprinted gene on the maternal chromosome, accompanied by alteration of the maternal epigenotype toward a paternal state spread over the PWS/AS domain. The functional significance of this acquired paternal pattern of gene expression was demonstrated by the ability to complement PWS phenotypes by maternal inheritance of the PWS-IC deletion, which is in stark contrast to paternal inheritance of the PWS-IC deletion that resulted in the PWS phenotypes. Importantly, low levels of expression of the paternally expressed imprinted genes are sufficient to rescue postnatal lethality and growth retardation in two PWS mouse models. These findings open the opportunity for a novel approach to the treatment of PWS

SnoRNA Snord116 (Pwcr1/MBII-85) Deletion Causes Growth Deficiency and Hyperphagia in Mice

Prader-Willi syndrome (PWS) is the leading genetic cause of obesity. After initial severe hypotonia, PWS children become hyperphagic and morbidly obese, if intake is not restricted. Short stature with abnormal growth hormone secretion, hypogonadism, cognitive impairment, anxiety and behavior problems are other features. PWS is caused by lack of expression of imprinted genes in a ∼4 mb region of chromosome band 15q11.2. Our previous translocation studies predicted a major role for the C/D box small nucleolar RNA cluster SNORD116 (PWCR1/HBII-85) in PWS. To test this hypothesis, we created a ∼150 kb deletion of the >40 copies of Snord116 (Pwcr1/MBII-85) in C57BL/6 mice. Snord116del mice with paternally derived deletion lack expression of this snoRNA. They have early-onset postnatal growth deficiency, but normal fertility and lifespan. While pituitary structure and somatotrophs are normal, liver Igf1 mRNA is decreased. In cognitive and behavior tests, Snord116del mice are deficient in motor learning and have increased anxiety. Around three months of age, they develop hyperphagia, but stay lean on regular and high-fat diet. On reduced caloric intake, Snord116del mice maintain their weight better than wild-type littermates, excluding increased energy requirement as a cause of hyperphagia. Normal compensatory feeding after fasting, and ability to maintain body temperature in the cold indicate normal energy homeostasis regulation. Metabolic chamber studies reveal that Snord116del mice maintain energy homeostasis by altered fuel usage. Prolonged mealtime and increased circulating ghrelin indicate a defect in meal termination mechanism. Snord116del mice, the first snoRNA deletion animal model, reveal a novel role for a non-coding RNA in growth and feeding regulation

Indirect exclusion of four candidate genes for generalized progressive retinal atrophy in several breeds of dogs

BACKGROUND: Generalized progressive retinal atrophy (gPRA) is a hereditary ocular disorder with progressive photoreceptor degeneration in dogs. Four retina-specific genes, ATP binding cassette transporter retina (ABCA4), connexin 36 (CX36), c-mer tyrosin kinase receptor (MERTK) and photoreceptor cell retinol dehydrogenase (RDH12) were investigated in order to identify mutations leading to autosomal recessive (ar) gPRA in 29 breeds of dogs. RESULTS: Mutation screening was performed initially by PCR and single strand conformation polymorphism (SSCP) analysis, representing a simple method with comparatively high reliability for identification of sequence variations in many samples. Conspicuous banding patterns were analyzed via sequence analyses in order to detect the underlying nucleotide variations. No pathogenetically relevant mutations were detected in the genes ABCA4, CX36, MERTK and RDH12 in 71 affected dogs of 29 breeds. Yet 30 new sequence variations were identified, both, in the coding regions and intronic sequences. Many of the sequence variations were in heterozygous state in affected dogs. CONCLUSION: Based on the ar transmittance of gPRA in the breeds investigated, informative sequence variations provide evidence allowing indirect exclusion of pathogenetic mutations in the genes ABCA4 (for 9 breeds), CX36 (for 12 breeds), MERTK (for all 29 breeds) and RDH12 (for 9 breeds)

Targeting the histone methyltransferase G9a activates imprinted genes and improves survival of a mouse model of Prader–Willi syndrome

Prader–Willi syndrome (PWS) is an imprinting disorder caused by a deficiency of paternally expressed gene(s) in the 15q11–q13 chromosomal region. The regulation of imprinted gene expression in this region is coordinated by an imprinting center (PWS-IC). In individuals with PWS, genes responsible for PWS on the maternal chromosome are present, but repressed epigenetically, which provides an opportunity for the use of epigenetic therapy to restore expression from the maternal copies of PWS-associated genes. Through a high-content screen (HCS) of >9,000 small molecules, we discovered that UNC0638 and UNC0642—two selective inhibitors of euchromatic histone lysine N-methyltransferase-2 (EHMT2, also known as G9a)—activated the maternal (m) copy of candidate genes underlying PWS, including the SnoRNA cluster SNORD116, in cells from humans with PWS and also from a mouse model of PWS carrying a paternal (p) deletion from small nuclear ribonucleoprotein N (Snrpn (S)) to ubiquitin protein ligase E3A (Ube3a (U)) (mouse model referred to hereafter as m+/pΔS−U). Both UNC0642 and UNC0638 caused a selective reduction of the dimethylation of histone H3 lysine 9 (H3K9me2) at PWS-IC, without changing DNA methylation, when analyzed by bisulfite genomic sequencing. This indicates that histone modification is essential for the imprinting of candidate genes underlying PWS. UNC0642 displayed therapeutic effects in the PWS mouse model by improving the survival and the growth of m+/pΔS−U newborn pups. This study provides the first proof of principle for an epigenetics-based therapy for PWS