Screening effects in a density functional theory based description of molecular junctions in the Coulomb blockade regime

We recently introduced a method based on density functional theory (DFT) and non-equilibrium Green's function techniques (NEGF) for calculating the addition energies of single molecule nano-junctions in the Coulomb blockade (CB) regime. Here we apply this approach to benzene molecules lying parallel and at various distances from two aluminum fcc (111) surfaces, and discuss the distance dependence in our calculations in terms of electrostatic screening effects. The addition energies near the surface are reduced by about a factor of two, which is comparable to previously reported calculations employing a computationally far more demanding quasi-particle description

Metastable States in High Order Short-Range Spin Glasses

The mean number of metastable states in higher order short-range spin glasses is estimated analytically using a variational method introduced by Tanaka and Edwards for very large coordination numbers. For lattices with small connectivities, numerical simulations do not show any significant dependence on the relative positions of the interacting spins on the lattice, indicating thus that these systems can be described by a few macroscopic parameters. As an extremely anisotropic model we consider the low autocorrelated binary spin model and we show through numerical simulations that its landscape has an exceptionally large number of local optima

Towards a theoretical description of molecular junctions in the Coulomb blockade regime based on density functional theory

Non-equilibrium Greens function techniques (NEGF) combined with Density Functional Theory (DFT) calculations have become a standard tool for the description of electron transport through single molecule nano-junctions in the coherent tunneling regime. However, the applicability of these methods for transport in the Coulomb blockade (CB) regime is still under debate. We present here NEGF-DFT calculations performed on simple model systems in the presence of an effective gate potential. The results show that: i) the CB addition energies can be predicted with such an approach with reasonable accuracy; ii) neither the magnitude of the Kohn-Sham gap nor the lack of a derivative discontinuity in the exchange-correlation functional represent a problem for this purpose

The architecture of chicken chromosome territories changes during differentiation

BACKGROUND: Between cell divisions the chromatin fiber of each chromosome is restricted to a subvolume of the interphase cell nucleus called chromosome territory. The internal organization of these chromosome territories is still largely unknown. RESULTS: We compared the large-scale chromatin structure of chromosome territories between several hematopoietic chicken cell types at various differentiation stages. Chromosome territories were labeled by fluorescence in situ hybridization in structurally preserved nuclei, recorded by confocal microscopy and evaluated visually and by quantitative image analysis. Chromosome territories in multipotent myeloid precursor cells appeared homogeneously stained and compact. The inactive lysozyme gene as well as the centromere of the lysozyme gene harboring chromosome located to the interior of the chromosome territory. In further differentiated cell types such as myeloblasts, macrophages and erythroblasts chromosome territories appeared increasingly diffuse, disaggregating to separable substructures. The lysozyme gene, which is gradually activated during the differentiation to activated macrophages, as well as the centromere were relocated increasingly to more external positions. CONCLUSIONS: Our results reveal a cell type specific constitution of chromosome territories. The data suggest that a repositioning of chromosomal loci during differentiation may be a consequence of general changes in chromosome territory morphology, not necessarily related to transcriptional changes

A multideterminant assessment of mean field methods for the description of electron transfer in the weak coupling regime

Multideterminant calculations have been performed on model systems to emphasize the role of many-body effects in the general description of charge quantization experiments. We show numerically and derive analytically that a closed-shell ansatz, the usual ingredient of mean-field methods, does not properly describe the step-like electron transfer characteristic in weakly coupled systems. With the multideterminant results as a benchmark, we have evaluated the performance of common ab initio mean field techniques, such as Hartree Fock (HF) and Density Functional Theory (DFT) with local and hybrid exchange correlation functionals, with a special focus on spin-polarization effects. For HF and hybrid DFT, a qualitatively correct open-shell solution with distinct steps in the electron transfer behaviour can be obtained with a spin-unrestricted (i.e., spin-polarized) ansatz though this solution differs quantitatively from the multideterminant reference. We also discuss the relationship between the electronic eigenvalue gap and the onset of charge transfer for both HF and DFT and relate our findings to recently proposed practical schemes for calculating the addition energies in the Coulomb blockade regime for single molecule junctions from closed-shell DFT within the local density approximation

Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation

BACKGROUND: Comparison of metabolic networks is typically performed based on the organisms' enzyme contents. This approach disregards functional replacements as well as orthologies that are misannotated. Direct comparison of the structure of metabolic networks can circumvent these problems. RESULTS: Metabolic networks are naturally represented as directed hypergraphs in such a way that metabolites are nodes and enzyme-catalyzed reactions form (hyper)edges. The familiar operations from set algebra (union, intersection, and difference) form a natural basis for both the pairwise comparison of networks and identification of distinct metabolic features of a set of algorithms. We report here on an implementation of this approach and its application to the procaryotes. CONCLUSION: We demonstrate that metabolic networks contain valuable phylogenetic information by comparing phylogenies obtained from network comparisons with 16S RNA phylogenies. The algebraic approach to metabolic networks is suitable to study metabolic innovations in two sets of organisms, free living microbes and Pyrococci, as well as obligate intracellular pathogens

Variational Monte Carlo Calculations of 3^3H and 4^4He with a relativistic Hamiltonian - II

In relativistic Hamiltonians the two-nucleon interaction is expressed as a sum of $\tilde{v}_{ij}$, the interaction in the ${\bf P}_{ij}=0$ rest frame, and the ``boost interaction'' $\delta v({\bf P}_{ij})$ which depends upon the total momentum ${\bf P}_{ij}$ and vanishes in the rest frame. The $\delta v$ can be regarded as a sum of four terms: $\delta v_{RE}$, $\delta v_{LC}$, $\delta v_{TP}$ and $\delta v_{QM}$; the first three originate from the relativistic energy-momentum relation, Lorentz contraction and Thomas precession, while the last is purely quantum. The contributions of $\delta v_{RE}$ and $\delta v_{LC}$ have been previously calculated with the variational Monte Carlo method for $^3$H and $^4$He. In this brief note we report the results of similar calculations for the contributions of $\delta v_{TP}$ and $\delta v_{QM}$. These are found to be rather small.Comment: 7 pages, P-94-09-07