Surface energy and stability of stress-driven discommensurate surface structures

A method is presented to obtain {\it ab initio} upper and lower bounds to surface energies of stress-driven discommensurate surface structures, possibly non-periodic or exhibiting very large unit cells. The instability of the stressed, commensurate parent of the discommensurate structure sets an upper bound to its surface energy; a lower bound is defined by the surface energy of an ideally commensurate but laterally strained hypothetical surface system. The surface energies of the phases of the Si(111):Ga and Ge(111):Ga systems and the energies of the discommensurations are determined within $\pm 0.2$ eV.Comment: 4 pages RevTeX. 2 Figures not included. Ask for a hard copy (through regular mail) to [email protected]

First-Principles Studies of Hydrogenated Si(111)--7×\times7

The relaxed geometries and electronic properties of the hydrogenated phases of the Si(111)-7$\times$7 surface are studied using first-principles molecular dynamics. A monohydride phase, with one H per dangling bond adsorbed on the bare surface is found to be energetically favorable. Another phase where 43 hydrogens saturate the dangling bonds created by the removal of the adatoms from the clean surface is found to be nearly equivalent energetically. Experimental STM and differential reflectance characteristics of the hydrogenated surfaces agree well with the calculated features.Comment: REVTEX manuscript with 3 postscript figures, all included in uu file. Also available at http://www.phy.ohiou.edu/~ulloa/ulloa.htm

Large Scale Electronic Structure Calculations with Multigrid Acceleration

We have developed a set of techniques for performing large scale ab initio calculations using multigrid accelerations and a real-space grid as a basis. The multigrid methods permit efficient calculations on ill-conditioned systems with long length scales or high energy cutoffs. The technique has been applied to systems containing up to 100 atoms, including a highly elongated diamond cell, an isolated C$_{60}$ molecule, and a 32-atom cell of GaN with the Ga d-states in valence. The method is well suited for implementation on both vector and massively parallel architectures.Comment: 4 pages, 1 postscript figur

Supercell technique for total-energy calculations of finite charged and polar systems

We study the behavior of total-energy supercell calculations for dipolar molecules and charged clusters. Using a cutoff Coulomb interaction within the framework of a plane-wave basis set formalism, with all other aspects of the method (pseudopotentials, basis set, exchange-correlation functional) unchanged, we are able to assess directly the interaction effects present in the supercell technique. We find that the supercell method gives structures and energies in almost total agreement with the results of calculations for finite systems, even for molecules with large dipole moments. We also show that the performance of finite-grid calculations can be improved by allowing a degree of aliasing in the Hartree energy, and by using a reciprocal space definition of the cutoff Coulomb interaction

Local Isoelectronic Reactivity of Solid Surfaces

The quantity w^N(r) = ( 1/ k^2 T_el)[partial n(r, T_el) / partial T_el]_(v(r),N) is introduced as a convenient measure of the local isoelectronic reactivity of surfaces. It characterizes the local polarizability of the surface and it can be calculated easily. The quantity w^N(r) supplements the charge transfer reactivity measured e.g. by the local softness to which it is closely related. We demonstrate the applicability and virtues of the function w^N(r) for the example of hydrogen dissociation and adsorption on Pd(100).Comment: RevTeX, 13 pages, 3 figures, to appear in Phys. Rev. Let

An Effective-Medium Tight-Binding Model for Silicon

A new method for calculating the total energy of Si systems is presented. The method is based on the effective-medium theory concept of a reference system. Instead of calculating the energy of an atom in the system of interest a reference system is introduced where the local surroundings are similar. The energy of the reference system can be calculated selfconsistently once and for all while the energy difference to the reference system can be obtained approximately. We propose to calculate it using the tight-binding LMTO scheme with the Atomic-Sphere Approximation(ASA) for the potential, and by using the ASA with charge-conserving spheres we are able to treat open system without introducing empty spheres. All steps in the calculational method is {\em ab initio} in the sense that all quantities entering are calculated from first principles without any fitting to experiment. A complete and detailed description of the method is given together with test calculations of the energies of phonons, elastic constants, different structures, surfaces and surface reconstructions. We compare the results to calculations using an empirical tight-binding scheme.Comment: 26 pages (11 uuencoded Postscript figures appended), LaTeX, CAMP-090594-

Combinatorial molecular optimization of cement hydrates

Despite its ubiquitous presence in the built environment, concrete’s molecular-level properties are only recently being explored using experimental and simulation studies. Increasing societal concerns about concrete’s environmental footprint have provided strong motivation to develop new concrete with greater specific stiffness or strength (for structures with less material). Herein, a combinatorial approach is described to optimize properties of cement hydrates. The method entails screening a computationally generated database of atomic structures of calcium-silicate-hydrate, the binding phase of concrete, against a set of three defect attributes: calcium-to-silicon ratio as compositional index and two correlation distances describing medium-range silicon-oxygen and calcium-oxygen environments. Although structural and mechanical properties correlate well with calcium-to-silicon ratio, the cross-correlation between all three defect attributes reveals an indentation modulus-to-hardness ratio extremum, analogous to identifying optimum network connectivity in glass rheology. We also comment on implications of the present findings for a novel route to optimize the nanoscale mechanical properties of cement hydrate.National Ready Mixed Concrete Association (Research sponsorship)Education Foundation (N.J.) (Research sponsorship)Portland Cement Association (Research sponsorship

Integrating evolution into ecological modelling: accommodating phenotypic changes in agent based models.

PMCID: PMC3733718This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Evolutionary change is a characteristic of living organisms and forms one of the ways in which species adapt to changed conditions. However, most ecological models do not incorporate this ubiquitous phenomenon. We have developed a model that takes a 'phenotypic gambit' approach and focuses on changes in the frequency of phenotypes (which differ in timing of breeding and fecundity) within a population, using, as an example, seasonal breeding. Fitness per phenotype calculated as the individual's contribution to population growth on an annual basis coincide with the population dynamics per phenotype. Simplified model variants were explored to examine whether the complexity included in the model is justified. Outputs from the spatially implicit model underestimated the number of individuals across all phenotypes. When no phenotype transitions are included (i.e. offspring always inherit their parent's phenotype) numbers of all individuals are always underestimated. We conclude that by using a phenotypic gambit approach evolutionary dynamics can be incorporated into individual based models, and that all that is required is an understanding of the probability of offspring inheriting the parental phenotype

The American Science Pipeline: Sustaining Innovation in a Time of Economic Crisis

Significant limitations have emerged in America's science training pipeline, including inaccessibility, inflexibility, financial limitations, and lack of diversity. We present three effective programs that collectively address these challenges. The programs are grounded in rigorous science and integrate through diverse disciplines across undergraduate, graduate, and postdoctoral students, and resonate with the broader community. We discuss these models in the context of current economic constraints on higher education and the urgent need for our institutions to recruit and retain diverse student populations and sustain the successful American record in scientific education and innovation

Influences of H on the Adsorption of a Single Ag Atom on Si(111)-7 × 7 Surface

The adsorption of a single Ag atom on both clear Si(111)-7 × 7 and 19 hydrogen terminated Si(111)-7 × 7 (hereafter referred as 19H-Si(111)-7 × 7) surfaces has been investigated using first-principles calculations. The results indicated that the pre-adsorbed H on Si surface altered the surface electronic properties of Si and influenced the adsorption properties of Ag atom on the H terminated Si surface (e.g., adsorption site and bonding properties). Difference charge density data indicated that covalent bond is formed between adsorbed Ag and H atoms on 19H-Si(111)-7 × 7 surface, which increases the adsorption energy of Ag atom on Si surface