5,316 research outputs found
Non-adiabatic Kohn-anomaly in a doped graphene monolayer
We compute, from first-principles, the frequency of the E2g, Gamma phonon
(Raman G-band) of graphene, as a function of the charge doping. Calculations
are done using i) the adiabatic Born-Oppenheimer approximation and ii)
time-dependent perturbation theory to explore dynamic effects beyond this
approximation. The two approaches provide very different results. While, the
adiabatic phonon frequency weakly depends on the doping, the dynamic one
rapidly varies because of a Kohn anomaly. The adiabatic approximation is
considered valid in most materials. Here, we show that doped graphene is a
spectacular example where this approximation miserably fails.Comment: 5 pages, 3 figures, Accepted by Phys. Rev. Let
Generalization of the density-matrix method to a non-orthogonal basis
We present a generalization of the Li, Nunes and Vanderbilt density-matrix
method to the case of a non-orthogonal set of basis functions. A representation
of the real-space density matrix is chosen in such a way that only the overlap
matrix, and not its inverse, appears in the energy functional. The generalized
energy functional is shown to be variational with respect to the elements of
the density matrix, which typically remains well localized.Comment: 11 pages + 2 postcript figures at the end (search for -cut here
Total energy global optimizations using non orthogonal localized orbitals
An energy functional for orbital based calculations is proposed, which
depends on a number of non orthogonal, localized orbitals larger than the
number of occupied states in the system, and on a parameter, the electronic
chemical potential, determining the number of electrons. We show that the
minimization of the functional with respect to overlapping localized orbitals
can be performed so as to attain directly the ground state energy, without
being trapped at local minima. The present approach overcomes the multiple
minima problem present within the original formulation of orbital based
methods; it therefore makes it possible to perform calculations for an
arbitrary system, without including any information about the system bonding
properties in the construction of the input wavefunctions. Furthermore, while
retaining the same computational cost as the original approach, our formulation
allows one to improve the variational estimate of the ground state energy, and
the energy conservation during a molecular dynamics run. Several numerical
examples for surfaces, bulk systems and clusters are presented and discussed.Comment: 24 pages, RevTex file, 5 figures available upon reques
Effect of dimensionality on the charge-density-wave in few-layers 2H-NbSe
We investigate the charge density wave (CDW) instability in single and double
layers, as well as in the bulk 2H-NbSe. We demonstrate that the density
functional theory correctly describes the metallic CDW state in the bulk
2H-NbSe. We predict that both mono- and bilayer NbSe undergo a CDW
instability. However, while in the bulk the instability occurs at a momentum
, in free-standing layers it
occurs at . Furthermore, while
in the bulk the CDW leads to a metallic state, in a monolayer the ground state
becomes semimetallic, in agreement with recent experimental data. We elucidate
the key role that an enhancement of the electron-phonon matrix element at
plays in forming the CDW ground state.Comment: 4 pages 5 figure
Electron-phonon coupling and phonon self-energy in MgB: do we really understand MgB Raman spectra ?
We consider a model Hamiltonian fitted on the ab-initio band structure to
describe the electron-phonon coupling between the electronic bands and
the phonon E mode in MgB. The model allows for analytical
calculations and numerical treatments using very large k-point grids. We
calculate the phonon self-energy of the E mode along two high symmetry
directions in the Brillouin zone. We demonstrate that the contribution of the
bands to the Raman linewidth of the E mode via the
electron-phonon coupling is zero. As a consequence the large resonance seen in
Raman experiments cannot be interpreted as originated from the mode at
. We examine in details the effects of Fermi surface singularities in
the phonon spectrum and linewidth and we determine the magnitude of finite
temperature effects in the the phonon self-energy. From our findings we suggest
several possible effects which might be responsible for the MgB Raman
spectra.Comment: 10 pages, 9 figure
All-electron magnetic response with pseudopotentials: NMR chemical shifts
A theory for the ab initio calculation of all-electron NMR chemical shifts in
insulators using pseudopotentials is presented. It is formulated for both
finite and infinitely periodic systems and is based on an extension to the
Projector Augmented Wave approach of Bloechl [P. E. Bloechl, Phys. Rev. B 50,
17953 (1994)] and the method of Mauri et al [F. Mauri, B.G. Pfrommer, and S.G.
Louie, Phys. Rev. Lett. 77, 5300 (1996)]. The theory is successfully validated
for molecules by comparison with a selection of quantum chemical results, and
in periodic systems by comparison with plane-wave all-electron results for
diamond.Comment: 25 pages, 4 tables, submitted to Physical Review
Large scale quantum simulations: C_60 impacts on a semiconducting surface
We present tight binding molecular dynamics simulations of C_60 collisions on
the reconstructed diamond(111) surface, carried out with an O(N) method and
with cells containing 1140 atoms. The results of our simulations are in very
good agreement with experiments performed under the same impact conditions.
Furthermore our calculations provide a detailed characterization of the
microscopic processes occuring during the collision, and allow the
identification of three impact regimes, as a function of the fullerene incident
energy. Finally, the study of the reactivity between the cluster and the
surface gives insight into the deposition mechanisms of C_60 on semiconducting
substrates
First principles calculation of vibrational Raman spectra in large systems: signature of small rings in crystalline SiO2
We present an approach for the efficient calculation of vibrational Raman
intensities in periodic systems within density functional theory. The Raman
intensities are computed from the second order derivative of the electronic
density matrix with respect to a uniform electric field. In contrast to
previous approaches, the computational effort required by our method for the
evaluation of the intensities is negligible compared to that required for the
calculation of vibrational frequencies. As a first application, we study the
signature of 3- and 4-membered rings in the the Raman spectra of several
polymorphs of SiO2, including a zeolite having 102 atoms per unit cell.Comment: 4 pages, 2 figures, revtex4 Minor corrections; accepted in Phys. Rev.
Let
Membrane Type 1 Matrix Metalloproteinase Regulates Monocyte Migration and Collagen Destruction in Tuberculosis
Tuberculosis (TB) remains a global pandemic and drug resistance is rising. Multicellular granuloma formation is the pathological hallmark of Mycobacterium tuberculosis infection. The membrane type 1 matrix metalloproteinase (MT1-MMP or MMP-14) is a collagenase that is key in leukocyte migration and collagen destruction. In patients with TB, induced sputum MT1-MMP mRNA levels were increased 5.1-fold compared with matched controls and correlated positively with extent of lung infiltration on chest radiographs (r = 0.483; p < 0.05). M. tuberculosis infection of primary human monocytes increased MT1-MMP surface expression 31.7-fold and gene expression 24.5-fold. M. tuberculosis-infected monocytes degraded collagen matrix in an MT1-MMP-dependent manner, and MT1-MMP neutralization decreased collagen degradation by 73%. In human TB granulomas, MT1-MMP immunoreactivity was observed in macrophages throughout the granuloma. Monocyte-monocyte networks caused a 17.5-fold increase in MT1-MMP surface expression dependent on p38 MAPK and G protein-coupled receptor-dependent signaling. Monocytes migrating toward agarose beads impregnated with conditioned media from M. tuberculosis-infected monocytes expressed MT1-MMP. Neutralization of MT1-MMP activity decreased this M. tuberculosis network-dependent monocyte migration by 44%. Taken together, we demonstrate that MT1-MMP is central to two key elements of TB pathogenesis, causing collagen degradation and regulating monocyte migration
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