264 research outputs found
Metric tensor as the dynamical variable for variable cell-shape molecular dynamics
We propose a new variable cell-shape molecular dynamics algorithm where the
dynamical variables associated with the cell are the six independent dot
products between the vectors defining the cell instead of the nine cartesian
components of those vectors. Our choice of the metric tensor as the dynamical
variable automatically eliminates the cell orientation from the dynamics.
Furthermore, choosing for the cell kinetic energy a simple scalar that is
quadratic in the time derivatives of the metric tensor, makes the dynamics
invariant with respect to the choice of the simulation cell edges. Choosing the
densitary character of that scalar allows us to have a dynamics that obeys the
virial theorem. We derive the equations of motion for the two conditions of
constant external pressure and constant thermodynamic tension. We also show
that using the metric as variable is convenient for structural optimization
under those two conditions. We use simulations for Ar with Lennard-Jones
parameters and for Si with forces and stresses calculated from first-principles
of density functional theory to illustrate the applications of the method.Comment: 10 pages + 6 figures, Latex, to be published in Physical Review
Ab initio molecular dynamics using density based energy functionals: application to ground state geometries of some small clusters
The ground state geometries of some small clusters have been obtained via ab
initio molecular dynamical simulations by employing density based energy
functionals. The approximate kinetic energy functionals that have been employed
are the standard Thomas-Fermi along with the Weizsacker correction
and a combination . It is shown that the functional
involving gives superior charge densities and bondlengths over the
standard functional. Apart from dimers and trimers of Na, Mg, Al, Li, Si,
equilibrium geometries for and clusters have also
been reported. For all the clusters investigated, the method yields the ground
state geometries with the correct symmetries with bondlengths within 5\% when
compared with the corresponding results obtained via full orbital based
Kohn-Sham method. The method is fast and a promising one to study the ground
state geometries of large clusters.Comment: 15 pages, 3 PS figure
Ab initio Pseudopotential Plane-wave Calculations of the Electronic Structure of YBa_2Cu_3O_7
We present an ab initio pseudopotential local density functional calculation
for stoichiometric high-Tc cuprate YBa_2Cu_3O_7 using the plane-wave basis set.
We have overcome well-known difficulties in applying pseudopotential methods to
first-row elements, transition metals, and rare-earth materials by carefully
generating norm-conserving pseudopotentials with excellent transferability and
employing an extremely efficient iterative diagonalization scheme optimized for
our purpose. The self-consistent band structures, the total and site-projected
densities of states, the partial charges and their symmetry-decompositions, and
some characteristic charge densities near E_f are presented. We compare our
results with various existing (F)LAPW and (F)LMTO calculations and establish
that the ab initio pseudopotential method is competitive with other methods in
studying the electronic structure of such complicated materials as high-Tc
cuprates. [8 postscript files in uuencoded compressed form]Comment: 14 pages, RevTeX v3.0, 8 figures (appended in postscript file), SNUTP
94-8
Charge-Induced Fragmentation of Sodium Clusters
The fission of highly charged sodium clusters with fissilities X>1 is studied
by {\em ab initio} molecular dynamics. Na_{24}^{4+} is found to undergo
predominantly sequential Na_{3}^{+} emission on a time scale of 1 ps, while
Na_{24}^{Q+} (5 \leq Q \leq 8) undergoes multifragmentation on a time scale
\geq 0.1 ps, with Na^{+} increasingly the dominant fragment as Q increases. All
singly-charged fragments Na_{n}^{+} up to size n=6 are observed. The observed
fragment spectrum is, within statistical error, independent of the temperature
T of the parent cluster for T \leq 1500 K. These findings are consistent with
and explain recent trends observed experimentally.Comment: To appear in Physical Review Letter
Evaluation of Exchange-Correlation Energy, Potential, and Stress
We describe a method for calculating the exchange and correlation (XC)
contributions to the total energy, effective potential, and stress tensor in
the generalized gradient approximation. We avoid using the analytical
expressions for the functional derivatives of E_xc*rho, which depend on
discontinuous second-order derivatives of the electron density rho. Instead, we
first approximate E_xc by its integral in a real space grid, and then we
evaluate its partial derivatives with respect to the density at the grid
points. This ensures the exact consistency between the calculated total energy,
potential, and stress, and it avoids the need of second-order derivatives. We
show a few applications of the method, which requires only the value of the
(spin) electron density in a grid (possibly nonuniform) and returns a
conventional (local) XC potential.Comment: 7 pages, 3 figure
Evolution of electronic and ionic structure of Mg-clusters with the growth cluster size
The optimized structure and electronic properties of neutral and singly
charged magnesium clusters have been investigated using ab initio theoretical
methods based on density-functional theory and systematic post-Hartree-Fock
many-body perturbation theory accounting for all electrons in the system. We
have systematically calculated the optimized geometries of neutral and singly
charged magnesium clusters consisting of up to 21 atoms, electronic shell
closures, binding energies per atom, ionization potentials and the gap between
the highest occupied and the lowest unoccupied molecular orbitals. We have
investigated the transition to the hcp structure and metallic evolution of the
magnesium clusters, as well as the stability of linear chains and rings of
magnesium atoms. The results obtained are compared with the available
experimental data and the results of other theoretical works.Comment: 30 pages, 10 figures, 3 table
Ionic structure and photoabsorption in medium sized sodium clusters
We present ground-state configurations and photoabsorption spectra of Na-7+,
Na-27+ and Na-41+. Both the ionic structure and the photoabsorption spectra of
medium-size sodium clusters beyond Na-20 have been calculated self-consistently
with a nonspherical treatment of the valence electrons in density functional
theory. We use a local pseudopotential that has been adjusted to experimental
bulk properties and the atomic 3s level of sodium. Our studies have shown that
both the ionic structure of the ground state and the positions of the plasmon
resonances depend sensitively on the pseudopotential used in the calculation,
which stresses the importance of its consistent use in both steps.Comment: 4 pages, 3 figures. Accepted for publication in PRB, tentatively July
15th, 1998 some typos corrected, brought to nicer forma
Overexpression of platelet-derived growth factor receptor α in breast cancer is associated with tumour progression
INTRODUCTION: Receptor tyrosine kinases have been extensively studied owing to their frequently abnormal activation in the development and progression of human cancers. Platelet-derived growth factor receptors (PDGFRs) are receptors with intrinsic tyrosine kinase activity that regulate several functions in normal cells and are widely expressed in a variety of malignancies. After the demonstration that gastrointestinal stromal tumours without c-Kit mutations harbour PDGFR-α-activating mutations and that PDGFR-α is also a therapeutic target for imatinib mesylate, the interest for this receptor has increased considerably. Because breast cancer is one of the most frequent neoplasias in women worldwide, and only one study has reported PDGFR-α expression in breast carcinomas, the aim of this work was to investigate the potential significance of PDGFR-α expression in invasive mammary carcinomas. METHODS: We used immunohistochemistry to detect PDGFR-α overexpression on a series of 181 formalin-fixed paraffin-embedded invasive ductal breast carcinomas and in two breast cancer cell lines: MCF-7 and HS578T. We associated its expression with known prognostic factors and we also performed polymerase chain reaction–single-stranded conformational polymorphism and direct sequencing to screen for PDGFR-α mutations. RESULTS: PDGFR-α expression was observed in 39.2% of the breast carcinomas and showed an association with lymph node metastasis (P = 0.0079), HER-2 expression (P = 0.0265) and Bcl2 expression (P = 0.0121). A correlation was also found with the expression of platelet-derived growth factor A (PDGF-A; P = 0.0194). The two cell lines tested did not express PDGFR-α. Screening for mutations revealed alterations in the PDGFR-α gene at the following locations: 2500A→G, 2529T→A and 2472C→T in exon 18 and 1701G→A in exon 12. We also found an intronic insertion IVS17-50insA at exon 18 in all sequenced cases. None of these genetic alterations was correlated with PDGFR-α expression. The cell lines did not reveal any alterations in the PDGFR-α gene sequence. CONCLUSION: PDGFR-α is expressed in invasive breast carcinomas and is associated with biological aggressiveness. The genetic alterations described were not correlated with protein expression, but other mechanisms such as gene amplification or constitutive activation of a signalling pathway inducing this receptor could still sustain PDGFR-α as a potential therapeutic target
A generalized finite-strain damage model for quasi-incompressible hyperelasticity using hybrid formulation
This is the accepted version of the following article: [Comellas, E., Bellomo, F. J., and Oller, S. (2015) A generalized finite-strain damage model for quasi-incompressible hyperelasticity using hybrid formulation. Int. J. Numer. Meth. Engng, doi: 10.1002/nme.5118.], which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1002/nme.5118/abstractA new generalized damage model for quasi-incompressible hyperelasticity in a total Lagrangian finite-strain framework is presented. A Kachanov-like reduction factor (1 - D) is applied on the deviatoric part of the hyperelastic constitutive model. Linear and exponential softening are defined as damage evolution laws, both describable in terms of only two material parameters. The model is formulated following continuum damage mechanics theory such that it can be particularized for any hyperelastic model based on the volumetric–isochoric split of the Helmholtz free energy. However, in the present work, it has been implemented in an in-house finite element code for neo-Hooke and Ogden hyperelasticity. The details of the hybrid formulation used are also described. A couple of three-dimensional examples are presented to illustrate the main characteristics of the damage model. The results obtained reproduce a wide range of softening behaviors, highlighting the versatility of the formulation proposed. The damage formulation has been developed to be used in conjunction with mixing theory in order to model the behavior of fibered biological tissues. As an example, the markedly different behaviors of the fundamental components of the rectus sheath were reproduced using the damage model, obtaining excellent correlation with the experimental results from literature.Peer ReviewedPostprint (author’s final draft
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