The Smallest Molecular Switch

Ab-initio total energy calculations reveal benzene-dithiolate (BDT) molecules on a gold surface, contacted by a monoatomic gold STM tip to have two classes of low energy conformations with differing symmetries. Lateral motion of the tip or excitation of the molecule cause it to change from one conformation class to the other and to switch between a strongly and a weakly conducting state. Thus, surprisingly, despite their apparent simplicity these Au/BDT/Au nanowires are shown to be electrically bi-stable switches, the smallest two-terminal molecular switches to date. Experiments with a conventional or novel self-assembled STM are proposed to test these predictions.Comment: 8 pages, 3 figure

Opportunities and limitations of transition voltage spectroscopy: a theoretical analysis

In molecular charge transport, transition voltage spectroscopy (TVS) holds the promise that molecular energy levels can be explored at bias voltages lower than required for resonant tunneling. We investigate the theoretical basis of this novel tool, using a generic model. In particular, we study the length dependence of the conducting frontier orbital and of the 'transition voltage' as a function of length. We show that this dependence is influenced by the amount of screening of the electrons in the molecule, which determines the voltage drop to be located at the contacts or across the entire molecule. We observe that the transition voltage depends significantly on the length, but that the ratio between the transition voltage and the conducting frontier orbital is approximately constant only in strongly screening (conjugated) molecules. Uncertainty about the screening within a molecule thus limits the predictive power of TVS. We furthermore argue that the relative length independence of the transition voltage for non-conjugated chains is due to strong localization of the frontier orbitals on the end groups ensuring binding of the rods to the metallic contacts. Finally, we investigate the characteristics of TVS in asymmetric molecular junctions. If a single level dominates the transport properties, TVS can provide a good estimate for both the level position and the degree of junction asymmetry. If more levels are involved the applicability of TVS becomes limited.Comment: 8 pages, 12 figure

Inelastic Scattering in Metal-H2-Metal Junctions

We present first-principles calculations of the dI/dV characteristics of an H2 molecule sandwiched between Au and Pt electrodes in the presence of electron-phonon interactions. The conductance is found to decrease by a few percentage at threshold voltages corresponding to the excitation energy of longitudinal vibrations of the H2 molecule. In the case of Pt electrodes, the transverse vibrations can mediate transport through otherwise non-transmitting Pt $d$-channels leading to an increase in the differential conductance even though the hydrogen junction is characterized predominately by a single almost fully open transport channel. In the case of Au, the transverse modes do not affect the dI/dV because the Au d-states are too far below the Fermi level. A simple explanation of the first-principles results is given using scattering theory. Finally, we compare and discuss our results in relation to experimental data.Comment: Accepted in Phys. Rev.

A stochastic spectral analysis of transcriptional regulatory cascades

The past decade has seen great advances in our understanding of the role of noise in gene regulation and the physical limits to signaling in biological networks. Here we introduce the spectral method for computation of the joint probability distribution over all species in a biological network. The spectral method exploits the natural eigenfunctions of the master equation of birth-death processes to solve for the joint distribution of modules within the network, which then inform each other and facilitate calculation of the entire joint distribution. We illustrate the method on a ubiquitous case in nature: linear regulatory cascades. The efficiency of the method makes possible numerical optimization of the input and regulatory parameters, revealing design properties of, e.g., the most informative cascades. We find, for threshold regulation, that a cascade of strong regulations converts a unimodal input to a bimodal output, that multimodal inputs are no more informative than bimodal inputs, and that a chain of up-regulations outperforms a chain of down-regulations. We anticipate that this numerical approach may be useful for modeling noise in a variety of small network topologies in biology

A statistical method for revealing form-function relations in biological networks

Over the past decade, a number of researchers in systems biology have sought to relate the function of biological systems to their network-level descriptions -- lists of the most important players and the pairwise interactions between them. Both for large networks (in which statistical analysis is often framed in terms of the abundance of repeated small subgraphs) and for small networks which can be analyzed in greater detail (or even synthesized in vivo and subjected to experiment), revealing the relationship between the topology of small subgraphs and their biological function has been a central goal. We here seek to pose this revelation as a statistical task, illustrated using a particular setup which has been constructed experimentally and for which parameterized models of transcriptional regulation have been studied extensively. The question "how does function follow form" is here mathematized by identifying which topological attributes correlate with the diverse possible information-processing tasks which a transcriptional regulatory network can realize. The resulting method reveals one form-function relationship which had earlier been predicted based on analytic results, and reveals a second for which we can provide an analytic interpretation. Resulting source code is distributed via http://formfunction.sourceforge.net.Comment: To appear in Proc. Natl. Acad. Sci. USA. 17 pages, 9 figures, 2 table

Creation and Reproduction of Model Cells with Semipermeable Membrane

A high activity of reactions can be confined in a model cell with a semipermeable membrane in the Schl\"ogl model. It is interpreted as a model of primitive metabolism in a cell. We study two generalized models to understand the creation of primitive cell systems conceptually from the view point of the nonlinear-nonequilibrium physics. In the first model, a single-cell system with a highly active state confined by a semipermeable membrane is spontaneously created from an inactive homogeneous state by a stochastic jump process. In the second model, many cell structures are reproduced from a single cell, and a multicellular system is created.Comment: 11 pages, 7 figure

Bacterial persisters are a stochastically formed subpopulation of low-energy cells.

Persisters represent a small subpopulation of non- or slow-growing bacterial cells that are tolerant to killing by antibiotics. Despite their prominent role in the recalcitrance of chronic infections to antibiotic therapy, the mechanism of their formation has remained elusive. We show that sorted cells of Escherichia coli with low levels of energy-generating enzymes are better able to survive antibiotic killing. Using microfluidics time-lapse microscopy and a fluorescent reporter for in vivo ATP measurements, we find that a subpopulation of cells with a low level of ATP survives killing by ampicillin. We propose that these low ATP cells are formed stochastically as a result of fluctuations in the abundance of energy-generating components. These findings point to a general "low energy" mechanism of persister formation

(Working title) Are We Meeting Oral Health Needs of Care Home Populations?

Aim: To evaluate care home (N) staff knowledge of oral care in comparison to NHS Quality Improvement Scotland (NHS QIS) guidelines. To identify barriers to delivering oral care and determine if Oral Health Educator (OHE) training had an effect upon staff knowledge of oral care delivery. Setting: The study was undertaken within Greater Glasgow, 2005 to 2007. Subjects and Methods: From 33 care homes (N), 28 participated in data gathering comprising 109 staff. A ‘knowledge check-list’ based upon daily oral care protocol from NHS QIS Best Practice Statement (BPS) served as template for knowledge assessment. An OHE undertook small group discussions related to the BPS in a sub-group of original participants and a second round of data collected. Results: The majority of staff (n=86, 79%) agreed that residents required assistance with oral care and placed oral care (n=85, 78%) as a moderate to high priority. Only 57% of managers and 49% of nurses had received training in oral care. Most staff (79% of managers, 85% of nurses) were unaware of the NHS QIS BPS. Deficiencies in knowledge of key areas within the BPS were identified. Between pre- and post-OHE training, significant differences were identified in prioritisation of oral care (p =0.009), perceived competence (p =0.005) and confidence giving advice (p =0.004). Following OHE intervention, knowledge of BPS protocol increased by 45%. Conclusion: Knowledge of oral care provision by carers for home residents requires substantial improvement. An OHE training programme structured around the NHS QIS BPS demonstrated a measurable increase in levels of staff knowledge of oral care

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