Raman frequency shift in oxygen functionalized carbon nanotubes

In terms of lattice dynamics theory, we study the vibrational properties of the oxygen-functionalized single wall carbon nanotubes (O-SWCNs). Due to the C-O and O-O interactions, many degenerate phonon modes are split and even some new phonon modes are obtained, different from the bare SWCNs. A distinct Raman shift is found in both the radial breathing mode and G modes, depending not only on the tube diameter and chirality but also on oxygen coverage and adsorption configurations. With the oxygen coverage increasing, interesting, a nonmonotonic up- and down-shift is observed in G modes, which is contributed to the competition between the bond expansion and contraction, there coexisting in the functionalized carbon nanotube.Comment: 4 pages, 3 figures, 1 tabl

Electronic structure of superconducting graphite intercalate compounds: The role of the interlayer state

Although not an intrinsic superconductor, it has been long--known that, when intercalated with certain dopants, graphite is capable of exhibiting superconductivity. Of the family of graphite--based materials which are known to superconduct, perhaps the most well--studied are the alkali metal--graphite intercalation compounds (GIC) and, of these, the most easily fabricated is the C${}_8$K system which exhibits a transition temperature $\bm{T_c\simeq 0.14}$K. By increasing the alkali metal concentration (through high pressure fabrication techniques), the transition temperature has been shown to increase to as much as $\bm 5$K in C${}_2$Na. Lately, in an important recent development, Weller \emph{et al.} have shown that, at ambient conditions, the intercalated compounds \cyb and \cca exhibit superconductivity with transition temperatures $\bm{T_c\simeq 6.5}$K and $\bm{11.5}$K respectively, in excess of that presently reported for other graphite--based compounds. We explore the architecture of the states near the Fermi level and identify characteristics of the electronic band structure generic to GICs. As expected, we find that charge transfer from the intercalant atoms to the graphene sheets results in the occupation of the $\bm\pi$--bands. Yet, remarkably, in all those -- and only those -- compounds that superconduct, we find that an interlayer state, which is well separated from the carbon sheets, also becomes occupied. We show that the energy of the interlayer band is controlled by a combination of its occupancy and the separation between the carbon layers.Comment: 4 Figures. Please see accompanying experimental manuscript "Superconductivity in the Intercalated Graphite Compounds C6Yb and C6Ca" by Weller et a

Chemotaxis When Bacteria Remember: Drift versus Diffusion

{\sl Escherichia coli} ({\sl E. coli}) bacteria govern their trajectories by switching between running and tumbling modes as a function of the nutrient concentration they experienced in the past. At short time one observes a drift of the bacterial population, while at long time one observes accumulation in high-nutrient regions. Recent work has viewed chemotaxis as a compromise between drift toward favorable regions and accumulation in favorable regions. A number of earlier studies assume that a bacterium resets its memory at tumbles -- a fact not borne out by experiment -- and make use of approximate coarse-grained descriptions. Here, we revisit the problem of chemotaxis without resorting to any memory resets. We find that when bacteria respond to the environment in a non-adaptive manner, chemotaxis is generally dominated by diffusion, whereas when bacteria respond in an adaptive manner, chemotaxis is dominated by a bias in the motion. In the adaptive case, favorable drift occurs together with favorable accumulation. We derive our results from detailed simulations and a variety of analytical arguments. In particular, we introduce a new coarse-grained description of chemotaxis as biased diffusion, and we discuss the way it departs from older coarse-grained descriptions.Comment: Revised version, journal reference adde

Electronic Structure and Optical Properties of the Co-doped Anatase TiO2_{2} Studied from First Principles

The Co-doped anatase TiO$_{2}$, a recently discovered room-temperature ferromagnetic insulator, has been studied by the first-principles calculations in the pseudo-potential plane-wave formalism within the local-spin-density approximation (LSDA), supplemented by the full-potential linear augmented plane wave (FP-LAPW) method. Emphasis is placed on the dependence of its electronic structures and linear optical properties on the Co-doping concentration and oxygen vacancy in the system in order to pursue the origin of its ferromagnetism. In the case of substitutional doping of Co for Ti, our calculated results are well consistent with the experimental data, showing that Co is in its low spin state. Also, it is shown that the oxygen vacancy enhances the ferromagnetism and has larger effect on both the electronic structure and optical properties than the Co-doping concentration only.Comment: 12 pages, 4 figure

Optimal transport on wireless networks

We present a study of the application of a variant of a recently introduced heuristic algorithm for the optimization of transport routes on complex networks to the problem of finding the optimal routes of communication between nodes on wireless networks. Our algorithm iteratively balances network traffic by minimizing the maximum node betweenness on the network. The variant we consider specifically accounts for the broadcast restrictions imposed by wireless communication by using a different betweenness measure. We compare the performance of our algorithm to two other known algorithms and find that our algorithm achieves the highest transport capacity both for minimum node degree geometric networks, which are directed geometric networks that model wireless communication networks, and for configuration model networks that are uncorrelated scale-free networks.Comment: 5 pages, 4 figure

Multi-component Transparent Conducting Oxides: Progress in Materials Modelling

Transparent conducting oxides (TCOs) play an essential role in modern optoelectronic devices through their combination of electrical conductivity and optical transparency. We review recent progress in our understanding of multi-component TCOs formed from solid-solutions of ZnO, In2O3, Ga2O3 and Al2O3, with a particular emphasis on the contributions of materials modelling, primarily based on Density Functional Theory. In particular, we highlight three major results from our work: (i) the fundamental principles governing the crystal structures of multi-component oxide structures including (In2O3)(ZnO)n, named IZO, and (In2O3)m(Ga2O3)l(ZnO)n, named IGZO; (ii) the relationship between elemental composition and optical and electrical behaviour, including valence band alignments; (iii) the high-performance of amorphous oxide semiconductors. From these advances, the challenge of the rational design of novel electroceramic materials is discussed.Comment: Part of a themed issue of Journal of Physics: Condensed Matter on "Semiconducting Oxides". In Press (2011

Effects of thermal fluctuation and the receptor-receptor interaction in bacterial chemotactic signalling and adaptation

Bacterial chemotaxis is controlled by the conformational changes of the receptors, in response to the change of the ambient chemical concentration. In a statistical mechanical approach, the signalling due to the conformational changes is a thermodynamic average quantity, dependent on the temperature and the total energy of the system, including both ligand-receptor interaction and receptor-receptor interaction. This physical theory suggests to biology a new understanding of cooperation in ligand binding and receptor signalling problems. How much experimental support of this approach can be obtained from the currently available data? What are the parameter values? What is the practical information for experiments? Here we make comparisons between the theory and recent experimental results. Although currently comparisons can only be semi-quantitative or qualitative, consistency is clearly shown. The theory also helps to sort a variety of data.Comment: 26 pages, revtex. Journal version. Analysis on another set of data on adaptation time is adde

Triggering of the 2014 M_w7.3 Papanoa earthquake by a slow slip event in Guerrero, Mexico

Since their discovery two decades ago, slow slip events have been shown to play an important role in accommodating strain in subduction zones. However, the physical mechanisms that generate slow slip and the relationships with earthquakes are unclear. Slow slip events have been recorded in the Guerrero segment of the Cocos–North America subduction zone. Here we use inversion of position time series recorded by a continuous GPS network to reconstruct the evolution of aseismic slip on the subduction interface of the Guerrero segment. We find that a slow slip event began in February 2014, two months before the magnitude (M_w) 7.3 Papanoa earthquake on 18 April. The slow slip event initiated in a region adjacent to the earthquake hypocentre and extended into the vicinity of the seismogenic zone. This spatio-temporal proximity strongly suggests that the Papanoa earthquake was triggered by the ongoing slow slip event. We demonstrate that the triggering mechanism could be either static stress increases in the hypocentral region, as revealed by Coulomb stress modelling, or enhanced weakening of the earthquake hypocentral area by the slow slip. We also show that the plate interface in the Guerrero area is highly coupled between slow slip events, and that most of the accumulated strain is released aseismically during the slow slip episodes

A 'resource allocator' for transcription based on a highly fragmented T7 RNA polymerase

Synthetic genetic systems share resources with the host, including machinery for transcription and translation. Phage RNA polymerases (RNAPs) decouple transcription from the host and generate high expression. However, they can exhibit toxicity and lack accessory proteins (σ factors and activators) that enable switching between different promoters and modulation of activity. Here, we show that T7 RNAP (883 amino acids) can be divided into four fragments that have to be co‐expressed to function. The DNA‐binding loop is encoded in a C‐terminal 285‐aa ‘σ fragment’, and fragments with different specificity can direct the remaining 601‐aa ‘core fragment’ to different promoters. Using these parts, we have built a resource allocator that sets the core fragment concentration, which is then shared by multiple σ fragments. Adjusting the concentration of the core fragment sets the maximum transcriptional capacity available to a synthetic system. Further, positive and negative regulation is implemented using a 67‐aa N‐terminal ‘α fragment’ and a null (inactivated) σ fragment, respectively. The α fragment can be fused to recombinant proteins to make promoters responsive to their levels. These parts provide a toolbox to allocate transcriptional resources via different schemes, which we demonstrate by building a system which adjusts promoter activity to compensate for the difference in copy number of two plasmids.United States. Office of Naval Research (N00014‐13‐1‐0074)National Institutes of Health (U.S.) (5R01GM095765)National Science Foundation (U.S.) (Synthetic Biology Engineering Research Center (SA5284‐11210))United States. Dept. of Defense (National Defense Science and Engineering Graduate Fellowship (NDSEG) Program))Hertz Foundation (Fellowship

Pulsed Feedback Defers Cellular Differentiation

Environmental signals induce diverse cellular differentiation programs. In certain systems, cells defer differentiation for extended time periods after the signal appears, proliferating through multiple rounds of cell division before committing to a new fate. How can cells set a deferral time much longer than the cell cycle? Here we study Bacillus subtilis cells that respond to sudden nutrient limitation with multiple rounds of growth and division before differentiating into spores. A well-characterized genetic circuit controls the concentration and phosphorylation of the master regulator Spo0A, which rises to a critical concentration to initiate sporulation. However, it remains unclear how this circuit enables cells to defer sporulation for multiple cell cycles. Using quantitative time-lapse fluorescence microscopy of Spo0A dynamics in individual cells, we observed pulses of Spo0A phosphorylation at a characteristic cell cycle phase. Pulse amplitudes grew systematically and cell-autonomously over multiple cell cycles leading up to sporulation. This pulse growth required a key positive feedback loop involving the sporulation kinases, without which the deferral of sporulation became ultrasensitive to kinase expression. Thus, deferral is controlled by a pulsed positive feedback loop in which kinase expression is activated by pulses of Spo0A phosphorylation. This pulsed positive feedback architecture provides a more robust mechanism for setting deferral times than constitutive kinase expression. Finally, using mathematical modeling, we show how pulsing and time delays together enable “polyphasic” positive feedback, in which different parts of a feedback loop are active at different times. Polyphasic feedback can enable more accurate tuning of long deferral times. Together, these results suggest that Bacillus subtilis uses a pulsed positive feedback loop to implement a “timer” that operates over timescales much longer than a cell cycle