44 research outputs found
Electronic properties of silica nanowires
Thin nanowires of silicon oxide were studied by pseudopotential density
functional electronic structure calculations using the generalized gradient
approximation. Infinite linear and zigzag Si-O chains were investigated. A wire
composed of three-dimensional periodically repeated Si4O8 units was also
optimized, but this structure was found to be of limited stability. The
geometry, electronic structure, and Hirshfeld charges of these silicon oxide
nanowires were computed. The results show that the Si-O chain is metallic,
whereas the zigzag chain and the Si4O8 nanowire are insulators
Photoelasticity of crystalline and amorphous silica from first principles
Based on density-functional perturbation theory we have computed from first
principles the photoelastic tensor of few crystalline phases of silica at
normal conditions and high pressure (quartz, -cristobalite,
-cristobalite) and of models of amorphous silica (containig up to 162
atoms), obtained by quenching from the melt in combined classical and
Car-Parrinello molecular dynamics simulations. The computational framework has
also been checked on the photoelastic tensor of crystalline silicon and MgO as
prototypes of covalent and ionic systems. The agreement with available
experimental data is good.
A phenomenological model suitable to describe the photoelastic properties of
different silica polymorphs is devised by fitting on the ab-initio data.Comment: ten figure
Relative energetics and structural properties of zirconia using a self-consistent tight-binding model
We describe an empirical, self-consistent, orthogonal tight-binding model for
zirconia, which allows for the polarizability of the anions at dipole and
quadrupole levels and for crystal field splitting of the cation d orbitals.
This is achieved by mixing the orbitals of different symmetry on a site with
coupling coefficients driven by the Coulomb potentials up to octapole level.
The additional forces on atoms due to the self-consistency and polarizabilities
are exactly obtained by straightforward electrostatics, by analogy with the
Hellmann-Feynman theorem as applied in first-principles calculations. The model
correctly orders the zero temperature energies of all zirconia polymorphs. The
Zr-O matrix elements of the Hamiltonian, which measure covalency, make a
greater contribution than the polarizability to the energy differences between
phases. Results for elastic constants of the cubic and tetragonal phases and
phonon frequencies of the cubic phase are also presented and compared with some
experimental data and first-principles calculations. We suggest that the model
will be useful for studying finite temperature effects by means of molecular
dynamics.Comment: to be published in Physical Review B (1 march 2000
Folliculin regulates mTORC1/2 and WNT pathways in early human pluripotency
The pathways involved in exit from pluripotency in human embryonic stem cells are poorly understood. Here, the authors performed a CRISPR-based screen to identify genes that promote exit from naĂŻve pluripotency and find a role for folliculin (FLCN) by regulating the mTOR and Wnt pathways
The physics of dynamical atomic charges: the case of ABO3 compounds
Based on recent first-principles computations in perovskite compounds,
especially BaTiO3, we examine the significance of the Born effective charge
concept and contrast it with other atomic charge definitions, either static
(Mulliken, Bader...) or dynamical (Callen, Szigeti...). It is shown that static
and dynamical charges are not driven by the same underlying parameters. A
unified treatment of dynamical charges in periodic solids and large clusters is
proposed. The origin of the difference between static and dynamical charges is
discussed in terms of local polarizability and delocalized transfers of charge:
local models succeed in reproducing anomalous effective charges thanks to large
atomic polarizabilities but, in ABO3 compounds, ab initio calculations favor
the physical picture based upon transfer of charges. Various results concerning
barium and strontium titanates are presented. The origin of anomalous Born
effective charges is discussed thanks to a band-by-band decomposition which
allows to identify the displacement of the Wannier center of separated bands
induced by an atomic displacement. The sensitivity of the Born effective
charges to microscopic and macroscopic strains is examined. Finally, we
estimate the spontaneous polarization in the four phases of barium titanate.Comment: 25 pages, 6 Figures, 10 Tables, LaTe
Free energy and molecular dynamics calculations for the cubic-tetragonal phase transition in zirconia
The high-temperature cubic-tetragonal phase transition of pure stoichiometric
zirconia is studied by molecular dynamics (MD) simulations and within the
framework of the Landau theory of phase transformations. The interatomic forces
are calculated using an empirical, self-consistent, orthogonal tight-binding
(SC-TB) model, which includes atomic polarizabilities up to the quadrupolar
level. A first set of standard MD calculations shows that, on increasing
temperature, one particular vibrational frequency softens. The temperature
evolution of the free energy surfaces around the phase transition is then
studied with a second set of calculations. These combine the thermodynamic
integration technique with constrained MD simulations. The results seem to
support the thesis of a second-order phase transition but with unusual, very
anharmonic behaviour above the transition temperature
Phonons and related properties of extended systems from density-functional perturbation theory
This article reviews the current status of lattice-dynamical calculations in
crystals, using density-functional perturbation theory, with emphasis on the
plane-wave pseudo-potential method. Several specialized topics are treated,
including the implementation for metals, the calculation of the response to
macroscopic electric fields and their relevance to long wave-length vibrations
in polar materials, the response to strain deformations, and higher-order
responses. The success of this methodology is demonstrated with a number of
applications existing in the literature.Comment: 52 pages, 14 figures, submitted to Review of Modern Physic
Mitochondrial physiology
As the knowledge base and importance of mitochondrial physiology to evolution, health and disease expands, the necessity for harmonizing the terminology concerning mitochondrial respiratory states and rates has become increasingly apparent. The chemiosmotic theory establishes the mechanism of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theoretical foundation of mitochondrial physiology and bioenergetics. We follow the latest SI guidelines and those of the International Union of Pure and Applied Chemistry (IUPAC) on terminology in physical chemistry, extended by considerations of open systems and thermodynamics of irreversible processes. The concept-driven constructive terminology incorporates the meaning of each quantity and aligns concepts and symbols with the nomenclature of classical bioenergetics. We endeavour to provide a balanced view of mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes. Uniform standards for evaluation of respiratory states and rates will ultimately contribute to reproducibility between laboratories and thus support the development of data repositories of mitochondrial respiratory function in species, tissues, and cells. Clarity of concept and consistency of nomenclature facilitate effective transdisciplinary communication, education, and ultimately further discovery
Mitochondrial physiology
As the knowledge base and importance of mitochondrial physiology to evolution, health and disease expands, the necessity for harmonizing the terminology concerning mitochondrial respiratory states and rates has become increasingly apparent. The chemiosmotic theory establishes the mechanism of energy transformation and coupling in oxidative phosphorylation. The unifying concept of the protonmotive force provides the framework for developing a consistent theoretical foundation of mitochondrial physiology and bioenergetics. We follow the latest SI guidelines and those of the International Union of Pure and Applied Chemistry (IUPAC) on terminology in physical chemistry, extended by considerations of open systems and thermodynamics of irreversible processes. The concept-driven constructive terminology incorporates the meaning of each quantity and aligns concepts and symbols with the nomenclature of classical bioenergetics. We endeavour to provide a balanced view of mitochondrial respiratory control and a critical discussion on reporting data of mitochondrial respiration in terms of metabolic flows and fluxes. Uniform standards for evaluation of respiratory states and rates will ultimately contribute to reproducibility between laboratories and thus support the development of data repositories of mitochondrial respiratory function in species, tissues, and cells. Clarity of concept and consistency of nomenclature facilitate effective transdisciplinary communication, education, and ultimately further discovery