Structural Building Blocks Research Articles

Early stages of growth of Pb, Sn and Ge on Ru(0001): A comparative density functional theory study

As has recently been shown experimentally, adatoms from group 14 exhibit distinct growth characteristics on Ru(0001) at submonolayer coverages. In particular, Pb and Sn atoms agglomerate in dense islands of the c(2 × 4) or c(2 × 8) symmetry with local coverage of 1/2 monolayer (ML), respectively, already for much lower deposition doses, whereas Ge atoms self-assemble in the dilute 21×21 structure with adatom density of 1/7 ML. To trace the observed differences, we employed ab-initio density-functional-theory simulations and followed the early stages of growth of Pb, Sn, and Ge on Ru(0001) in a systematic manner by examining the potential energy surfaces for successive adsorption of up to several atoms of each element within a large surface unit cell. This way the effective lateral interactions between adatoms were recognized in the low-coverage regime, and their most favorable dimer and trimer configurations were identified. Interpreting them as initial building blocks of the adsorbate structure enabled us to clarify the tendency of various considered elements towards formation of a dense or dilute ordered overlayer on Ru(0001) at low nominal coverages.

Correlating dynamical properties of organic aerogel with increased sound insulation of sandwich wallboard systems

Low thermal conductivity of classical aerogels has long been exploited, while their dynamic properties are yet to be further investigated. This work investigates a new class of acoustic materials based on porous hierarchical three-dimensional assemblies of organic nanoparticles. Primary polymer nanoparticles are formed via chemical reactions in solution and self-assemble to fractal porous secondary particles, which in turn become the fundamental building blocks of larger globular, fibrous or hybrid structures that form the microscopic network of highly porous monolithic materials referred to as polymer-crosslinked (or X-) aerogels. Their low-cost, thin-panel form has found potential applications as constrained damping layers integrated into gypsum wallboards. The standardized chamber-based random-incident tests demonstrate drastically increased sound transmission losses without significantly increasing the board thickness and weight when light-weight X-aerogel panels of less than 1 cm in thickness are integrated into gypsum wallboards in sandwich structure. For better understanding of its excellent effect as constrained damping layers, this paper discusses experimental investigations on broadband dynamic properties of X-aerogels with the intention to correlate their intriguing dynamic properties with increased sound insulations which will have high potentials as emerging building materials for advanced noise and vibration controls and beyond.

High-Temperature, High-Pressure Hydrothermal Synthesis of Ba3[B6O10(OH)2](CO3) and Ba6[B12O21(OH)2](CO3)2, Two Barium Borate Carbonates with 2D Layer and 3D Framework Structures.

Two new barium borate carbonates, Ba3[B6O10(OH)2](CO3) (1) and Ba6[B12O21(OH)2](CO3)2 (2), have been synthesized by high-temperature, high-pressure hydrothermal methods at 460 °C and 600 bar and structurally characterized by single-crystal X-ray diffraction, TGA, IR, and MAS 11B NMR spectroscopy. The descriptors of the fundamental building blocks (FBB) of both structures are 2Δ4□:⟨Δ2□⟩=⟨4□⟩=⟨Δ2□⟩. The FBB of 1 has a chair conformation, and the FBBs of 2 have both chair and boat conformations. Compound 1 adopts a noncentrosymmetric 2D layer structure with the Ba2+ cations and CO32- anions between the layers, whereas compound 2 has a centrosymmetric 3D framework structure containing 9- and 10-ring channels with the Ba2+ cations and CO32- anions at the center or on the edges of the channels. The two structures are two of the few examples where the carbonate groups are isolated and occupy their own independent sites.

THERMAL PROPERTIES OF TPD-BASED ORGANIC GLASSES

Glassy materials are condensed matter systems showing physical properties in between solids and liquids and retaining information about the thermal history they have been subjected to and the way they have been prepared. Formally, this implies that their configurational energy landscape is a complex multi-dimensional surface, showing quite a few basins with different depths, widths, and shapes: the system can be trapped in any of them, assuming very unlike physical properties. Recently, it has been demonstrated experimentally that a glassy system can be grown by physical vapor deposition of organic molecules on a substrate. The physics of such organic glasses is enriched by a new feature, namely: the anisotropic molecular structure of the basic building blocks used to assemble the film. TPD-based organic glasses have been generated by atomistic simulations that mimic vapor deposition and their thermal properties have been accordingly calculated. Simulations generate a rational phenomenology, providing robust evidence that heat transfer is not isotropic but, rather, correlated to an inherent molecular property, namely the axial structure of the TPD molecule. Furthermore, we present the first theoretical prediction of the specific heat trend versus temperature, showing in the quantum regime an intriguing anomaly with respect to crystalline systems.

Study of specific nanoenvironments containing α-helices in all-α and (α+β)+(α/β) proteins.

Protein secondary structure elements (PSSEs) such as α-helices, β-strands, and turns are the primary building blocks of the tertiary protein structure. Our primary interest here is to reveal the characteristics of the nanoenvironment formed by both PSSEs and their surrounding amino acid residues (AARs), which might contribute to the general understanding of how proteins fold. The characteristics of such nanoenvironments must be specific to each secondary structure element, and we have set our goal here to gather the fullest possible description of the α-helical nanoenvironment. In general, this postulate (the existence of specific nanoenvironments for specific protein substructures/neighbourhoods/regions with distinct functionality) was already successfully explored and confirmed for some protein regions, such as protein-protein interfaces and enzyme catalytic sites. Consequently, PSSEs were the obvious next choice for additional work for further evidence showing that specific nanoenvironments (having characteristics fully describable by means of structural and physical chemical descriptors) do exist for the corresponding and determined intraprotein regions. The nanoenvironment of α-helices (nEoαH) is defined as any region of the protein where this secondary structure element type is detected. The nEoαH, therefore, includes not only the α-helix amino acid residues but also the residues immediately around the α-helix. The hypothesis that motivated this work is that it might in fact be possible to detect a postulated “signal” or “signature” that distinguishes the specific location of α-helices. This “signal” must be discernible by tracking differences in the values of physical, chemical, physicochemical, structural and geometric descriptors immediately before (or after) the PSSE from those in the region along the α-helices. The search for this specific nanoenvironment “signal” was made possible by aligning previously selected α-helices of equal length. Afterward, we calculated the average value, standard deviation and mean square error at each aligned residue position for each selected descriptor. We applied Student’s t-test, the Kolmogorov-Smirnov test and MANOVA statistical tests to the dataset constructed as described above, and the results confirmed that the hypothesized “signal”/“signature” is both existing/identifiable and capable of distinguishing the presence of an α-helix inside the specific nanoenvironment, contextualized as a specific region within the whole protein. However, such conclusion might rarely be reached if only one descriptor is considered at a time. A more accurate signal with broader coverage is achieved only if one applies multivariate analysis, which means that several descriptors (usually approximately 10 descriptors) should be considered at the same time. To a limited extent (up to a maximum of 15% of cases), such conclusion is also possible with only a single descriptor, and the conclusion is also possible in general for up to 50–80% of cases when no less than 5 nonlinear descriptors are selected and considered. Using all the descriptors considered in this work, provided all assumptions about data characteristics for this analysis are met, multivariate analysis regularly reached a coverage and accuracy above 90%. Understanding how secondary structure elements are formed and maintained within a protein structure could enable a more detailed understanding of how proteins reach their final 3D structure and consequently, their function. Likewise, this knowledge may also improve the tools used to determine how good a structure is by means of comparing the “signal” around a selected PSSE with the one obtained from the best (resolution and quality wise) protein structures available.

Topology of Disconnected Elementary Band Representations.

Elementary band representations are the fundamental building blocks of atomic limit band structures. They have the defining property that at partial filling they cannot be both gapped and trivial. Here, we give two examples-one each in a symmorphic and a nonsymmorphic space group-of elementary band representations realized with an energy gap. In doing so, we explicitly construct a counterexample to a claim by Michel and Zak that single-valued elementary band representations in nonsymmorphic space groups with time-reversal symmetry are connected. For each example, we construct a topological invariant to explicitly demonstrate that the valence bands are nontrivial. We discover a new topological invariant: a movable but unremovable Dirac cone in the "Wilson Hamiltonian" and a bent-Z_{2} index.

Localised streak solutions for a Blasius boundary layer

Streaks are a common feature of disturbed boundary-layer flows. They play a central role in transient growth mechanisms and are a building block of self-sustained structures. Most theoretical work has focused on streaks that are periodic in the spanwise direction, but in this work we consider a single spatially localised streak embedded into a Blasius boundary layer. For small streak amplitudes, we show the perturbation can be described in terms of a set of eigenmodes that correspond to an isolated streak/roll structure. These modes are new, and arise from a bi-global eigenvalue calculation; they decay algebraically downstream and may be viewed as the natural three-dimensional extension of the classical two-dimensional Libby & Fox (J. Fluid Mech., vol. 17 (3), 1963, pp. 433–449) solutions. Despite their bi-global nature, we show that a subset of these eigenmodes (including the slowest decaying) is fundamentally related to the solutions first presented by Luchini (J. Fluid Mech., vol. 327, 1996, pp. 101–116), as derived for spanwise-periodic disturbances (at small spanwise wavenumber). This surprising connection is made by an analysis of the far-field decay of the bi-global state. We also address the fully non-parallel downstream development of nonlinear streaks, confirming that the aforementioned eigenmodes are recovered as the streak/roll decays downstream. Encouraging comparisons are made with available experimental data.

Spiky electric and magnetic field structures in flux rope experiments

Magnetic flux ropes are structures that are common in the corona of the sun and presumably all stars. They can be thought of as the building blocks of solar structures. They have been observed in Earth's magnetotail and near Mars and Venus. When multiple flux ropes are present magnetic field line reconnection, which converts magnetic energy to other forms, can occur when they collide. The structure of multiple magnetic ropes, the interactions between multiple ropes, and their topological properties such as helicity and writhing have been studied theoretically and in laboratory experiments. Here, we report on spiky potential and magnetic fields associated with the ropes. We show that the potential structures are chaotic for a range of their temporal half-widths and the probability density function (PDF) of their widths resembles the statistical distribution of crumpled paper. The spatial structure of the magnetic spikes is revealed using a correlation counting method. Computer simulation suggests that the potential structures are the nonlinear end result of an instability involving relative drift between ions and electrons.

Cellulose crystals plastify by localized shear.

Cellulose microfibrils are the principal structural building blocks of wood and plants. Their crystalline domains provide outstanding mechanical properties. Cellulose microfibrils have thus a remarkable potential as eco-friendly fibrous reinforcements for structural engineered materials. However, the elastoplastic properties of cellulose crystals remain poorly understood. Here, we use atomistic simulations to determine the plastic shear resistance of cellulose crystals and analyze the underpinning atomic deformation mechanisms. In particular, we demonstrate how the complex and adaptable atomic structure of crystalline cellulose controls its anisotropic elastoplastic behavior. For perfect crystals, we show that shear occurs through localized bands along with noticeable dilatancy. Depending on the shear direction, not only noncovalent interactions between cellulose chains but also local deformations, translations, and rotations of the cellulose macromolecules contribute to the response of the crystal. We also reveal the marked effect of crystalline defects like dislocations, which decrease both the yield strength and the dilatancy, in a way analogous to that of metallic crystals.

Biomedicine: Programmable and Multifunctional DNA‐Based Materials for Biomedical Applications (Adv. Mater. 24/2018)

In article number 1703658, Yuezhou Zhang, Hongbo Zhang, and co-workers discuss the biomedical applications of DNA-based materials. Due to the well understood interactions of four types of nucleotides, which serve as the building blocks of DNA, the programmable and versatile structure is readily achieved and multifaceted functionalities are assigned. DNA nanomaterials are very promising in biomedical applications.

Beyond the pre-communicative medium: A cross-behavioral prospective study on the role of gesture in language and play development

This study prospectively explored the role of declarative and imperative gestures in the development of language and symbolic play milestones using a multi-measure micro-analytic approach. Nine infants were observed in their natural home environments once a month for a one hour session between the ages of 8–16 months by recording their spontaneous pre-lingual and lingual form usages and symbolic play acts. This framework enabled the coding of object- and human-directed vocalization, babbling, speech, declarative and imperative gestures, and four types of symbolic play acts: single-object play, single-object sequences, multi-object play, and multi-object sequences. The relative degree of usage of each type of behavior was examined. The results showed that declarative and imperative gestures frequency of usage are related to all language milestones for the short and long term. The infants’ gestures were related to symbolic play for the long term; their declarative gestures supported most of the levels of symbolic acts and their imperative gestures supported multi-object sequences. The results are explained in terms of the structural building blocks and contextual framework of gestures, which may scaffold infants’ preliminary symbolic behavior.

Synthesis of Molybdenum Carbide and Formation of an Epitaxial Mo2c/MoS2 Hybrid Structure Via Carburization of Molybdenum Disulfide

The epitaxial formation of metallic molybdenum carbide (Mo2C, a 2D MXene material) is achieved via chemical conversion of molybdenum disulfide with thermal annealing under CH4 and H2. A fully converted metallic Mo2C and Mo2C/MoS2 hybrid junctions could be provided with the adjusting of synthesis area of Mo2C the thermal annealing period. Mo2C film shows a metallic property as the outstanding electrode with a low sheet resistance (123.6 Ω/cm2) and carrier concentration of 5.84Х1013 /cm2. Mo2C/MoS2 hybrid junctions display a low contact resistance (1.2 kΩ∙μm) and low Schottky barrier height (26 meV), indicating the material’s potential utility as a critical hybrid structural building block in future device applications. Mo2C grows and forms a Mo2C/MoS2 hybrid structure were simulated by density functional theory calculations to model the mechanisms. The results show that Mo2C conversion is initiated at the MoS2 edge and undergoes sequential hydrodesulfurization and carbide conversion steps, and an atomically sharp interface with MoS2 forms through epitaxial growth of Mo2C. This work provides the area-controllable synthesis of a manufacturable MXene from a transition metal dichalcogenide (TMD) material and the formation of a metal/semiconductor junction structure. The present results will be of critical importance for future 2D heterojunction structures and functional device applications.

Imide-Based Polymers of Intrinsic Microporosity: Probing the Microstructure in Relation to CO2 Sorption Characteristics.

A range of microporous, imide-based polymers were newly synthesized using two-step poly-condensation reactions of bis(carboxylic anhydride) and various aromatic diamines for CO2 gas capture and storage applications. In this report, we attempted to assess the relative significance of molecular structural aspects through the manipulation of the conformational characteristics of the building blocks of the polymeric structures, the spiro-containing acid anhydride and the aromatic amines, to induce greater intrinsic microporosity and higher surface areas for the resulting solids. Results obtained from this study were thus used to outline a working relationship between the structural diversity of the constructed porous solids and their performance as CO2 sorbents.

Untangling the drivers of community cohesion in small-scale fisheries

Sustainable fisheries require strong management and effective governance. However, small-scale fisheries (SFF) often lack formal institutions, leaving management in the hands of local users in the form of various governance approaches (e.g., local, traditional, or co-management). The effectiveness of these approaches inherently relies upon some level of cohesion among resource users to facilitate agreement on common policies and practices regarding common pool fishery resources. Understanding the factors driving the formation and maintenance of community cohesion in SSF is therefore critical if we are to devise more effective participatory governance approaches and encourage and empower decentralized, localized, and community-based resource management approaches. Here, we adopt a social relational network perspective to propose a suite of hypothesized drivers that lead to the establishment of social ties among fishers that build the foundation for community cohesion. We then draw on detailed data from Jamaica’s small-scale fishery to empirically test these drivers by employing a set of nested exponential random graph models (ERGMs) based on specific structural building blocks (i.e., network configurations) theorized to influence the establishment of social ties. Our results demonstrate that multiple drivers are at play, but that collectively, gear-based homophily, geographic proximity, and leadership play particularly important roles. We discuss the extent to which these drivers help explain previous experiences, as well as their implications for future and sustained collective action in SSF in Jamaica and elsewhere.

Self-Assembling of Fmoc-GC Peptide Nucleic Acid Dimers into Highly Fluorescent Aggregates.

The study of molecules that self-assemble through noncovalent interactions is one of the most attractive topics in supramolecular chemistry. The use of short peptides or modified nucleotides as building blocks for the aggregates is particularly intriguing because these are very easy to synthesize; moreover, subtle changes in the chemical structure of such building blocks may drastically affect the properties of the aggregates. The ability of peptide nucleic acids (PNA) to aggregate has been very little explored, despite its practical applications. In this work we investigated the self-assembling properties of a PNA dimer, conjugated at the N-terminus to a fluorenylmethoxycarbonyl group. This PNA dimer forms nano-aggregates at low concentration in CHCl3 /CH3 OH mixtures. The aggregates retain very interesting fluorescent properties (high quantum yield in the visible region with lifetimes on the nanosecond scale), which make them promising materials for applications in optoelectronics.

4-Diphenylaminocarbazole: Switching Substituent Position for Voltage Reduction and Efficiency Enhancement of OLEDs

Simple but exceptionally efficient 4-diphenylaminocarbazole host material, 4-DPACz, is presented and compared with its positional isomer, 1-DPACz. The shift of diphenylamino substituent from the 1-position to 4-position of carbazole resulted in an increase in the HOMO energy level as well as an increase in triplet energy level. Having a high triplet energy level (2.76 eV) and well-matched HOMO energy level (-5.61 eV), 4-DPACz showed reduced driving voltage and higher efficiencies for solution-processed green PhOLEDs compated to PVK as well as 1-DPACz. Maximum luminous, power, and external quantum efficiencies reaching to 47.9 cd A-1, 25.2 lm W-1, and 14.3%, respectively, were achieved with a device configuration of [ITO/PEDOT:PSS/4-DPACz:Ir(mppy)3/TPBi/CsF/Al]. Additional enhancement of efficiencies of 4-DPACz was verified when incorporating another dopant, Ir(Si-bppy)2(acac), resulting in 59.1 cd A-1, 29.5 lm W-1, and 15.8%. Furthermore, reduced efficiency roll-off was clearly observed for 4-DPACz compared with PVK. Such improved device characteristics of 4-DPACz were attributed to its high hole mobility and charge balance inside the emitting layer therof. The excellent results using such a simple-structured 4-DPACz could promote various applications of this 4-DPACz unit as a building block structure for further possible oligomeric, dendritic, and polymeric materials.

Waggawagga-CLI: A command-line tool for predicting stable single α-helices (SAH-domains), and the SAH-domain distribution across eukaryotes.

Stable single-alpha helices (SAH-domains) function as rigid connectors and constant force springs between structural domains, and can provide contact surfaces for protein-protein and protein-RNA interactions. SAH-domains mainly consist of charged amino acids and are monomeric and stable in polar solutions, characteristics which distinguish them from coiled-coil domains and intrinsically disordered regions. Although the number of reported SAH-domains is steadily increasing, genome-wide analyses of SAH-domains in eukaryotic genomes are still missing. Here, we present Waggawagga-CLI, a command-line tool for predicting and analysing SAH-domains in protein sequence datasets. Using Waggawagga-CLI we predicted SAH-domains in 24 datasets from eukaryotes across the tree of life. SAH-domains were predicted in 0.5 to 3.5% of the protein-coding content per species. SAH-domains are particularly present in longer proteins supporting their function as structural building block in multi-domain proteins. In human, SAH-domains are mainly used as alternative building blocks not being present in all transcripts of a gene. Gene ontology analysis showed that yeast proteins with SAH-domains are particular enriched in macromolecular complex subunit organization, cellular component biogenesis and RNA metabolic processes, and that they have a strong nuclear and ribonucleoprotein complex localization and function in ribosome and nucleic acid binding. Human proteins with SAH-domains have roles in all types of RNA processing and cytoskeleton organization, and are predicted to function in RNA binding, protein binding involved in cell and cell-cell adhesion, and cytoskeletal protein binding. Waggawagga-CLI allows the user to adjust the stabilizing and destabilizing contribution of amino acid interactions in i,i+3 and i,i+4 spacings, and provides extensive flexibility for user-designed analyses.

Epitaxial Synthesis of Molybdenum Carbide and Formation of a Mo2C/MoS2 Hybrid Structure via Chemical Conversion of Molybdenum Disulfide.

The epitaxial synthesis of molybdenum carbide (Mo2C, a 2D MXene material) via chemical conversion of molybdenum disulfide (MoS2) with thermal annealing under CH4 and H2 is reported. The experimental results show that adjusting the thermal annealing period provides a fully converted metallic Mo2C from MoS2 and an atomically sharp metallic/semiconducting hybrid structure via partial conversion of the semiconducting 2D material. Mo2C/MoS2 hybrid junctions display a low contact resistance (1.2 kΩ·μm) and low Schottky barrier height (26 meV), indicating the material's potential utility as a critical hybrid structural building block in future device applications. Density functional theory calculations are used to model the mechanisms by which Mo2C grows and forms a Mo2C/MoS2 hybrid structure. The results show that Mo2C conversion is initiated at the MoS2 edge and undergoes sequential hydrodesulfurization and carbide conversion steps, and an atomically sharp interface with MoS2 forms through epitaxial growth of Mo2C. This work provides the area-controllable synthesis of a manufacturable MXene from a transition metal dichalcogenide material and the formation of a metal/semiconductor junction structure. The present results will be of critical importance for future 2D heterojunction structures and functional device applications.

Shape Transformation of Constituent Building Blocks within Self-Assembled Nanosheets and Nano-origami.

Self-assembly of nanoparticles represents a simple yet efficient route to synthesize designer materials with unusual properties. However, the previous assembled structures whether by surfactants, polymer, or DNA ligands are "static" or "frozen" building block structures. Here, we report the growth of transformable self-assembled nanosheets which could enable reversible switching between two types of nanosheets and even evolving into diverse third generation nanosheet structures without losing pristine periodicity. Such in situ transformation of nanoparticle building blocks can even be achieved in a free-standing two-dimensional system and three-dimensional origami. The success in such in situ nanocrystal transformation is attributed to robust "plant-cell-wall-like" ion-permeable reactor arrays from densely packed polymer ligands, which spatially define and confine nanoscale nucleation/growth/etching events. Our strategy enables efficient fabrication of nanocrystal nanosheets with programmable building blocks for innovative applications in adaptive tactile metamaterials, optoelectronic devices, and sensors.

Morphological and elemental analysis of alpaca hair (Vicugna pacos) using scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM – EDX)

The aim of studies was to evaluate the microstructure and elemental compositions of alpaca hair. The hair from eight alpacas, which came from different part of Poland, were analyzed by scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDX). The quantitive analysis was performed for nutritionally important elements (calcium and phosphorous), elements, which are part of building blocks of hair structure (silicon and sulfur) and trace elements (copper, zinc, selenium). Moreover, the elemental mapping was carried out. The SEM images showed that microstructure of hair is irregular and rough. The average diameter of hair is 32,27 ± 4,06 µm. The obtained results showed content of elements in hair and also their distribution in the structure of hair. This findings can be a good benchmark for further studies. .