Nano-wires with surface disorder: Giant localization lengths and dynamical tunneling in the presence of directed chaos

We investigate electron quantum transport through nano-wires with one-sided surface roughness in the presence of a perpendicular magnetic field. Exponentially diverging localization lengths are found in the quantum-to-classical crossover regime, controlled by tunneling between regular and chaotic regions of the underlying mixed classical phase space. We show that each regular mode possesses a well-defined mode-specific localization length. We present analytic estimates of these mode localization lengths which agree well with the numerical data. The coupling between regular and chaotic regions can be determined by varying the length of the wire leading to intricate structures in the transmission probabilities. We explain these structures quantitatively by dynamical tunneling in the presence of directed chaos.Comment: 15 pages, 12 figure

Nano-wires with surface disorder: Giant localization lengths and quantum-to-classical crossover

We investigate electronic quantum transport through nano-wires with one-sided surface roughness. A magnetic field perpendicular to the scattering region is shown to lead to exponentially diverging localization lengths in the quantum-to-classical crossover regime. This effect can be quantitatively accounted for by tunneling between the regular and the chaotic components of the underlying mixed classical phase space.Comment: 4 pages, 3 figures; final version (including added references

Reflection resonances in surface-disordered waveguides: strong higher-order effects of the disorder

We study coherent wave scattering through waveguides with a step-like surface disorder and find distinct enhancements in the reflection coefficients at well-defined resonance values. Based on detailed numerical and analytical calculations, we can unambiguously identify the origin of these reflection resonances to be higher-order correlations in the surface disorder profile which are typically neglected in similar studies of the same system. A remarkable feature of this new effect is that it relies on the longitudinal correlations in the step profile, although individual step heights are random and thus completely uncorrelated. The corresponding resonances are very pronounced and robust with respect to ensemble averaging, and lead to an enhancement of wave reflection by more than one order of magnitude

Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli.

The genome-scale model (GEM) of metabolism in the bacterium Escherichia coli K-12 has been in development for over a decade and is now in wide use. GEM-enabled studies of E. coli have been primarily focused on six applications: (1) metabolic engineering, (2) model-driven discovery, (3) prediction of cellular phenotypes, (4) analysis of biological network properties, (5) studies of evolutionary processes, and (6) models of interspecies interactions. In this review, we provide an overview of these applications along with a critical assessment of their successes and limitations, and a perspective on likely future developments in the field. Taken together, the studies performed over the past decade have established a genome-scale mechanistic understanding of genotype–phenotype relationships in E. coli metabolism that forms the basis for similar efforts for other microbial species. Future challenges include the expansion of GEMs by integrating additional cellular processes beyond metabolism, the identification of key constraints based on emerging data types, and the development of computational methods able to handle such large-scale network models with sufficient accuracy

Thermalization and Cooling of Plasmon-Exciton Polaritons: Towards Quantum Condensation

We present indications of thermalization and cooling of quasi-particles, a precursor for quantum condensation, in a plasmonic nanoparticle array. We investigate a periodic array of metallic nanorods covered by a polymer layer doped with an organic dye at room temperature. Surface lattice resonances of the array---hybridized plasmonic/photonic modes---couple strongly to excitons in the dye, and bosonic quasi-particles which we call plasmon-exciton-polaritons (PEPs) are formed. By increasing the PEP density through optical pumping, we observe thermalization and cooling of the strongly coupled PEP band in the light emission dispersion diagram. For increased pumping, we observe saturation of the strong coupling and emission in a new weakly coupled band, which again shows signatures of thermalization and cooling.Comment: 8 pages, 5 figures including supplemental material. The newest version includes new measurements and corrections to the interpretation of the result

MultiMetEval: comparative and multi-objective analysis of genome-scale metabolic models

Comparative metabolic modelling is emerging as a novel field, supported by the development of reliable and standardized approaches for constructing genome-scale metabolic models in high throughput. New software solutions are needed to allow efficient comparative analysis of multiple models in the context of multiple cellular objectives. Here, we present the user-friendly software framework Multi-Metabolic Evaluator (MultiMetEval), built upon SurreyFBA, which allows the user to compose collections of metabolic models that together can be subjected to flux balance analysis. Additionally, MultiMetEval implements functionalities for multi-objective analysis by calculating the Pareto front between two cellular objectives. Using a previously generated dataset of 38 actinobacterial genome-scale metabolic models, we show how these approaches can lead to exciting novel insights. Firstly, after incorporating several pathways for the biosynthesis of natural products into each of these models, comparative flux balance analysis predicted that species like Streptomyces that harbour the highest diversity of secondary metabolite biosynthetic gene clusters in their genomes do not necessarily have the metabolic network topology most suitable for compound overproduction. Secondly, multi-objective analysis of biomass production and natural product biosynthesis in these actinobacteria shows that the well-studied occurrence of discrete metabolic switches during the change of cellular objectives is inherent to their metabolic network architecture. Comparative and multi-objective modelling can lead to insights that could not be obtained by normal flux balance analyses. MultiMetEval provides a powerful platform that makes these analyses straightforward for biologists. Sources and binaries of MultiMetEval are freely available from https://github.com/PiotrZakrzewski/MetEv​al/downloads

Characterization of growth and metabolism of the haloalkaliphile Natronomonas pharaonis

Natronomonas pharaonis is an archaeon adapted to two extreme conditions: high salt concentration and alkaline pH. It has become one of the model organisms for the study of extremophilic life. Here, we present a genome-scale, manually curated metabolic reconstruction for the microorganism. The reconstruction itself represents a knowledge base of the haloalkaliphile's metabolism and, as such, would greatly assist further investigations on archaeal pathways. In addition, we experimentally determined several parameters relevant to growth, including a characterization of the biomass composition and a quantification of carbon and oxygen consumption. Using the metabolic reconstruction and the experimental data, we formulated a constraints-based model which we used to analyze the behavior of the archaeon when grown on a single carbon source. Results of the analysis include the finding that Natronomonas pharaonis, when grown aerobically on acetate, uses a carbon to oxygen consumption ratio that is theoretically near-optimal with respect to growth and energy production. This supports the hypothesis that, under simple conditions, the microorganism optimizes its metabolism with respect to the two objectives. We also found that the archaeon has a very low carbon efficiency of only about 35%. This inefficiency is probably due to a very low P/O ratio as well as to the other difficulties posed by its extreme environment