Constraints on the phase diagram of molybdenum from first-principles free-energy calculations

We use first-principles techniques to re-examine the suggestion that transitions seen in high-P experiments on Mo are solid-solid transitions from the bcc structure to either the fcc or hcp structures. We confirm that in the harmonic approximation the free energies of fcc and hcp structures become lower than that of bcc at P > 325 GPa and T below the melting curve, as reported recently. However, we show that if anharmonic effects are fully included this is no longer true. We calculate fully anharmonic free energies of high-T crystal phases by integration of the thermal average stress with respect to strain as structures are deformed into each other, and also by thermodynamic integration from harmonic reference systems to the fully anharmonic system. Our finding that fcc is thermodynamically less stable than bcc in the relevant high-P/high-T region is supported by comparing the melting curves of the two structures calculated using the first-principles reference-coexistence technique. We present first-principles simulations based on the recently proposed Z method which also support the stability of bcc over fcc.Comment: 33 pages, 10 figure

Hsp-90 and the biology of nematodes

BACKGROUND: Hsp-90 from the free-living nematode Caenorhabditis elegans is unique in that it fails to bind to the specific Hsp-90 inhibitor, geldanamycin (GA). Here we surveyed 24 different free-living or parasitic nematodes with the aim of determining whether C. elegans Hsp-90 was the exception or the norm amongst the nematodes. We combined these data with codon evolution models in an attempt to identify whether hsp-90 from GA-binding and non-binding species has evolved under different evolutionary constraints.<BR/>RESULTS: We show that GA-binding is associated with life history: free-living nematodes and those parasitic species with free-living larval stages failed to bind GA. In contrast, obligate parasites and those worms in which the free-living stage in the environment is enclosed within a resistant egg, possess a GA-binding Hsp-90. We analysed Hsp-90 sequences from fifteen nematode species to determine whether nematode hsp-90s have undergone adaptive evolution that influences GA-binding. Our data provide evidence of rapid diversifying selection in the evolution of the hsp-90 gene along three separate lineages, and identified a number of residues showing significant evidence of adaptive evolution. However, we were unable to prove that the selection observed is correlated with the ability to bind geldanamycin or not.<BR/>CONCLUSION: Hsp-90 is a multi-functional protein and the rapid evolution of the hsp-90 gene presumably correlates with other key cellular functions. Factors other than primary amino acid sequence may influence the ability of Hsp-90 to bind to geldanamycin

Quantum atomic delocalization vs. structural disorder in amorphous silicon

Quantum effects on the atom delocalization in amorphous silicon have been studied by path-integral Monte Carlo simulations from 30 to 800 K. The quantum delocalization is appreciable vs. topological disorder, as seen from structural observables such as the radial distribution function (RDF). At low temperatures, the width of the first peak in the RDF increases by a factor of 1.5 due to quantum effects. The overall anharmonicity of the solid vibrations at finite temperatures in amorphous silicon is clearly larger than in the crystalline material. Low-energy vibrational modes are mainly located on coordination defects in the amorphous material.Comment: 5 pages, 5 PS figures, REVTE

Probing Disordered Substrates by Imaging the Adsorbate in its Fluid Phase

Several recent imaging experiments access the equilibrium density profiles of interacting particles confined to a two-dimensional substrate. When these particles are in a fluid phase, we show that such data yields precise information regarding substrate disorder as reflected in one-point functions and two-point correlations of the fluid. Using Monte Carlo simulations and replica generalizations of liquid state theories, we extract unusual two-point correlations of time-averaged density inhomogeneities induced by disorder. Distribution functions such as these have not hitherto been measured but should be experimentally accessible.Comment: 10 pages revtex 4 figure

A Self-Consistent First-Principles Technique Having Linear Scaling

An algorithm for first-principles electronic structure calculations having a computational cost which scales linearly with the system size is presented. Our method exploits the real-space localization of the density matrix, and in this respect it is related to the technique of Li, Nunes and Vanderbilt. The density matrix is expressed in terms of localized support functions, and a matrix of variational parameters, L, having a finite spatial range. The total energy is minimized with respect to both the support functions and the elements of the L matrix. The method is variational, and becomes exact as the ranges of the support functions and the L matrix are increased. We have tested the method on crystalline silicon systems containing up to 216 atoms, and we discuss some of these results.Comment: 12 pages, REVTeX, 2 figure

Coexistence and Criticality in Size-Asymmetric Hard-Core Electrolytes

Liquid-vapor coexistence curves and critical parameters for hard-core 1:1 electrolyte models with diameter ratios lambda = sigma_{-}/\sigma_{+}=1 to 5.7 have been studied by fine-discretization Monte Carlo methods. Normalizing via the length scale sigma_{+-}=(sigma_{+} + sigma_{-})/2 relevant for the low densities in question, both Tc* (=kB Tc sigma_{+-}/q^2 and rhoc* (= rhoc sigma _{+-}^{3}) decrease rapidly (from ~ 0.05 to 0.03 and 0.08 to 0.04, respectively) as lambda increases. These trends, which unequivocally contradict current theories, are closely mirrored by results for tightly tethered dipolar dimers (with Tc* lower by ~ 0-11% and rhoc* greater by 37-12%).Comment: 4 pages, 5 figure

Towards a Linear-Scaling DFT Technique: The Density Matrix Approach

A recently proposed linear-scaling scheme for density-functional pseudopotential calculations is described in detail. The method is based on a formulation of density functional theory in which the ground state energy is determined by minimization with respect to the density matrix, subject to the condition that the eigenvalues of the latter lie in the range [0,1]. Linear-scaling behavior is achieved by requiring that the density matrix should vanish when the separation of its arguments exceeds a chosen cutoff. The limitation on the eigenvalue range is imposed by the method of Li, Nunes and Vanderbilt. The scheme is implemented by calculating all terms in the energy on a uniform real-space grid, and minimization is performed using the conjugate-gradient method. Tests on a 512-atom Si system show that the total energy converges rapidly as the range of the density matrix is increased. A discussion of the relation between the present method and other linear-scaling methods is given, and some problems that still require solution are indicated.Comment: REVTeX file, 27 pages with 4 uuencoded postscript figure

Basis Functions for Linear-Scaling First-Principles Calculations

In the framework of a recently reported linear-scaling method for density-functional-pseudopotential calculations, we investigate the use of localized basis functions for such work. We propose a basis set in which each local orbital is represented in terms of an array of `blip functions'' on the points of a grid. We analyze the relation between blip-function basis sets and the plane-wave basis used in standard pseudopotential methods, derive criteria for the approximate equivalence of the two, and describe practical tests of these criteria. Techniques are presented for using blip-function basis sets in linear-scaling calculations, and numerical tests of these techniques are reported for Si crystal using both local and non-local pseudopotentials. We find rapid convergence of the total energy to the values given by standard plane-wave calculations as the radius of the linear-scaling localized orbitals is increased.Comment: revtex file, with two encapsulated postscript figures, uses epsf.sty, submitted to Phys. Rev.

Resolution of Biphasic Binding of the Opioid Antagonist Naltrexone in Brain Membranes

In synaptosomal membranes from rat brain cortex, in the presence of 150 m M NaC1, the opioid antagonist [ 3 H] naltrexone bound to two populations of receptor sites with affinities of 0.27 and 4.3 n M , respectively. Guanosine-5′-(3-thiotriphosphate) had little modulating effect and did not alter the biphasic nature of ligand binding. On the other hand, receptor-selective opioids differentially inhibited the two binding components of [ 3 H] naltrexone. As shown by nonlinear least-squares analysis, the Μ opioids Tyr-D-Ala-Gly-(Me)Phe-Gly-ol or sufentanil abolished high-affinity [ 3 H] naltrexone binding, whereas the Δ-selective ligands [D- Pen 2 , D-Pen 5 ] enkephalin, ICI 174, 864, and oxymorphindole inhibited and eventually eliminated the low-affinity component in a concentration-dependent manner. These results indicate that, in contrast to the guanine nucleotide-sensitive biphasic binding of opioid-alkaloid agonists, the heterogeneity of naltrexone binding in brain membranes reflects ligand interaction with different opioid-receptor types.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/66340/1/j.1471-4159.1991.tb08288.x.pd

Molar volume of solid isotopic helium mixtures

Solid isotopic helium mixtures have been studied by path-integral Monte Carlo simulations in the isothermal-isobaric ensemble. This method allowed us to study the molar volume as a function of temperature, pressure, and isotopic composition. At 25 K and 0.2 GPa, the relative difference between molar volumes of isotopically-pure crystals of 3He and 4He is found to be about 3%. This difference decreases under pressure, and for 12 GPa it is smaller than 1%. For isotopically-mixed crystals, a linear relation between lattice parameters and concentrations of helium isotopes is found, in agreement with Vegard's law. The virtual crystal approximation, valid for isotopic mixtures of heavier atoms, does not give reliable results for solid solutions of helium isotopes.Comment: 7 pages, 5 figure