Commensurate Unit Research Articles

Using fuzzy logic to compare species distribution models developed on the basis of expert knowledge and sampling records

BackgroundExperts use knowledge to infer the distribution of species based on fuzzy logical assumptions about the relationship between species and the environment. Thus, expert knowledge is amenable to fuzzy logic modelling, which give to propositions a continuous truth value between 0 and 1. In species distribution modelling, fuzzy logic may also be used to model, from a number of records, the degree to which conditions are favourable to the occurrence of a species. Therefore, fuzzy logic operations can be used to compare and combine models based on expert knowledge and species records. Here, we applied fuzzy logic modelling to the distribution of amphibians in Uruguay as inferred from expert knowledge and from observed records to infer favourable locations, with favourability being the commensurable unit for both kinds of data sources. We compared the results for threatened species, species considered by experts to be ubiquitous, and non-threatened, non-ubiquitous species. We calculated the fuzzy intersection of models based on both knowledge sources to obtain a unified prediction of favourable locations.ResultsModels based on expert knowledge involved a larger number of variables and were less affected by sampling bias. Models based on experts had the same overprediction rate for the three types of species, whereas models based on species records had a lower prediction rate for ubiquitous species. Models based on expert knowledge performed equally as well or better than corresponding models based on species records for threatened species, even when they had to discriminate and classify the same set of records used to build the models based on species records. For threatened species, expert models predicted more restrictive favourable territories than those predicted based on records. Observed records generated the best-fitted models for non-threatened non-ubiquitous species, and ubiquitous species.ConclusionsFuzzy modelling permitted the objective comparison of the potential of expert knowledge and incomplete distribution records to infer the territories favourable for different species. Distribution of threatened species was able to be better explained by subjective expert knowledge, while for generalist species models based on observed data were more accurate. These results have implications for the correct use of expert knowledge in conservation planning.

Electric-field-tunable band gap in commensurate twisted bilayer graphene

Bernal bilayer graphene exhibits a band gap that is tunable through the infrared with an electric field. We show that sublattice odd commensurate twisted bilayer graphene (C-TBG) exhibits a band gap that is tunable through the terahertz with an electric field. We show that from the perspective of terahertz optics the sublattice odd and even forms of C-TBG are ``inflated'' versions of Bernal and AA-stacked bilayer graphene, respectively, with energy scales reduced by a factor of 110 for the $21.{79}^{\ensuremath{\circ}}$ commensurate unit cell. This lower energy scale is accompanied by a correspondingly smaller gate voltage, which means that the strong-field regime is more easily accessible than in the Bernal case. Finally, we show that the interlayer coherence energy is a directly accessible experimental quantity through the position of a power-law divergence in the optical conductivity.

SYSTEMATIC APPROACH TO WORK SAFETY MANAGEMENT IN THE WORKPLACE

Occupational safety management in our country no longer meets modern requirements for occupational safety in the workplace and needs to be improved, in particular through the introduction of a risk-oriented approach to the assessment of production factors. The use of risk-oriented approach system to safety management in the workplace is substantiated in this work, and it is the primary link in the management system of labor protection and its optimal (comfortable) organization significantly affects the production environment, safety and staff productivity. A structural and logical model of the incident at the workplace is proposed and possible dangerous events, the development of which in space and time can lead to its implementation are identified. Dangerous events can be caused by both - the actions of the employer and the employee, as well as external factors. All considered dangerous events are random in nature, so methods of general theory of random process control, simulation and Boolean algebra are used for their analysis. According to this model, workplace safety management involves identifying the factors that are most likely to be present in the workplace and justifying measures to reduce the frequency of their occurrence and increase the level of safety. It is shown that the use of a systemic risk-oriented approach to safety management in the workplace will allow to identify the factors that are most likely to cause accidents and to develop appropriate measures to eliminate them. In a market economy, an important point in occupational safety management at all levels is to resolve the compromise between the economic feasibility of economic activity and social responsibility of the state in a way that reduces production risk, namely - maintaining human-centric economic development. Finding such a compromise is difficult and problematic, as it is difficult to compare in commensurate units the economic performance of economic activities with social losses due to accidents and occupational diseases at work. In the conditions of decentralization, when the role of supervisory bodies over the state of labor protection is reduced, it is very important to form elements of labor protection culture in employees and managers. Improving public and cultural education on occupational safety remains a priority of our country's public policy, in particular through higher education, which trains highly qualified workers and senior managers who are personally responsible for occupational safety at each workplace.

Understanding parapatry: How do environment and competitive interactions shape Iberian vipers’ distributions?

ABSTRACTAimAs parapatric distributions are traditionally studied by pairs of species, this study aims to evaluate the causes of the maintenance of parapatry, specifically to assess whether the case of the three viper species present in the Iberian Peninsula is mainly caused by environmental conditions, historical events, interspecific competition among them, or a combination of these factors.LocationThe Iberian Peninsula.TaxonVipera aspis, V. latastei and V. seoanei..MethodsWe applied the concept of favourability of occurrence to produce commensurate distribution units unaffected by the prevalence of different species in the Iberian Peninsula. We compared the favourability of each species individually with the favourability of occurrence of more than one species co‐occurring in their overlapping ranges, and identified the areas in which sympatric coexistence, environmental segregation and competitive exclusion are predicted to occur.ResultsThe main driver of the parapatric pattern was competitive exclusion, which was mediated by gradual changes in the environmental conditions favouring each species. The para‐Mediterranean V. aspis presented fragmented favourable areas outside its range that seemed to be unoccupied due to competitive exclusion by the other vipers. The Mediterranean V. latastei appeared to be limited by competition with the other viper species and by the environment in north‐western Iberia. V. seoanei prevented the other two species becoming established in the north‐western quarter of the Iberian Peninsula due to its better adaption to the humid conditions in this region. Some areas of sustainable coexistence were detected, mainly in the upper reaches of the River Ebro.Main conclusionsEach species is better adapted to particular conditions. However, the existence of ecotones forces them to occur sympatrically and compete for resources. The parapatric pattern is a result of the evolutionary history of the species and of strong competitive interactions between them, which form ‘competitive‐exclusion barriers’. However, these barriers are environmentally dependent, so changes in the environment could rapidly affect the limits of the species distribution.

Disobedient Things

Analysis of the Deepwater Horizon disaster and the accumulatory decline of BP demonstrates both the analytical efficacy of the capital-as-power approach to value theory, and the irreducible role of objects in the process of accumulation. Rather than productivity per se, accumulation depends on control of productivity. Capital as power focuses on capitalization as an expression of the assessment by owners of their own power. In this article, I argue that the power of owners translated into capital values is over both the human and non-human components of systems of production. Power is actualized through entities defined as cultural and political, as well as economic. Capitalization translates the irreducible social order – including objects – that bear on accumulation into commensurable units of capital. The decline of BP’s capital valuation in the wake of the disaster expressed the market’s falling confidence in the obedience of the entities that bear on its profits, including the things that comprise the company’s productive capacity.

Spinel- and Högbomite-Supergroup Minerals from Sulfide-Free Endogenic Pb–Zn–Sb–As Assemblage in the Pelagonian Massif, Republic of North Macedonia

Sulfide-free mineral assemblages with the chalcophile element minerals from occurrences associated with altered rocks of Pelagonian massif, Republic of North Macedonia have been studied. The inputting sequence of various ore-forming constituents has been revealed on the basis of morphological features, zoning of the spinel-group minerals, and the hogbomite supergroup minerals. Conclusions about the inputting consequences of various ore-forming components have shown that these minerals easily form epitaxial and syntaxial intergrowths with each other and with nežilovite due to commensurable unit cell parameters. Some potentially new minerals were identified belonging to the hogbomite supergroup.

Phylogenetic Comparative Methods and the Evolution of Multivariate Phenotypes

Evolutionary biology is multivariate, and advances in phylogenetic comparative methods for multivariate phenotypes have surged to accommodate this fact. Evolutionary trends in multivariate phenotypes are derived from distances and directions between species in a multivariate phenotype space. For these patterns to be interpretable, phenotypes should be characterized by traits in commensurate units and scale. Visualizing such trends, as is achieved with phylomorphospaces, should continue to play a prominent role in macroevolutionary analyses. Evaluating phylogenetic generalized least squares (PGLS) models (e.g., phylogenetic analysis of variance and regression) is valuable, but using parametric procedures is limited to only a few phenotypic variables. In contrast, nonparametric, permutation-based PGLS methods provide a flexible alternative and are thus preferred for high-dimensional multivariate phenotypes. Permutation-based methods for evaluating covariation within multivariate phenotypes are also well established and can test evolutionary trends in phenotypic integration. However, comparing evolutionary rates and modes in multivariate phenotypes remains an important area of future development.

Commensurate lattice constant dependent thermal conductivity of misoriented bilayer graphene

Misorientation of two layers of bilayer graphene leaves distinct signatures in the electronic properties and the phonon modes. The effect on the thermal conductivity has received the least attention and is the least well understood. In this work, the in-plane thermal conductivity of misoriented bilayer graphene (m-BLG) is investigated as a function of temperature and interlayer misorientation angle using nonequilibrium molecular dynamics (NEMD). The central result is that the calculated thermal conductivities decrease approximately linearly with the increasing lattice constant of the commensurate m-BLG unit cell. Comparisons of the phonon dispersions show that misorientation has negligible affect on the low-energy phonon frequencies and velocities. However, the larger periodicity of m-BLG reduces the Brillouin zone size to the extent that the zone edge acoustic phonons are thermally populated. This allows Umklapp scattering to reduce the lifetimes of the phonons contributing to the thermal transport, and consequently, to reduce the thermal conductivity. This explanation is supported by direct calculation of reduced phonon lifetimes in m-BLG based on density functional theory (DFT).

Bulk-boundary correspondence from the intercellular Zak phase

The Zak phase $\gamma$, the generalization of the Berry phase to Bloch wave functions in solids, is often used to characterize inversion-symmetric 1D topological insulators; however, since its value can depend on the choice of real-space origin and unit cell, only the difference between the Zak phase of two regions is believed to be relevant. Here, we show that one can extract an origin-independent part of $\gamma$, the so-called inter-cellular Zak phase $\gamma^{\mathrm{inter}}$, which can be used as a bulk quantity to predict the number of surface modes as follows: a neutral finite 1D tight-binding system has $n_s = \gamma^{\mathrm{inter}}/\pi$ (mod 2) number of in-gap surface modes below the Fermi level if there exists a commensurate bulk unit cell that respects inversion symmetry. We demonstrate this by first verifying that $\pm e\gamma^{\mathrm{inter}}/2\pi$ (mod $e$) is equal to the extra charge accumulation in the surface region for a general translationally invariant 1D insulator, while the remnant part of $\gamma$, the intra-cellular Zak phase $\gamma^{\mathrm{intra}}$, corresponds to the electronic part of the dipole moment of the bulk's unit cell. Second, we show that the extra charge accumulation can be related to the number of surface modes when the unit cell is inversion symmetric. This bulk-boundary correspondence using $\gamma^{\mathrm{inter}}$ reduces to the conventional one using $\gamma$ when the real-space origin is at the inversion center. Our work thereby clarifies the usage of $\gamma$ in the bulk-boundary correspondence. We study several tight binding models to quantitatively check the relation between the extra charge accumulation and the inter-cellular Zak phase as well as the bulk-boundary correspondence using the inter-cellular Zak phase.

Atomistic modeling of phonon transport in turbostratic graphitic structures

Thermal transport in turbostratic graphitic systems is investigated by using an atomistic analytical model based on the 4th-nearest-neighbor force constant approximation and a registry-dependent interlayer potential. The developed model is shown to produce an excellent agreement with the experimental data and ab initio results in the calculation of bulk properties. Subsequent analysis of phonon transport in combination with the Green's function method illustrates the significant dependence of key characteristics on the misorientation angle, clearly indicating the importance of this degree of freedom in multi-stacked structures. Selecting three angles with the smallest commensurate unit cells, the thermal resistance is evaluated at the twisted interface between two AB stacked graphite. The resulting values in the range of 35 × 10−10 K m2/W to 116 × 10−10 K m2/W are as large as those between two dissimilar material systems such as a metal and graphene. The strong rotational effect on the cross-plane thermal transport may offer an effective means of phonon engineering for applications such as thermoelectric materials.

CellMatch: Combining two unit cells into a common supercell with minimal strain

Recent emergence of 2D materials (the so-called van der Waals materials), of which graphene is the most famous one, opens new routes in creation of novel materials by mere layer-by-layer combinations. Moreover, a growth of such materials is typically done on a substrate. In both cases structures appear that are periodical in the plane but the periodicity is very different from simple 1×1 commensurate unit cells combinations which appears for materials with very similar values of lattice constants. Much more common is the case in which a new periodic cell is of a moiré type—such as 10×10 over 9×9 in case of graphene on Ir(111). Once the shape of the common supercell for 2 different 2D materials, or a material and the surface is found–it is easy to do a computational treatment with appropriate method for electronic structure–such as density functional theory, tight binding or some other. The purpose of the CellMatch code is to generate such common supercell given the two unit cells of selected materials. The CellMatch code searches within given combinatorial space and sorts results by the strain imposed on one of the components, while the other component experiences zero strain. Program summaryProgram title: CellMatchCatalogue identifier: AEYD_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEYD_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.htmlNo. of lines in distributed program, including test data, etc.: 18603No. of bytes in distributed program, including test data, etc.: 129294Distribution format: tar.gzProgramming language: Python.Computer: Any architecture with a python interpreter.Operating system: Linux, AIX.RAM: Even for large systems almost negligible usage of memory.Classification: 7.3.Nature of problem: Contracting a common supercell that fits the atoms of two unit cells with minimal strain. This is used as input for any total energy or electronic structure code.Solution method: Straightforward systematic search in the phase space of combinations of unit cell vectors.Unusual features: Output, atomic structure of the supercell, can be used in any total energy program.Running time: Usually very short (seconds) if the search parameters are kept at reasonable values.

Self-assembly of indole-2-carboxylic acid at graphite and gold surfaces.

Model systems are critical to our understanding of self-assembly processes. As such, we have studied the surface self-assembly of a small and simple molecule, indole-2-carboxylic acid (I2CA). We combine density functional theory gas-phase (DFT) calculations with scanning tunneling microscopy to reveal details of I2CA assembly in two different solvents at the solution/solid interface, and on Au(111) in ultrahigh vacuum (UHV). In UHV and at the trichlorobenzene/highly oriented pyrolytic graphite (HOPG) interface, I2CA forms epitaxial lamellar structures based on cyclic OH⋯O carboxylic dimers. The structure formed at the heptanoic acid/HOPG interface is different and can be interpreted in a model where heptanoic acid molecules co-adsorb on the substrate with the I2CA, forming a bicomponent commensurate unit cell. DFT calculations of dimer energetics elucidate the basic building blocks of these structures, whereas calculations of periodic two-dimensional assemblies reveal the epitaxial effects introduced by the different substrates.

Biodiversity offsetting: what are the challenges, opportunities and research priorities for animal conservation?

[Extract] Governments, businesses, financial institutions and local communities are increasingly using biodiversity offsets, also known as compensatory mitigation, as a putative mechanism to achieve 'no net loss' (NNL) of biodiversity as a result of specific development projects (McKenney & Kiesecker, 2010; Quetier & Lavorel, 2011; Gardner et al., 2013). The Business and Biodiversity Offsets Programme (BBOP), an international collaboration for the development of offset methodologies, defines biodiversity offsets as 'the measurable conservation outcomes resulting from actions designed to compensate for significant residual adverse biodiversity impacts arising from project development after appropriate prevention and mitigation measures have been taken. The goal of biodiversity offsets is to achieve no net loss and preferably a net gain of biodiversity on the ground with respect to species composition, habitat structure, ecosystem function and people's use and cultural values associated with biodiversity' (BBOP, 2009). Proposals are already proceeding in the European Union (EU) for a NNL initiative as part of the 'EU Biodiversity Strategy to 2020' – with possible operational principles that include offsetting schemes (see http://ec.europa.eu/environment/nature/biodiversity/nnl/index_en.htm). Madsen et al. (2011) identified legislation mandating compensatory biodiversity conservation mechanisms (including offsets) in 45 countries, with a further 27 under development and this number is likely to have grown since.

Growth of Si on Ag(111) and determination of large commensurate unit cell of high-temperature phase

We studied the structural transition for silicon adsorption on Ag(111) by using low-energy electron diffraction (LEED) and Auger electron spectroscopy at various substrate temperatures during deposition. We obtained a single phase of the (4 × 4) structure at 520 K, which was reported as a silicene. At 620 K, the (4 × 4) structure changed to a high-temperature phase which was determined as by LEED, while in preceding works, it was assigned to a quasi or structure. Although the high-temperature phase had not been observed as a single phase, we obtained LEED patterns with a single phase for it, which enabled us to explain all the diffraction spots on the basis of the kinematic theory including double diffraction. The was obtained by the multiplication of a subunit cell. We concluded that the and phases could instead be represented as a phase, and we proposed a possible atomic model.

LEED studies on modulated surface structures

Abstract The problems occurring in structure analyses of modulated surfaces by LEED or X-ray diffraction are briefly discussed. In previous LEED studies of modulated surfaces a commensurate unit cell and Fourier coefficients to describe the modulation function has been used. The wave length of the modulation and the size of the supercell are limited in this way by the computational effort of the multiple scattering calculations. To overcome this problem an approximation is proposed allowing the analysis of commensurate or incommensurate surface modulations with long wave lengths.

Band structure of silicene on zirconium diboride (0001) thin-film surface: Convergence of experiment and calculations in the one-Si-atom Brillouin zone

So far, it represents a challenging task to reproduce angle-resolved photoelectron (ARPES) spectra of epitaxial silicene by first-principles calculations. Here, we report on the resolution of the previously controversial issue related to the structural configuration of silicene on the ZrB$_2$(0001) surface and its band structure. In particular, by representing the band structure in a large Brillouin zone associated with a single Si atom, it is found that the imaginary part of the one-particle Green's function follows the spectral weight observed in ARPES spectra. By additionally varying the in-plane lattice constant, the results of density functional theory calculations and ARPES data obtained in a wide energy range converge into the "planar-like" phase and provide the orbital character of electronic states in the vicinity of the Fermi level. It is anticipated that the choice of a smaller commensurate unit cell for the representation of the electronic structure will be useful for the study of epitaxial two-dimensional materials on various substrates in general.

CuPc/Au(1 1 0): Determination of the azimuthal alignment by a combination of angle-resolved photoemission and density functional theory

Here we report on a combined experimental and theoretical study on the structural and electronic properties of a monolayer of Copper-Phthalocyanine (CuPc) on the Au(110) surface. Low-energy electron diffraction reveals a commensurate overlayer unit cell containing one adsorbate species. The azimuthal alignment of the CuPc molecule is revealed by comparing experimental constant binding energy (kxky)-maps using angle-resolved photoelectron spectroscopy with theoretical momentum maps of the free molecule's highest occupied molecular orbital (HOMO). This structural information is confirmed by total energy calculations within the framework of van-der-Waals corrected density functional theory. The electronic structure is further analyzed by computing the molecule-projected density of states, using both a semi-local and a hybrid exchange-correlation functional. In agreement with experiment, the HOMO is located about 1.2eV below the Fermi-level, while there is no significant charge transfer into the molecule and the CuPc LUMO remains unoccupied on the Au(110) surface.

Substrate selected polymorphism of epitaxially aligned tetraphenyl-porphyrin thin films

Porphyrin molecules, of interest as versatile materials for organic electronics, are highly prone to formation of significantly different polymorphic phases. To elucidate the determinants for the specific polymorphic phase formed in thin films as well as for the arrangement of the molecules on a given substrate two different anisotropic substrate surfaces have been selected: KCl(100) and the oxygen reconstructed Cu(110) surface. We observe that the crystal structure of the thin films depends on the substrate, whereas the relative molecular orientations in both cases are similar. X-Ray and transmission electron diffraction of 30 nm thick tetraphenyl-porphyrin (H(2)TPP) and platinum tetraphenyl-porphyrin (PtTPP) thin films deposited on KCl(100) surfaces reveals that both kinds of molecules crystallize in a tetragonal polymorph with the (001) lattice planes, i.e. with their macrocycles, parallel to the substrate. Films deposited on the oxygen reconstructed Cu(110)-(2 × 1)O surface exhibit in contrast the triclinic polymorph even though molecules again align nearly parallel to the substrate surface as observed by LEED and X-ray diffraction. On both substrates we identify two driving forces for the epitaxial alignment of porphyrins: (i) molecules aligning with their macrocycles (nearly) parallel to the substrate surface and (ii) the porphyrin molecules forming a commensurate unit cell with the respective substrate. The polymorphic phase meeting both requirements is the most favorable to be formed on a given substrate and due to this structural flexibility in both cases well-ordered, epitaxially aligned porphyrin thin films are achieved.

Reconstructing Iron Age Community Dynamics in Eskişehir Province, Central Turkey

Current understanding of the Iron Age polity of Phrygia in Central Anatolia is primarily based on excavations and survey in the region of the Phrygian capital of Gordion. In order to expand our knowledge of the Phrygian polity, we assess the scale and nature of Iron Age communities in the western (Eskisehir) region of Phrygia. We address the challenge of interpreting ceramics derived from large-scale archaeological survey by utilizing Neutron Activation Analysis (NAA) of ceramics from 12 sites across the region collected by the Eskisehir archaeological survey project as well as an excavated assemblage from Şar Hoyuk. While the uniformity in ceramic technology and styles suggest the region is part of the larger Phrygian community, NAA results reveal that (a) ceramic production was regionally highly localized with limited evidence of standardization during the Iron Age and (b) based on evidence of community interaction it is possible to establish a partial chronological sequence of development. These results have implications not only for understanding the internal dynamics within the Phrygian core but also for developing a methodology for comparing ancient polities using commensurate units of interacting communities. The present study is part of the larger Anatolian Iron Age Ceramics project ( http://www.une.edu.au/a-ia ).

Adsorption ofα-sexithiophene on Au(001): Molecule-induced partial lifting of the substrate reconstruction

Ultrathin films of the organic molecule $\ensuremath{\alpha}$-sexithiophene (6T) on Au(001) have been studied by variable-temperature scanning tunneling microscopy. Upon adsorption at room temperature, the monolayer forms two highly ordered and enantiomeric pure structures of flat-lying molecules arranged in rows. While one structural phase is related to quenching of the underlying substrate reconstruction, the quasihexagonal Au(001) reconstruction is conserved for the other one. This leads to two different substrate symmetries for the two molecular structures. Detailed analysis reveals a commensurate unit cell identical to a 6T monolayer on Ag(001) for one structure and an incommensurate 6T arrangement for the other structure strikingly similar to 6T on Au(111). In situ measurements at elevated temperatures show a thermally induced order-disorder transition due to molecular diffusion processes at approximately 400 K.