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 $O(N)$ 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 $O(N)$ methods; it therefore makes it possible to perform $O(N)$ 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-NbSe2_2

We investigate the charge density wave (CDW) instability in single and double layers, as well as in the bulk 2H-NbSe$_{2}$. We demonstrate that the density functional theory correctly describes the metallic CDW state in the bulk 2H-NbSe$_{2}$. We predict that both mono- and bilayer NbSe$_{2}$ undergo a CDW instability. However, while in the bulk the instability occurs at a momentum $\mathbf{q}_{CDW}\approx{2/3}\mathbf{\Gamma M}$, in free-standing layers it occurs at $\mathbf{q}_{CDW}\approx{1/2}\mathbf{\Gamma M}$. 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 $\mathbf{q}\approx\mathbf{q}_{CDW}$ plays in forming the CDW ground state.Comment: 4 pages 5 figure

Electron-phonon coupling and phonon self-energy in MgB2_2: do we really understand MgB2_2 Raman spectra ?

We consider a model Hamiltonian fitted on the ab-initio band structure to describe the electron-phonon coupling between the electronic $\sigma-$bands and the phonon E$_{2g}$ mode in MgB$_2$. The model allows for analytical calculations and numerical treatments using very large k-point grids. We calculate the phonon self-energy of the E$_{2g}$ mode along two high symmetry directions in the Brillouin zone. We demonstrate that the contribution of the $\sigma$ bands to the Raman linewidth of the E$_{2g}$ 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 $E_{2g}$ mode at $\Gamma$. 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$_2$ 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