First-principles based force-field for the interaction of proteins with Au(100)(5 x 1): an extension of GolP-CHARMM

Noncovalent recognition between peptides and inorganic materials is an established phenomenon. Key to exploiting these interactions in a wide range of materials self-assembly applications would be to harness the facet-selective control of peptide binding onto these materials. Fundamental understanding of what drives facet-selectivity in peptide binding is developing, but as yet is not sufficient to enable design of predictable facet-specific sequences. Computational simulation of the aqueous peptide-gold interface, commonly used to understand the mechanisms driving adsorption at an atomic level, has thus far neglected the role that surface reconstruction might play in facet specificity. Here the polarizable GolP-CHARMM suite of force fields is extended to include the reconstructed Au(100) surface. The force field, compatible with the bio-organic force field CHARMM, is parametrized using first-principles data. Our extended force field is tailored to reproduce the heterogeneity of weak chemisorbing N and S species to specific locations in the Au(100)(5 × 1) surface identified from the first-principles calculations. We apply our new model to predict and compare the three-dimensional structure of liquid water at Au(111), Au(100)(1 × 1), and Au(100)(5 × 1) interfaces. Using molecular dynamics simulations, we predict an increased likelihood for water-mediated peptide adsorption at the aqueous-Au(100)(1 × 1) interface compared with the Au(100)(5 × 1) interface. Therefore, our findings suggest that peptide binding can discriminate between the native and reconstructed Au(100) interfaces and that the role of reconstruction on binding at the Au(100) interface should not be neglected. © 2013 American Chemical Society.

Differentiation from first principles using spreadsheets

The article demonstrates the ability of spreadsheets to fit a polynomial to a set of discrete points. It is noted that such an ability enables students to not just evaluate a gradient at a single point, but at a whole family of points, which generates the analytical global gradient function of secants without doing any algebraic manipulations. One of the advantages of such an approach is that it enables the class to focus on the concepts being taught, rather than being hindered by the mechanics of trying to factorise a cubic polynomial.

Structural phase transformations of Mg3N2 at high pressure : experimental and theoretical studies

The structural behavior of Mg₃N₂ has been investigated up to 40.7 GPa at room temperature by means of angle-dispersive X-ray diffraction. A reversible, first-order structural phase transition from the ambient cubic phase (Ia3̅) to a high-pressure monoclinic phase (C2/m) is found to start at ~ 20.6 GPa and complete at ~ 32.5 GPa for the first time. The equation of state determined from our experiments yields bulk moduli of 110.7(2) and 171.5(1) GPa for the cubic and monoclinic phases, respectively, indicating higher incompressibility of the high-pressure phase of Mg₃N₂. First-principles calculations reproduced the phase stability and transition pressure determined in our experiment. In addition, a second phase transition from the monoclinic phase to a hexagonal phase (P3̅m₁) was predicted around 67 GPa for Mg₃N₂. The electronic band structures of three phases of Mg₃N₂ are also calculated and discussed.

Scandium-doped AlN 1D hexagonal nanoprisms : a class of room-temperature ferromagnetic materials

Pretty vacancy: The formation energy of Al vacancies in aluminum nitride is decreased by doping with nonmagnetic scandium ions. These vacancies are shown to be the cause of the room-temperature ferromagnetism in the resulting 1D hexagonal nanoprisms of AlN:Sc, a result that is confirmed by first-principles calculations. The doping approach provides a new route to dilute magnetic semiconductor materials.

Dielectric screening in atomically thin boron nitride nanosheets

Two-dimensional (2D) hexagonal boron nitride (BN) nanosheets are excellent dielectric substrate for graphene, molybdenum disulfide, and many other 2D nanomaterial-based electronic and photonic devices. To optimize the performance of these 2D devices, it is essential to understand the dielectric screening properties of BN nanosheets as a function of the thickness. Here, electric force microscopy along with theoretical calculations based on both state-of-the-art first-principles calculations with van der Waals interactions under consideration, and nonlinear Thomas-Fermi theory models are used to investigate the dielectric screening in high-quality BN nanosheets of different thicknesses. It is found that atomically thin BN nanosheets are less effective in electric field screening, but the screening capability of BN shows a relatively weak dependence on the layer thickness.

Oxygen-doped boron nitride nanosheets with excellent performance in hydrogen storage

Hydrogen is considered one of the best energy sources. However, the lack of effective, stable, and safe storage materials has severely prevented its practical application. Strong effort has been made to try new nanostructured materials as new storage materials. In this study, oxygen-doped boron nitride (BN) nanosheets with 2-6 atomic layers, synthesized by a facile sol-gel method, show a storage capacity of 5.7wt% under 5MPa at room temperature, which is the highest hydrogen storage ever reported for any BN materials. Importantly, 89% of the stored hydrogen can be released when the hydrogen pressure is reduced to ambient conditions. Furthermore, the BN nanosheets exhibit an excellent storage cycling stability due to the stable two-dimensional nanostructure. The first principles calculations reveal that the high hydrogen storage mainly origins from the oxygen-doping of the BN nanosheets with increased adsorption energies of H2 on BN by 20-80% over pure BN sheets at the different coverage. © 2014 Elsevier Ltd.

Prediction of a superhard carbon-rich C-N compound comparable to diamond

Until now, it has been a challenge both in experiment and in theory to design new superhard materials with high hardness values that are comparable to that of diamond. Here, by using first-principles calculations, we have introduced two new phases for a carbon-rich C-N compound with stoichiometry C3N, which is predicted to be energetically stable or metastable with respect to graphite and solid N2 at ambient pressure. It is found that C3N has a layered structure containing graphitic layers sandwiched with freely rotated N2 molecules. The layer-structured C3N is calculated to transform into a three-dimensional C2221 structure at 9 GPa with sp3-hybridized C atoms and sp2-hybridized N atoms. Phonon dispersion and elastic constant calculations reveal the dynamical and mechanical stability of the C2221 phase of C3N at ambient pressure. Significantly, first-principles ideal strength calculations indicate that the C2221 phase of C3N is a superhard material with an estimated Vickers hardness (∼76 GPa) comparable to that of diamond (60-120 GPa). The present results shed strong light on designing new superhard materials in the C-N system.

Non-covalent adsorption of amino acid analogues on noble-metal nanoparticles: influence of edges and vertices

The operation of many nanostructured biomolecular sensors and catalysts critically hinges on the manipulation of non-covalent adsorption of biomolecules on unfunctionalised noble-metal nanoparticles (NMNPs). Molecular-level structural details of the aqueous biomolecule/NMNP interface are pivotal to the successful realisation of these technologies, but such experimental data are currently scarce and challenging to obtain. Molecular simulations can generate these details, but are limited by the assumption of non-preferential adsorption to NMNP features. Here, via first principles calculations using a vdW-DF functional, and based on nanoscale sized NMNPs, we demonstrate that adsorption preferences to NP features vary with adsorbate chemistry. These results show a clear distinction between hydrocarbons, that prefer adsorption to facets over edges/vertices, over heteroatomic molecules that favour adsorption onto vertices over facets. Our data indicate the inability of widely used force-fields to correctly capture the adsorption of biomolecules onto NMNP surfaces under aqueous conditions. Our findings introduce a rational basis for the development of new force-fields that will reliably capture these phenomena.

Response : A defensible and workable approach to the income tax treatment of financial instruments

It is a privilege to have the opportunity to respond to the comments on my monograph1 provided by Mark Gergen, Glenn May, and Gordon Longhouse. Their comments, which are inevitably coloured by their very different perspectives, reflect the considerable expertise that each one of them has in the area of the income taxation of financial instruments. Indeed, it is with some hesitation that I offer a response in defence of various portions of the analysis presented in my monograph in support of some pretty modest proposals in this extremely difficult area of income tax law. Although I spent considerable time exploring some necessary first principles and their implications for the design of a system for the income taxation of financial instruments, I made several concessions to certain practical constraints that led me to support, in some measure, the status quo reflected in certain of the existing literature, as well as the legislation in a select group of countries. On the assumption that many readers may be unfamiliar with the monograph, I propose to respond by outlining much of my analysis in the monograph and the proposals that are the logical outcome. Throughout the outline, I will highlight and respond to what I see as the important points of difference emphasized by Gergen, May, and Longhouse.

Evolutionary approach to revising modernization theory : an introduction to the credible polity

The future global distribution of the political regimes of countries, just like that of their economic incomes, displays a surprising tendency for polarization into only two clubs of convergence at the extrema. This, in itself, is a persuasive reason to analyze afresh the logical validity of an endogenous theory for political and economic development inherent in modernization theory. I suggest how adopting a simple evolutionary game theoretic view on the subject allows an explanation for these parallel clubs of convergence in political regimes and economic income within the framework of existing research in democratization theory. I also suggest how instrumental action can be methodically introduced into such a setup using learning strategies adopted by political actors. These strategies, based on the first principles of political competition, are motivated by introducing the theoretical concept of a Credible Polity.