Inelastic transport theory from first-principles: methodology and applications for nanoscale devices

We describe a first-principles method for calculating electronic structure, vibrational modes and frequencies, electron-phonon couplings, and inelastic electron transport properties of an atomic-scale device bridging two metallic contacts under nonequilibrium conditions. The method extends the density-functional codes SIESTA and TranSIESTA that use atomic basis sets. The inelastic conductance characteristics are calculated using the nonequilibrium Green's function formalism, and the electron-phonon interaction is addressed with perturbation theory up to the level of the self-consistent Born approximation. While these calculations often are computationally demanding, we show how they can be approximated by a simple and efficient lowest order expansion. Our method also addresses effects of energy dissipation and local heating of the junction via detailed calculations of the power flow. We demonstrate the developed procedures by considering inelastic transport through atomic gold wires of various lengths, thereby extending the results presented in [Frederiksen et al., Phys. Rev. Lett. 93, 256601 (2004)]. To illustrate that the method applies more generally to molecular devices, we also calculate the inelastic current through different hydrocarbon molecules between gold electrodes. Both for the wires and the molecules our theory is in quantitative agreement with experiments, and characterizes the system-specific mode selectivity and local heating.Comment: 24 pages, 17 figure

Perturbation Study of the Conductance through an Interacting Region Connected to Multi-Mode Leads

We study the effects of electron correlation on transport through an interacting region connected to multi-mode leads based on the perturbation expansion with respect to the inter-electron interaction. At zero temperature the conductance defined in the Kubo formalism can be written in terms of a single-particle Green's function at the Fermi energy, and it can be mapped onto a transmission coefficient of the free quasiparticles described by an effective Hamiltonian. We apply this formulation to a two-dimensional Hubbard model of finite size connected to two noninteracting leads. We calculate the conductance in the electron-hole symmetric case using the order $U^2$ self-energy. The conductance shows several maximums in the $U$ dependence in some parameter regions of $t_y/t_x$, where $t_x$ ($t_y$) is the hopping matrix element in the $x$- ($y$-) directions. This is caused by the resonance occurring in some of the subbands, and is related with the $U$ dependence of the eigenvalues of the effective Hamiltonian.Comment: 17 pages, 12 figures, to be published in J.Phys.Soc.Jpn. 71(2002)No.

Nonlinear climatic sensitivity to greenhouse gases over past 4 glacial/interglacial cycles.

The paleoclimatic sensitivity to atmospheric greenhouse gases (GHGs) has recently been suggested to be nonlinear, however a GHG threshold value associated with deglaciation remains uncertain. Here, we combine a new sea surface temperature record spanning the last 360,000 years from the southern Western Pacific Warm Pool with records from five previous studies in the equatorial Pacific to document the nonlinear relationship between climatic sensitivity and GHG levels over the past four glacial/interglacial cycles. The sensitivity of the responses to GHG concentrations rises dramatically by a factor of 2-4 at atmospheric CO2 levels of >220 ppm. Our results suggest that the equatorial Pacific acts as a nonlinear amplifier that allows global climate to transition from deglacial to full interglacial conditions once atmospheric CO2 levels reach threshold levels

Studies of molecular-beam epitaxy growth of GaAs on porous Si substrates

GaAs has been grown on porous Si directly and on Si buffer layer–porous Si substrates by molecular-beam epitaxy. In the case of GaAs growth on porous Si, transmission electron microscopy (TEM) reveals that the dominant defects in GaAs layers grown on porous Si are microtwins and stacking faults, which originate from the GaAs/porous Si interface. GaAs is found to penetrate into the porous Si layers. By using a thin Si buffer layer (50 nm), GaAs penetration diminishes and the density of microtwins and stacking faults is largely reduced and localized at the GaAs/Si buffer interface. However, there is a high density of threading dislocations remaining. Both Si (100) aligned and four tilted substrates have been examined in this study. TEM results show no observable effect of the tilted substrates on the quality of the GaAs epitaxial layer

Green function techniques in the treatment of quantum transport at the molecular scale

The theoretical investigation of charge (and spin) transport at nanometer length scales requires the use of advanced and powerful techniques able to deal with the dynamical properties of the relevant physical systems, to explicitly include out-of-equilibrium situations typical for electrical/heat transport as well as to take into account interaction effects in a systematic way. Equilibrium Green function techniques and their extension to non-equilibrium situations via the Keldysh formalism build one of the pillars of current state-of-the-art approaches to quantum transport which have been implemented in both model Hamiltonian formulations and first-principle methodologies. We offer a tutorial overview of the applications of Green functions to deal with some fundamental aspects of charge transport at the nanoscale, mainly focusing on applications to model Hamiltonian formulations.Comment: Tutorial review, LaTeX, 129 pages, 41 figures, 300 references, submitted to Springer series "Lecture Notes in Physics

Dvl2-Dependent Activation of Daam1 and RhoA Regulates Wnt5a-Induced Breast Cancer Cell Migration

The Dishevelled (Dvl) and Dishevelled-associated activator of morphogenesis 1 (Daam1) pathway triggered by Wnt5a regulates cellular polarity during development and tissue homoeostasis. However, Wnt5a signaling in breast cancer progression remains poorly defined.We showed here that Wnt5a activated Dvl2, Daam1 and RhoA, and promoted migration of breast cancer cells, which was, however, abolished by Secreted Frizzled-related protein 2 (sFRP2) pretreatment. Dominant negative Dvl2 mutants or Dvl2 siRNA significantly decreased Wnt5a-induced Daam1/RhoA activation and cell migration. Ectopic expression of N-Daam1, a dominant negative mutant, or Daam1 siRNA remarkably inhibited Wnt5a-induced RhoA activation, stress fiber formation and cell migration. Ectopic expression of dominant negative RhoA (N19) or C3 exoenzyme transferase, a Rho inhibitor, decreased Wnt5a-induced stress fiber formation and cell migration.Taken together, we demonstrated for the first time that Wnt5a promotes breast cancer cell migration via Dvl2/Daam1/RhoA

Neuronal differentiation of hair-follicle-bulge-derived stem cells co-cultured with mouse cochlear modiolus explants

Stem-cell-based repair of auditory neurons may represent an attractive therapeutic option to restore sensorineural hearing loss. Hair-follicle-bulge-derived stem cells (HFBSCs) are promising candidates for this type of therapy, because they (1) have migratory properties, enabling migration after transplantation, (2) can differentiate into sensory neurons and glial cells, and (3) can easily be harvested in relatively high numbers. However, HFBSCs have never been used for this purpose. We hypothesized that HFBSCs can be used for cell-based repair of the auditory nerve and we have examined their migration and incorporation into cochlear modiolus explants and their subsequent differentiation. Modiolus explants obtained from adult wild-type mice were cultured in the presence of EF1α-copGFP-transduced HFBSCs, constitutively expressing copepod green fluorescent protein (copGFP). Also, modiolus explants without hair cells were co-cultured with DCX-copGFP-transduced HFBSCs, which demonstrate copGFP upon doublecortin expression during neuronal differentiation. Velocity of HFBSC migration towards modiolus explants was calculated, and after two weeks, co-cultures were fixed and processed for immunohistochemical staining. EF1α-copGFP HFBSC migration velocity was fast: 80.5 ± 6.1 μm/h. After arrival in the explant, the cells formed a fascicular pattern and changed their phenotype into an ATOH1-positive neuronal cell type. DCX-copGFP HFBSCs became green-fluorescent after integration into the explants, confirming neuronal differentiation of the cells. These results show that HFBSC-derived neuronal progenitors are migratory and can integrate into cochlear modiolus explants, while adapting their phenotype depending on this micro-environment. Thus, HFBSCs show potential to be employed in cell-based therapies for auditory nerve repair

Quasi-particle description for the transport through a small interacting system

We study effects of electron correlation on the transport through a small interacting system connected to reservoirs using an effective Hamiltonian which describes the free quasi-particles of a Fermi liquid. The effective Hamiltonian is defined microscopically with the value of the self-energy at $\omega=0$. Specifically, we apply the method to a Hubbard chain of finite size $N$ ($=1, 2, 3, ...$), and calculate the self-energy within the second order in $U$ in the electron-hole symmetric case. When the couplings between the chain and the reservoirs on the left and right are small, the conductance for even $N$ decreases with increasing $N$ showing a tendency toward a Mott-Hubbard insulator. This is caused by the off-diagonal element of the self-energy, and this behavior is qualitatively different from that in the special case examined in the previous work. We also study the effects of the asymmetry in the two couplings. While the perfect transmission due to the Kondo resonance occurs for any odd $N$ in the symmetric coupling, the conductance for odd $N$ decreases with increasing $N$ in the case of the asymmetric coupling.Comment: 27 pages, RevTeX, 14 figures, to be published in Phys. Rev.