Structural Building Blocks Research Articles

Dynamic responses in shocked Cu-Zr nanoglasses with gradient microstructure

Shock is one of the physical processes that materials are most likely to suffer during applications, therefore the elusive shock properties of nanoglasses are unacceptable. Additionally, establishing gradient microstructure is a promising approach to optimize mechanics properties further. Here, shock characteristics of Cu64Zr36 nanoglasses with gradient microstructures are systematically investigated by molecular dynamics simulations in the particle velocity range of 0.5 to 5 km/s. Two types of gradient nanoglasses (GNGs) along the shock direction are prepared and analyzed, i.e., a negative gradient structure (S1) in contrast with a positive gradient structure (S2). The results show that the number of mechanically stable <0,0,12,0> and <0,1,10,2> atomic Voronoi polyhedra, which are typical building blocks of the amorphous structure in terms of Voronoi tessellation method, in grain interfaces is significantly less than that in grain interiors. As a result, the local free volume gradually changes along the shock direction by the designed gradient structure, which causes a significant impact on the shock wave profiles of shear strain, stress, configurational entropy, and temperature in the GNGs. However, due to a similar chemically-disordered feature in grain interiors and interfaces, the shock wave speeds of nanoglasses are not sensitive to grain sizes under the same shock strength, contrary to the usual shock wave speed mechanism in conventional polycrystalline. Thus, unlike traditional polycrystalline with grain size gradient, the indirect free-surface method of estimating spall strength is still applicable to the GNGs. Finally, the positive gradient structure results in lower temperature and free volume in the spall region, which causes the spall strengths of the S2 sample higher than those of the S1 sample.

The next 50 years in database indexing or

Index structures are a building block of query processing and computer science in general. Since the dawn of computer technology there have been index structures. And since then, a myriad of index structures are being invented and published each and every year. In this paper we argue that the very idea of "inventing an index" is a misleading concept in the first place. It is the analogue of "inventing a physical query plan". This paper is a paradigm shift in which we propose to drop the idea to handcraft index structures (as done for binary search trees over B-trees to any form of learned index) altogether. We present a new automatic index breeding framework coined Genetic Generic Generation of Index Structures (GENE) . It is based on the observation that almost all index structures are assembled along three principal dimensions: (1) structural building blocks, e.g., a B-tree is assembled from two different structural node types (inner and leaf nodes), (2) a couple of invariants, e.g., for a B-tree all paths have the same length, and (3) decisions on the internal layout of nodes (row or column layout, etc.). We propose a generic indexing framework that can mimic many existing index structures along those dimensions. Based on that framework we propose a generic genetic index generation algorithm that, given a workload and an optimization goal, can automatically assemble and mutate, in other words 'breed' new index structure 'species'. In our experiments we follow multiple goals. We reexamine some good old wisdom from database technology. Given a specific workload, will GENE even breed an index that is equivalent to what our textbooks and papers currently recommend for such a workload? Or can we do even more? Our initial results strongly indicate that generated indexes are the next step in designing index structures.

Graphene Suspension from Modified Electrochemical Exfoliation of Graphite

Graphene has emerged as one of the most exciting materials since its discovery in 2004. Graphene is a term used for one to ten layers of sp2 hybridized carbon atoms arranged in a hexagonal pattern. Monolayer graphene is the building block of all graphitic structures and has high electron mobility, high thermal conductivity, high specific surface area, extremely high resistance to gas permeation and high optical transmittance. These exceptional properties make monolayer graphene attractive for potential applications as a catalyst or catalyst support in direct methanol fuel cells (DMFC), proton exchange membrane fuel cells (PEMFC), electrode in lithium-ion batteries, supercapacitors, as well as in thermally and electrically conductive sensors. AB-stacked bilayer and trilayer graphene have applications in the electronic industry, such as fabrication of field-effect transistors (FEts) and light detectors, due to an induced bandgap in the presence of an applied electric field. In addition, graphene finds major applications in the optoelectronic industry, such as electrode materials in solar cells, supercapacitors and transparent LCDs.Graphene is traditionally synthesized using the simple mechanical exfoliation of graphite, which is not scalable, or from chemical vapour deposition of a carbon source on a suitable substrate, which is both a complex and an expensive method. Hence, a scalable and economic graphene synthesis method is needed to harness the remarkable properties of graphene. The electrochemical exfoliation of graphite provides a promising route for the bulk production of graphene because it provides graphene flakes with the largest size and a smaller defect density than the well-known chemical synthesis methods such as Hummer or modified Hummer processes. The large size flakes resulting from electrochemical exfoliation are suitable for scalable electronic device fabrication methods. Electrochemical exfoliation proceeds via intercalation of the ions present in the electrolyte and is followed by the subsequent expansion and later exfoliation of graphite. However, this strategy produces graphene with a scatter in the layer numbers. A polydisperse suspension of graphene is undesirable because the electronic properties of graphene change with the number of layers. The intermediate graphite intercalation compounds are formed by the insertion of intercalants between the layers of the graphite host material. The intercalants can be atoms, ions or molecules. Graphite intercalation occurs in stages where the stage number indicates the number of graphene layers between the two nearest intercalant layers. In the present study, a modified electrochemical exfoliation route of graphite is explored, which proceeds through the exfoliation of a stage pure graphite intercalation compound followed by low-intensity ultrasonication. The modified electrochemical exfoliation of graphite is capable of providing a monodisperse graphene suspension

Modular Evolution of the Drosophila Metabolome.

Comparative phylogenetic studies offer a powerful approach to study the evolution of complex traits. Although much effort has been devoted to the evolution of the genome and to organismal phenotypes, until now relatively little work has been done on the evolution of the metabolome, despite the fact that it is composed of the basic structural and functional building blocks of all organisms. Here we explore variation in metabolite levels across 50 My of evolution in the genus Drosophila, employing a common garden design to measure the metabolome within and among 11 species of Drosophila. We find that both sex and age have dramatic and evolutionarily conserved effects on the metabolome. We also find substantial evidence that many metabolite pairs covary after phylogenetic correction, and that such metabolome coevolution is modular. Some of these modules are enriched for specific biochemical pathways and show different evolutionary trajectories, with some showing signs of stabilizing selection. Both observations suggest that functional relationships may ultimately cause such modularity. These coevolutionary patterns also differ between sexes and are affected by age. We explore the relevance of modular evolution to fitness by associating modules with lifespan variation measured in the same common garden. We find several modules associated with lifespan, particularly in the metabolome of older flies. Oxaloacetate levels in older females appear to coevolve with lifespan, and a lifespan-associated module in older females suggests that metabolic associations could underlie 50 My of lifespan evolution.

Chimeric single α-helical domains as rigid fusion protein connections for protein nanotechnology and structural biology

Chimeric fusion proteins are essential tools for protein nanotechnology. Non-optimized protein-protein connections are usually flexible and therefore unsuitable as structural building blocks. Here we show that the ER/K motif, a single α-helical domain (SAH), can be seamlessly fused to terminal helices of proteins, forming an extended, partially free-standing rigid helix. This enables the connection of two domains at a defined distance and orientation. We designed three constructs termed YFPnano, T4Lnano, and MoStoNano. Analysis of experimentally determined structures and molecular dynamics simulations reveals a certain degree of plasticity in the connections that allows the adaptation to crystal contact opportunities. Our data show that SAHs can be stably integrated into designed structural elements, enabling new possibilities for protein nanotechnology, for example, to improve the exposure of epitopes on nanoparticles (structural vaccinology), to engineer crystal contacts with minimal impact on construct flexibility (for the study of protein dynamics), and to design novel biomaterials.

Sa Bayan ng Meycauayan (In the Town of Meycauayan) – the Quarries, the People and Their Church

The Meycauayan quarries are important sources of cut stones during the Colonial Period. Piedra de meycauayan became the building blocks of many historic structures in Luzon. This article sheds light into the relationship of the townsfolk of Meycauayan to their church, specifically their response in sustaining the church by renewing the deed of donation of quarries made by their forefathers. This will be done by examining a 1731 manuscript from the Archivo Franciscano Ibero-Oriental (AFIO) – a rare document in the vernacular that offers perspective from the natives rather than the colonizers. All these are framed within the historical development of the famed quarries.

Halogenated benzothiadiazole-based conjugated polymers as efficient photocatalysts for dye degradation and oxidative coupling of benzylamines

Donor-acceptor (D-A) conjugated polymers are widely used in photovoltaic applications and heterogeneous catalysis due to their tunable building block and pre-designable structures. Here, a series of adjustable Donor-acceptor (D-A) benzothiodiazole-based conjugated polymers were designed and synthesized. The photocatalytic performance could be improved by fine-tuning the chemical structure by halogen substitution (F or Cl). The polymers exhibited excellent optoelectronic properties and were effective photocatalysts for the degradation of RhB and MO dyes, as well as promoting the oxidative coupling of benzylamines. Complete degradation of RhB and MO occurred in 30 min under visible light radiation, while the yield of benzylamine coupling mediated by superoxide anion was as high as 82%. Systematic characterization methods were used to gain insights on the unique photocatalytic performance of the polymers. Our findings provide further insights into the design and synthesis of benzothiadiazole-based conjugated polymers as promising organic photocatalysts for solar energy conversion.

Tailored Synthesis of Iron Oxide Nanocrystals for Formation of Cuboid Mesocrystals.

In this work, we systematically studied the shape- and size-controlled monodisperse synthesis of iron oxide nanocrystals (IONCs) for their use as building blocks in the formation of mesocrystals. For this aim, on understanding the influence of the oleic acid concentration, iron-oleate concentration, and heating rate on the synthesis of robust and reproducible IONCs with desired sizes and shapes, we synthesized highly monodisperse ∼11 nm sized nanocubes and nanospheres. Magnetic measurements of both cubic and spherical IONCs revealed the presence of mixed paramagnetic and superparamagnetic phases in these nanocrystals. Moreover, we observed that the magnetic moments of the nanocubes are more substantial compared to their spherical counterparts. We then demonstrated a simple magnetic-field-assisted assembly of nanocubes into three-dimensional (3D) cuboid mesocrystals while nanospheres did not form any mesocrystals. These findings indicate that small cubic nanocrystals hold great promise as potential building blocks of 3D magnetic hierarchical structures with their superior magnetic properties and mesocrystal assembly capability, which may have high relevance in various fields ranging from high-density data storage to biomedical applications.

Wallpaper group kirigami

Kirigami, the art of paper cutting, has become a paradigm for mechanical metamaterials in recent years. The basic building blocks of any kirigami structures are repetitive deployable patterns that derive inspiration from geometric art forms and simple planar tilings. Here, we complement these approaches by directly linking kirigami patterns to the symmetry associated with the set of 17 repeating patterns that fully characterize the space of periodic tilings of the plane. We start by showing how to construct deployable kirigami patterns using any of the wallpaper groups, and then design symmetry-preserving cut patterns to achieve arbitrary size changes via deployment. We further prove that different symmetry changes can be achieved by controlling the shape and connectivity of the tiles and connect these results to the underlying kirigami-based lattice structures. All together, our work provides a systematic approach for creating a broad range of kirigami-based deployable structures with any prescribed size and symmetry properties.

Follow the Hatred: The Production of Negative Feeling in Emily Brontë'sWuthering Heights

Follow the Hatred: The Production of Negative Feeling in Emily Brontë's<i>Wuthering Heights</i>

Molecular library of OLED host materials—Evaluating the multiscale simulation workflow

Amorphous small-molecule organic materials are utilized in organic light emitting diodes (OLEDs), with device performance relying on appropriate chemical design. Due to the vast number of contending materials, a symbiotic experimental and simulation approach would be greatly beneficial in linking chemical structure to macroscopic material properties. We review simulation approaches proposed for predicting macroscopic properties. We then present a library of OLED hosts, containing input files, results of simulations, and experimentally measured references of quantities relevant to OLED materials. We find that there is a linear proportionality between simulated and measured glass transition temperatures, despite a quantitative disagreement. Computed ionization energies are in excellent agreement with the ultraviolet photoelectron and photoemission spectroscopy in air measurements. We also observe a linear correlation between calculated electron affinities and ionization energies and cyclic voltammetry measurements. Computed energetic disorder correlates well with thermally stimulated luminescence measurements and charge mobilities agree remarkably well with space charge–limited current measurements. For the studied host materials, we find that the energetic disorder has the greatest impact on the charge carrier mobility. Our library helps to swiftly evaluate properties of new OLED materials by providing well-defined structural building blocks. The library is public and open for improvements. We envision the library expanding and the workflow providing guidance for future OLED material design.

Pegylation of phenothiazine – A synthetic route towards potent anticancer drugs

IntroductionCancer is a big challenge of the 21 century, whose defeat requires efficient antitumor drugs. ObjectivesThe paper aims to investigate the synergistic effect of two structural building blocks, phenothiazine and poly(ethylene glycol), towards efficient antitumor drugs. MethodsTwo PEGylated phenothiazine derivatives were synthetized by attaching poly(ethylene glycol) of 550 Da to the nitrogen atom of phenothiazine by ether or ester linkage. Their antitumor activity has been investigated on five human tumour lines and a mouse tumor line as well, by determination of IC50. The in vivo toxicity was determined by measuring the LD50 in BALB/c mice by the sequential method and the in vivo antitumor potential was measured by the tumours growth test. The antitumor mechanism was investigated by complexation studies of zinc and magnesium ions characteristic to the farnesyltransferase enzyme, by studies of self-aggregation in the cells proximity and by investigation of the antitumor properties of the acid species resulted by enzymatic cleavage of the PEGylated derivatives. ResultsThe two compounds showed antitumor activity, with IC50 against mouse colon carcinoma cell line comparable with that of the traditional antitumor drugs 5-Fluorouracil and doxorubicin. The phenothiazine PEGylation resulted in a significant toxicity diminishing, the LD50 in BALB/c mice increasing from 952.38 up to 1450 mg/kg, in phenothiazine equivalents. Both compounds inflicted a 92% inhibition of the tumour growth for doses much smaller than LD50. The investigation of the possible tumour inhibition mechanism suggested the nanoaggregate formation and the cleavage of ester bonds as key factors for the inhibition of cancer cell proliferation and biocompatibility improvement. ConclusionPhenothiazine and PEG building blocks have a synergetic effect working for both tumour growth inhibition and biocompatibility improvement. All these findings recommend the PEGylated phenothiazine derivatives as a valuable workbench for a next generation of antitumor drugs.

Building blocks of protein structures: Physics meets biology.

The native state structures of globular proteins are stable and well packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry of the building blocks of protein structures-α helices and strands assembled into β sheets-with no adjustable parameters, no amino acid sequence information, and no chemistry. There is an almost perfect fit between the dictates of mathematics and physics and the rules of quantum chemistry. Protein evolution is facilitated by sequence-independent platforms, which can elaborate sequence-dependent functional diversity. Our work highlights the vital role of discreteness in life and may have implications for the creation of artificial life and on the nature of life elsewhere in the cosmos.

Optimization of Magnetic Flux Ropes Modeled with the Regularized Biot–Savart Law Method

The so-called regularized Biot-Savart laws (RBSLs) provide an efficient and flexible method for modeling pre-eruptive magnetic configurations of coronal mass ejections (CMEs) whose characteristics are constrained by observational images and magnetic-field data. This method allows one to calculate the field of magnetic flux ropes (MFRs) with small circular cross-sections and an arbitrary axis shape. The field of the whole configuration is constructed as a superposition of (1) such a flux-rope field and (2) an ambient potential field derived, for example, from an observed magnetogram. The RBSL kernels are determined from the requirement that the MFR field for a straight cylinder must be exactly force-free. For a curved MFR, however, the magnetic forces are generally unbalanced over the whole path of the MFR. To minimize these forces, we apply a modified Gauss-Newton method to find optimal MFR parameters. This is done by iteratively adjusting the MFR axis path and axial current. We then try to relax the resulting optimized configuration in a subsequent line-tied zero-beta magnetohydrodynamic simulation toward a force-free equilibrium. By considering two models of the sigmoidal pre-eruption configuration for the 2009 February 13 CME, we demonstrate how this approach works and what it is capable of. We show, in particular, that the building blocks of the core magnetic structure described by these models match to morphological features typically observed in such type of configurations. Our method will be useful for both the modeling of particular eruptive events and theoretical studies of idealized pre-eruptive MFR configurations.

V-Shape Pneumatic Torsional Actuator: A Building Block for Soft Grasper and Manipulator.

Robotic joints are fundamental components in artificial graspers and manipulators, and they are designed to achieve high dexterity to carry out various tasks. Traditional robotic hands are often driven by rigid joints, such as tendons and electric motors, resulting in bulky and complex designs. Soft robotics, composed of flexible and compliant materials, offers promising solutions to mimic the human hands and handle delicate objects safely. In this article, we propose a simple yet effective V-shape pneumatic torsional actuator (V-PTA) as the building blocks of soft grasper and manipulators. The proposed actuator is capable of producing large angular changes and twisting torque, responding fast to pneumatic changes, and scaling to appropriate dimensions easily. Because the design is generic and modular in nature, these lightweight actuators could also be assembled to form a variety of patterns of structures to suit the needs of individual tasks. We further fabricated robotic graspers and manipulators based on multiple V-PTA and demonstrated that our design could offer solutions to execute daily laboratory operations that interact with small and irregular components. Experimental data confirmed that the V-PTA building block structure could potentially pave the path forward for miniature robotic automation in laboratory or industrial settings.

The scaling of social interactions across animal species

Social animals self-organise to create groups to increase protection against predators and productivity. One-to-one interactions are the building blocks of these emergent social structures and may correspond to friendship, grooming, communication, among other social relations. These structures should be robust to failures and provide efficient communication to compensate the costs of forming and maintaining the social contacts but the specific purpose of each social interaction regulates the evolution of the respective social networks. We collate 611 animal social networks and show that the number of social contacts E scales with group size N as a super-linear power-law E=CN^beta for various species of animals, including humans, other mammals and non-mammals. We identify that the power-law exponent beta varies according to the social function of the interactions as beta = 1+a/4, with a approx {1,2,3,4}. By fitting a multi-layer model to our data, we observe that the cost to cross social groups also varies according to social function. Relatively low costs are observed for physical contact, grooming and group membership which lead to small groups with high and constant social clustering. Offline friendship has similar patterns while online friendship shows weak social structures. The intermediate case of spatial proximity (with beta =1.5 and clustering dependency on network size quantitatively similar to friendship) suggests that proximity interactions may be as relevant for the spread of infectious diseases as for social processes like friendship.

Longer charged amino acids favor β-strand formation in hairpin peptides.

Interactions between charged amino acids significantly influence the structure and function of proteins. The encoded charged amino acids Asp, Glu, Arg, and Lys have different number of hydrophobic methylenes linking the backbone to the charged functionality. It remains to be fully understood how does this difference in the number of methylenes affect protein structure stability. Protein secondary structures are the fundamental three-dimensional building blocks of protein structures. β-Sheet structures are particularly interesting, because these structures have been associated with a number of protein misfolding diseases. Herein, we report the effect of charged amino acid side chain length at two β-strand positions individually on the stability of a β-hairpin. The charged amino acids include side chains with a carboxylate, an ammonium, or a guanidinium group. The experimental peptides, fully folded reference peptides, and fully unfolded reference peptides were synthesized by solid phase peptide synthesis and analyzed by 2D NMR methods including TOCSY, DQF-COSY, and ROESY. Sequence specific assignments were performed for all peptides. The chemical shift data were used to derive the fraction folded population and the folding free energy for the experimental peptides. Results showed that the fraction folded population increased with increasing charged amino acid side chain length. These results should be useful for developing functional peptides that adopt the β-conformation.

Cluster‐assembled materials: Ordered structures with advanced properties

AbstractCluster‐assembled materials (CAMs) present delicate structures and tailored properties, which have gained extensive interest in recent years. Due to the noncovalent linkage and size of sub‐1 nm, clusters present polymer‐like solution behaviors distinct from conventional nanocrystals, whereby a variety of CAMs with different constructions have been fabricated. To our knowledge, the morphologies and properties of CAMs are closely connected, which are strongly dependent on the structure and coordination state of cluster building blocks. For the CAMs with superior performances, the specific arrangement and surroundings of clusters at subnanometer scale usually result in well‐organized structures. In this review, we will summarize the recent progress of CAMs with highly ordered structures and advanced properties, where polyoxometalate cluster assemblies as well as cluster–nuclei co‐assemblies are involved. The application potentials of CAMs are then discussed, especially on the cluster arrangements and interactions at subnanometer scale. However, current researches are far from reaching the point, and future efforts are needed before the nature of cluster‐based nanostructures can be sufficiently revealed. We hope this article can offer unique insights and instructive understanding to the CAMs.

(Invited) Negative Volume Compressibility in Sc3n@C80–Cubane Cocrystal with Charge Transfer

According to the laws of thermodynamics, materials normally exhibit contraction or expansion along the directions of the applied pressure or tension. Here, we show that a man-made cocrystal of a metallofullerene and highly energetic cubane, with strained sp3 bonding, may exhibit an anomalous negative volume compressibility. In this cocrystal, the freely rotating fullerene Sc3N@C80 acts as a structural building block while static cubane molecules fill the lattice interstitial sites. Under high pressure, Sc3N@C80 keeps stable and preserves the crystalline framework of the materials, while the cubane undergoes a progressive configurational transformation above 6.5 GPa, probably promoted by charge transfer from fullerene to cubane. A further configurational change of the cubane into a low-density configuration at higher pressure results in an anomalous pressure-driven lattice expansion of the cocrystal (∼1.8% volume expansion). Such unusual negative compressibility has previously only been predicted by theory and suggested to appear in mechanical metamaterials.

A medium-range structure motif linking amorphous and crystalline states.

Amorphous materials have no long-range order, but there are ordered structures at short range (2-5 Å), medium range (5-20 Å) and even longer length scales1-5. While regular6,7 and semiregular polyhedra8-10 are often found as short-range ordering in amorphous materials, the nature of medium-range order has remained elusive11-14. Consequently, it is difficult to determine whether there exists any structural link at medium range or longer length scales between the amorphous material and its crystalline counterparts. Moreover, an amorphous material often crystallizes into a phase of different composition15, with very different underlying structural building blocks, further compounding the issue. Here, we capture an intermediate crystalline cubic phase in a Pd-Ni-P amorphous alloy and reveal the structure of the medium-range order, a six-membered tricapped trigonal prism cluster (6M-TTP) with a length scale of 12.5 Å. We find that the 6M-TTP can pack periodically to several tens of nanometres to form the cube phase. Our experimental observations provide evidence of a structural link between the amorphous and crystalline phases in a Pd-Ni-P alloy at the medium-range length scale and suggest that it is the connectivity of the 6M-TTP clusters that distinguishes the crystalline and amorphous phases. These findings will shed light on the structure of amorphous materials at extended length scales beyond that of short-range order.