Dislocations in stacking and commensurate-incommensurate phase transition in bilayer graphene and hexagonal boron nitride

Dislocations corresponding to a change of stacking in two-dimensional hexagonal bilayers, graphene and boron nitride, and associated with boundaries between commensurate domains are investigated using the two-chain Frenkel-Kontorova model on top of ab initio calculations. Structural transformations of bilayers in which the bottom layer is stretched and the upper one is left to relax freely are considered for gradually increased elongation of the bottom layer. Formation energies of dislocations, dislocation width and orientation of the boundary between commensurate domains are analyzed depending on the magnitude and direction of elongation. The second-order phase transition from the commensurate phase to the incommensurate one with multiple dislocations is predicted to take place at some critical elongation. The order parameter for this transition corresponds to the density of dislocations, which grows continuously upon increasing the elongation of the bottom layer above the critical value. In graphene and metastable boron nitride with the layers aligned in the same direction, where elementary dislocations are partial, this transition, however, is preceded by formation of the first dislocation at the elongation smaller than the critical one. The phase diagrams including this intermediate state are plotted in coordinates of the magnitude and direction of elongation of the bottom layer.Comment: 15 pages, 9 figure

Comparison of performance of van der Waals-corrected exchange-correlation functionals for interlayer interaction in graphene and hexagonal boron nitride

Exchange-correlation functionals with corrections for van der Waals interactions (PBE-D2, PBE-D3, PBE-D3(BJ), PBE-TS, optPBE-vdW and vdW-DF2) are tested for graphene and hexagonal boron nitride, both in the form of bulk and bilayer. The characteristics of the potential energy surface, such as the barrier to relative sliding of the layers and magnitude of corrugation, and physically measurable properties associated with relative in-plane and out-of-plane motion of the layers including the shear modulus and modulus for axial compression, shear mode frequency and frequency of out-of-plane vibrations are considered. The PBE-D3(BJ) functional gives the best results for the stackings of hexagonal boron nitride and graphite that are known to be ground-state from the experimental studies. However, it fails to describe the order of metastable states of boron nitride in energy. The PBE-D3 and vdW-DF2 functionals, which reproduce this order correctly, are identified as the optimal choice for general studies. The vdW-DF2 functional is preferred for evaluation of the modulus for axial compression and frequency of out-of-plane vibrations, while the PBE-D3 functional is somewhat more accurate in calculations of the shear modulus and shear mode frequency. The best description of the latter properties, however, is achieved also using the vdW-DF2 functional combined with consideration of the experimental interlayer distance. In the specific case of graphene, the PBE-D2 functional works very well and can be further improved by adjustment of the parameters.Comment: 22 pages, 4 figue

NCS-constrained exhaustive search using oligomeric models

Copyright © 2008 International Union of CrystallographyThe efficiency of the cross-rotation function step of molecular replacement (MR) is intrinsically limited as it uses only a fraction of the Patterson vectors. Along with general techniques extending the boundaries of the method, there are approaches that utilize specific features of a given structure. In special cases, where the directions of noncrystallographic symmetry axes can be unambiguously derived from the self-rotation function and the structure of the homologue protein is available in a related oligomeric state, the cross-rotation function step of MR can be omitted. In such cases, a small number of yet unknown parameters defining the orientation of the oligomer and/or its internal organization can be optimized using an exhaustive search. Three difficult MR cases are reported in which these parameters were determined and the oligomer was positioned according to the maximal value of the correlation coefficient in a series of translation searches.NI

Structure and energetics of carbon, hexagonal boron nitride and carbon/hexagonal boron nitride single-layer and bilayer nanoscrolls

Single-layer and bilayer carbon and hexagonal boron nitride nanoscrolls as well as nanoscrolls made of bilayer graphene/hexagonal boron nitride heterostructure are considered. Structures of stable states of the corresponding nanoscrolls prepared by rolling single-layer and bilayer rectangular nanoribbons are obtained based on the analytical model and numerical calculations. The lengths of nanoribbons for which stable and energetically favorable nanoscrolls are possible are determined. Barriers to rolling of single-layer and bilayer nanoribbons into nanoscrolls and barriers to nanoscroll unrolling are calculated. Based on the calculated barriers nanoscroll lifetimes in the stable state are estimated. Elastic constants for bending of graphene and hexagonal boron nitride layers used in the model are found by density functional theory calculations.Comment: 9 pages, 6 figure

Effect of electric field on the photoluminescence of polymer-inorganic nanoparticles composites

We report on the effect of electric field on the photoluminescence, PL, from a composite consisting of a conjugated polymer mixed with zinc oxide nanoparticles. We have found that in the absence of electric field PL emission from the composite film has two maxima in the blue and green-yellow regions. Application of a voltage bias to planar gold electrodes suppresses the green-yellow emission and shifts the only PL emission maximum towards the blue region. Current-voltage characteristics of the polymer-nanoparticles composite exhibit the non-linear behavior typical of non-homogeneous polymer-inorganic structures. Generation of excited states in the composite structure implies the presence of several radiative recombination mechanisms including formation of polymer-nanoparticle complexes including exciplex states and charge transfer between the polymer and nanoparticle that can be controlled by an electric field.Comment: 5 pages, 5 figures. accepted for publication in Solid State Communication

Surprises and pitfalls arising from (pseudo)symmetry

The presence of pseudosymmetry can cause problems in structure determination and refinement. The relevant background and representative examples are presented

Conformational flexibility and molecular interactions of an archaeal homologue of the Shwachman-Bodian-Diamond syndrome protein

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.Abstract Background Defects in the human Shwachman-Bodian-Diamond syndrome (SBDS) protein-coding gene lead to the autosomal recessive disorder characterised by bone marrow dysfunction, exocrine pancreatic insufficiency and skeletal abnormalities. This protein is highly conserved in eukaryotes and archaea but is not found in bacteria. Although genomic and biophysical studies have suggested involvement of this protein in RNA metabolism and in ribosome biogenesis, its interacting partners remain largely unknown. Results We determined the crystal structure of the SBDS orthologue from Methanothermobacter thermautotrophicus (mthSBDS). This structure shows that SBDS proteins are highly flexible, with the N-terminal FYSH domain and the C-terminal ferredoxin-like domain capable of undergoing substantial rotational adjustments with respect to the central domain. Affinity chromatography identified several proteins from the large ribosomal subunit as possible interacting partners of mthSBDS. Moreover, SELEX (Systematic Evolution of Ligands by EXponential enrichment) experiments, combined with electrophoretic mobility shift assays (EMSA) suggest that mthSBDS does not interact with RNA molecules in a sequence specific manner. Conclusion It is suggested that functional interactions of SBDS proteins with their partners could be facilitated by rotational adjustments of the N-terminal and the C-terminal domains with respect to the central domain. Examination of the SBDS protein structure and domain movements together with its possible interaction with large ribosomal subunit proteins suggest that these proteins could participate in ribosome function.Published versio

Papillomavirus E1 helicase assembly maintains an asymmetric state in the absence of DNA and nucleotide cofactors

Concerted, stochastic and sequential mechanisms of action have been proposed for different hexameric AAA+ molecular motors. Here we report the crystal structure of the E1 helicase from bovine papillomavirus, where asymmetric assembly is for the first time observed in the absence of nucleotide cofactors and DNA. Surprisingly, the ATP-binding sites adopt specific conformations linked to positional changes in the DNA-binding hairpins, which follow a wave-like trajectory, as observed previously in the E1/DNA/ADP complex. The protein's assembly thus maintains such an asymmetric state in the absence of DNA and nucleotide cofactors, allowing consideration of the E1 helicase action as the propagation of a conformational wave around the protein ring. The data imply that the wave's propagation within the AAA+ domains is not necessarily coupled with a strictly sequential hydrolysis of ATP. Since a single ATP hydrolysis event would affect the whole hexamer, such events may simply serve to rectify the direction of the wave's motion