Complex-band structure: a method to determine the off-resonant electron transport in oligomers

We validate that off-resonant electron transport across {\it ultra-short} oligomer molecular junctions is characterised by a conductance which decays exponentially with length, and we discuss a method to determine the damping factor via the energy spectrum of a periodic structure as a function of complex wavevector. An exact mapping to the complex wavevector is demonstrated by first-principle-based calculations of: a) the conductance of molecular junctions of phenyl-ethynylene wires covalently bonded to graphitic ribbons as a function of the bridge length, and b) the complex-band structure of poly-phenyl-ethynylene.Comment: version to appear in Chem Phys Lett; 8 pages, 4 figures; minor changes to the 06/08/03 submission (nomenclature and added concluding remark

Pathway level analysis of gene expression using singular value decomposition

BACKGROUND: A promising direction in the analysis of gene expression focuses on the changes in expression of specific predefined sets of genes that are known in advance to be related (e.g., genes coding for proteins involved in cellular pathways or complexes). Such an analysis can reveal features that are not easily visible from the variations in the individual genes and can lead to a picture of expression that is more biologically transparent and accessible to interpretation. In this article, we present a new method of this kind that operates by quantifying the level of 'activity' of each pathway in different samples. The activity levels, which are derived from singular value decompositions, form the basis for statistical comparisons and other applications. RESULTS: We demonstrate our approach using expression data from a study of type 2 diabetes and another of the influence of cigarette smoke on gene expression in airway epithelia. A number of interesting pathways are identified in comparisons between smokers and non-smokers including ones related to nicotine metabolism, mucus production, and glutathione metabolism. A comparison with results from the related approach, 'gene-set enrichment analysis', is also provided. CONCLUSION: Our method offers a flexible basis for identifying differentially expressed pathways from gene expression data. The results of a pathway-based analysis can be complementary to those obtained from one more focused on individual genes. A web program PLAGE (Pathway Level Analysis of Gene Expression) for performing the kinds of analyses described here is accessible at

Identifying differential expression in multiple SAGE libraries: an overdispersed log-linear model approach

BACKGROUND: In testing for differential gene expression involving multiple serial analysis of gene expression (SAGE) libraries, it is critical to account for both between and within library variation. Several methods have been proposed, including the t test, t(w )test, and an overdispersed logistic regression approach. The merits of these tests, however, have not been fully evaluated. Questions still remain on whether further improvements can be made. RESULTS: In this article, we introduce an overdispersed log-linear model approach to analyzing SAGE; we evaluate and compare its performance with three other tests: the two-sample t test, t(w )test and another based on overdispersed logistic linear regression. Analysis of simulated and real datasets show that both the log-linear and logistic overdispersion methods generally perform better than the t and t(w )tests; the log-linear method is further found to have better performance than the logistic method, showing equal or higher statistical power over a range of parameter values and with different data distributions. CONCLUSION: Overdispersed log-linear models provide an attractive and reliable framework for analyzing SAGE experiments involving multiple libraries. For convenience, the implementation of this method is available through a user-friendly web-interface available at

Complex band structure and plasmon lattice Green's function of a periodic metal-nanoparticle chain

When the surface plasmon resonance in a metal-nanoparticle chain is excited at one point, the response signal will generally decay down the chain due to absorption and radiation losses. The decay length is a key parameter in such plasmonic systems. By studying the plasmon lattice Green's function, we found that the decay length is generally governed by two exponential decay constants with phase factors corresponding to guided Bloch modes and one power-law decay with a phase factor corresponding to that of free space photons. The results show a high level of similarity between the absorptive and radiative decay channels. By analyzing the poles (and the corresponding residues) of the Green's function in a transformed complex reciprocal space, the dominant decay channel of the real-space Green's function is understood.Comment: 19 pages, 3 figure

Analytical study of non-linear transport across a semiconductor-metal junction

In this paper we study analytically a one-dimensional model for a semiconductor-metal junction. We study the formation of Tamm states and how they evolve when the semi-infinite semiconductor and metal are coupled together. The non-linear current, as a function of the bias voltage, is studied using the non-equilibrium Green's function method and the density matrix of the interface is given. The electronic occupation of the sites defining the interface has strong non-linearities as function of the bias voltage due to strong resonances present in the Green's functions of the junction sites. The surface Green's function is computed analytically by solving a quadratic matrix equation, which does not require adding a small imaginary constant to the energy. The wave function for the surface states is given

Amine-Gold Linked Single-Molecule Junctions: Experiment and Theory

The measured conductance distribution for single molecule benzenediamine-gold junctions, based on 59,000 individual conductance traces recorded while breaking a gold point contact in solution, has a clear peak at 0.0064 G$_{0}$ with a width of $\pm$ 40%. Conductance calculations based on density functional theory (DFT) for 15 distinct junction geometries show a similar spread. Differences in local structure have a limited influence on conductance because the amine-Au bonding motif is well-defined and flexible. The average calculated conductance (0.046 G$_{0}$) is seven times larger than experiment, suggesting the importance of many-electron corrections beyond DFT

MCM-test: a fuzzy-set-theory-based approach to differential analysis of gene pathways

Abstract Background Gene pathway can be defined as a group of genes that interact with each other to perform some biological processes. Along with the efforts to identify the individual genes that play vital roles in a particular disease, there is a growing interest in identifying the roles of gene pathways in such diseases. Results This paper proposes an innovative fuzzy-set-theory-based approach, Multi-dimensional Cluster Misclassification test (MCM-test), to measure the significance of gene pathways in a particular disease. Experiments have been conducted on both synthetic data and real world data. Results on published diabetes gene expression dataset and a list of predefined pathways from KEGG identified OXPHOS pathway involved in oxidative phosphorylation in mitochondria and other mitochondrial related pathways to be deregulated in diabetes patients. Our results support the previously supported notion that mitochondrial dysfunction is an important event in insulin resistance and type-2 diabetes. Conclusion Our experiments results suggest that MCM-test can be successfully used in pathway level differential analysis of gene expression datasets. This approach also provides a new solution to the general problem of measuring the difference between two groups of data, which is one of the most essential problems in most areas of research

Romantic Relationship Quality and Mental Health in Pregnancy During the COVID-19 Pandemic

Introduction: Social capital is important for good mental health and the quality of close relationships is one key indicator of social capital. Examining the association between relationship quality and mental health may be particularly important during pregnancy as mental health concerns during this period pose significant risk to families. The COVID-19 pandemic has contributed to increased mental health problems among pregnant individuals. The resulting lockdown protocols of the pandemic has also disrupted larger social networks and couples spent more time together in the context of ongoing chronic stress, highlighting the particular importance of romantic relationship quality. This study explored longitudinal associations between relationship satisfaction, depression, and anxiety among pregnant individuals during the first wave of the COVID-19 pandemic. Methods: Pregnant individuals (n = 1842) from the Pregnancy During the Pandemic Study were surveyed monthly (April-July 2020). Depression and anxiety symptoms, and relationship satisfaction were self-reported. Cross-lagged panel models were conducted to examine bidirectional associations between relationship satisfaction and mental health symptoms over time. Results: Relationship satisfaction was significantly correlated with depression and anxiety at all time points. Longitudinally, relationship satisfaction predicted later depression and anxiety symptoms, but depressive and anxiety symptoms did not predict later relationship satisfaction. Discussion: This study suggests that poor relationship satisfaction was linked to subsequent elevations in prenatal depressive and anxiety symptoms during the COVID-19 pandemic. Relationship enhancement interventions during pregnancy may be a means of improving the mental health of pregnant individuals, and interrupting transgenerational transmission, during times of prolonged psychological distress.Social Sciences and Humanities Research Council (SSHRC)Alberta Innovates - Research GrantCanadian Institutes of Health Research (CIHR)Othe

Current-Induced Effects in Nanoscale Conductors

We present an overview of current-induced effects in nanoscale conductors with emphasis on their description at the atomic level. In particular, we discuss steady-state current fluctuations, current-induced forces, inelastic scattering and local heating. All of these properties are calculated in terms of single-particle wavefunctions computed using a scattering approach within the static density-functional theory of many-electron systems. Examples of current-induced effects in atomic and molecular wires will be given and comparison with experimental results will be provided when available.Comment: revtex, 10 pages, 8 figure