Derivation of the Supermolecular Interaction Energy from the Monomer Densities in the Density Functional Theory

The density functional theory (DFT) interaction energy of a dimer is rigorously derived from the monomer densities. To this end, the supermolecular energy bifunctional is formulated in terms of mutually orthogonal sets of orbitals of the constituent monomers. The orthogonality condition is preserved in the solution of the Kohn-Sham equations through the Pauli blockade method. Numerical implementation of the method provides interaction energies which agree with those obtained from standard supermolecular calculations within less than 0.1% error for three example functionals: Slater-Dirac, PBE0 and B3LYP, and for two model van der Waals dimers: Ne2 and (C2H4)2, and two model H-bond complexes: (HF)2 and (NH3)2.Comment: 6 pages, 1 figure, REVTeX

Molecular structural order and anomalies in liquid silica

The present investigation examines the relationship between structural order, diffusivity anomalies, and density anomalies in liquid silica by means of molecular dynamics simulations. We use previously defined orientational and translational order parameters to quantify local structural order in atomic configurations. Extensive simulations are performed at different state points to measure structural order, diffusivity, and thermodynamic properties. It is found that silica shares many trends recently reported for water [J. R. Errington and P. G. Debenedetti, Nature 409, 318 (2001)]. At intermediate densities, the distribution of local orientational order is bimodal. At fixed temperature, order parameter extrema occur upon compression: a maximum in orientational order followed by a minimum in translational order. Unlike water, however, silica's translational order parameter minimum is broad, and there is no range of thermodynamic conditions where both parameters are strictly coupled. Furthermore, the temperature-density regime where both structural order parameters decrease upon isothermal compression (the structurally anomalous regime) does not encompass the region of diffusivity anomalies, as was the case for water.Comment: 30 pages, 8 figure

A test of non-equilibrium thermodynamics in glassy systems: the soft-sphere case

The scaling properties of the soft-sphere potential allow the derivation of an exact expression for the pressure of a frozen liquid, i.e., the pressure corresponding to configurations which are local minima in its multidimensional potential energy landscape. The existence of such a relation offers the unique possibility for testing the recently proposed extension of the liquid free energy to glassy out-of-equilibrium conditions and the associated expression for the temperature of the configurational degrees of freedom. We demonstrate that the non-equilibrium free energy provides an exact description of the soft-sphere pressure in glass states

Electrification of granular systems of identical insulators

Insulating particles can become highly electrified during powder handling, volcanic eruptions, and the wind-blown transport of dust, sand, and snow. Measurements in these granular systems have found that smaller particles generally charge negatively, while larger particles charge positively. These observations are puzzling, since particles in these systems are generally chemically identical, and thus have no contact potential difference. We show here that simple geometry leads to a net transfer of electrons from larger to smaller particles, in agreement with these observations. We integrate this charging mechanism into the first quantitative charging scheme for a granular system of identical insulators, and show that its predictions are in agreement with measurements. Our theory thus seems to provide an explanation for the hitherto puzzling phenomenon of the size-dependent charging of granular systems of identical insulators.Comment: 8 pages, 5 figures, published in Physical Review

Shear yielding of amorphous glassy solids: Effect of temperature and strain rate

We study shear yielding and steady state flow of glassy materials with molecular dynamics simulations of two standard models: amorphous polymers and bidisperse Lennard-Jones glasses. For a fixed strain rate, the maximum shear yield stress and the steady state flow stress in simple shear both drop linearly with increasing temperature. The dependence on strain rate can be described by a either a logarithm or a power-law added to a constant. In marked contrast to predictions of traditional thermal activation models, the rate dependence is nearly independent of temperature. The relation to more recent models of plastic deformation and glassy rheology is discussed, and the dynamics of particles and stress in small regions is examined in light of these findings

Density-functional embedding using a plane-wave basis

The constrained electron density method of embedding a Kohn-Sham system in a substrate system (first described by P. Cortona, Phys. Rev. B {\bf 44}, 8454 (1991) and T.A. Wesolowski and A. Warshel, J. Phys. Chem {\bf 97}, 8050 (1993)) is applied with a plane-wave basis and both local and non-local pseudopotentials. This method divides the electron density of the system into substrate and embedded electron densities, the sum of which is the electron density of the system of interest. Coupling between the substrate and embedded systems is achieved via approximate kinetic energy functionals. Bulk aluminium is examined as a test case for which there is a strong interaction between the substrate and embedded systems. A number of approximations to the kinetic-energy functional, both semi-local and non-local, are investigated. It is found that Kohn-Sham results can be well reproduced using a non-local kinetic energy functional, with the total energy accurate to better than 0.1 eV per atom and good agreement between the electron densities.Comment: 11 pages, 4 figure

Locally Preferred Structure and Frustration in Glassforming Liquids: A Clue to Polyamorphism?

We propose that the concept of liquids characterized by a given locally preferred structure (LPS) could help in understanding the observed phenomenon of polyamorphism. ``True polyamorphism'' would involve the competition between two (or more) distinct LPS, one favored at low pressure because of its low energy and one favored at high pressure because of its small specific volume, as in tetrahedrally coordinated systems. ``Apparent polyamorphism'' could be associated with the existence of a poorly crystallized defect-ordered phase with a large unit cell and small crystallites, which may be illustrated by the metastable glacial phase of the fragile glassformer triphenylphosphite; the apparent polyamorphism might result from structural frustration, i. e., a competition between the tendency to extend the LPS and a global constraint that prevents tiling of the whole space by the LPS.Comment: 11, 6 figures, Proceedings of the Conference "Horizons in Complex Systems", Messina; in honor of the 60th birthday of H.E. Stanle

Sheared Solid Materials

We present a time-dependent Ginzburg-Landau model of nonlinear elasticity in solid materials. We assume that the elastic energy density is a periodic function of the shear and tetragonal strains owing to the underlying lattice structure. With this new ingredient, solving the equations yields formation of dislocation dipoles or slips. In plastic flow high-density dislocations emerge at large strains to accumulate and grow into shear bands where the strains are localized. In addition to the elastic displacement, we also introduce the local free volume {\it m}. For very small $m$ the defect structures are metastable and long-lived where the dislocations are pinned by the Peierls potential barrier. However, if the shear modulus decreases with increasing {\it m}, accumulation of {\it m} around dislocation cores eventually breaks the Peierls potential leading to slow relaxations in the stress and the free energy (aging). As another application of our scheme, we also study dislocation formation in two-phase alloys (coherency loss) under shear strains, where dislocations glide preferentially in the softer regions and are trapped at the interfaces.Comment: 16pages, 11figure

Effects of deletion of the Streptococcus pneumoniae lipoprotein diacylglyceryl transferase gene lgt on ABC transporter function and on growth in vivo

Lipoproteins are an important class of surface associated proteins that have diverse roles and frequently are involved in the virulence of bacterial pathogens. As prolipoproteins are attached to the cell membrane by a single enzyme, prolipoprotein diacylglyceryl transferase (Lgt), deletion of the corresponding gene potentially allows the characterisation of the overall importance of lipoproteins for specific bacterial functions. We have used a Δlgt mutant strain of Streptococcus pneumoniae to investigate the effects of loss of lipoprotein attachment on cation acquisition, growth in media containing specific carbon sources, and virulence in different infection models. Immunoblots of triton X-114 extracts, flow cytometry and immuno-fluorescence microscopy confirmed the Δlgt mutant had markedly reduced lipoprotein expression on the cell surface. The Δlgt mutant had reduced growth in cation depleted medium, increased sensitivity to oxidative stress, reduced zinc uptake, and reduced intracellular levels of several cations. Doubling time of the Δlgt mutant was also increased slightly when grown in medium with glucose, raffinose and maltotriose as sole carbon sources. These multiple defects in cation and sugar ABC transporter function for the Δlgt mutant were associated with only slightly delayed growth in complete medium. However the Δlgt mutant had significantly reduced growth in blood or bronchoalveolar lavage fluid and a marked impairment in virulence in mouse models of nasopharyngeal colonisation, sepsis and pneumonia. These data suggest that for S. pneumoniae loss of surface localisation of lipoproteins has widespread effects on ABC transporter functions that collectively prevent the Δlgt mutant from establishing invasive infection

Jamming at Zero Temperature and Zero Applied Stress: the Epitome of Disorder

We have studied how 2- and 3- dimensional systems made up of particles interacting with finite range, repulsive potentials jam (i.e., develop a yield stress in a disordered state) at zero temperature and applied stress. For each configuration, there is a unique jamming threshold, $\phi_c$, at which particles can no longer avoid each other and the bulk and shear moduli simultaneously become non-zero. The distribution of $\phi_c$ values becomes narrower as the system size increases, so that essentially all configurations jam at the same $\phi$ in the thermodynamic limit. This packing fraction corresponds to the previously measured value for random close-packing. In fact, our results provide a well-defined meaning for "random close-packing" in terms of the fraction of all phase space with inherent structures that jam. The jamming threshold, Point J, occurring at zero temperature and applied stress and at the random close-packing density, has properties reminiscent of an ordinary critical point. As Point J is approached from higher packing fractions, power-law scaling is found for many quantities. Moreover, near Point J, certain quantities no longer self-average, suggesting the existence of a length scale that diverges at J. However, Point J also differs from an ordinary critical point: the scaling exponents do not depend on dimension but do depend on the interparticle potential. Finally, as Point J is approached from high packing fractions, the density of vibrational states develops a large excess of low-frequency modes. All of these results suggest that Point J may control behavior in its vicinity-perhaps even at the glass transition.Comment: 21 pages, 20 figure