The conductance of a multi-mode ballistic ring: beyond Landauer and Kubo

The Landauer conductance of a two terminal device equals to the number of open modes in the weak scattering limit. What is the corresponding result if we close the system into a ring? Is it still bounded by the number of open modes? Or is it unbounded as in the semi-classical (Drude) analysis? It turns out that the calculation of the mesoscopic conductance is similar to solving a percolation problem. The "percolation" is in energy space rather than in real space. The non-universal structures and the sparsity of the perturbation matrix cannot be ignored.Comment: 7 pages, 8 figures, with the correct version of Figs.6-

Total Quantum Zeno effect and Intelligent States for a two level system in a squeezed bath

In this work we show that by frequent measurements of adequately chosen observables, a complete suppression of the decay in an exponentially decaying two level system interacting with a squeezed bath is obtained. The observables for which the effect is observed depend on the the squeezing parameters of the bath. The initial states which display Total Zeno Effect are intelligent states of two conjugate observables associated to the electromagnetic fluctuations of the bath.Comment: 5 pages, 3 figure

Rate of energy absorption by a closed ballistic ring

We make a distinction between the spectroscopic and the mesoscopic conductance of closed systems. We show that the latter is not simply related to the Landauer conductance of the corresponding open system. A new ingredient in the theory is related to the non-universal structure of the perturbation matrix which is generic for quantum chaotic systems. These structures may created bottlenecks that suppress the diffusion in energy space, and hence the rate of energy absorption. The resulting effect is not merely quantitative: For a ring-dot system we find that a smaller Landauer conductance implies a smaller spectroscopic conductance, while the mesoscopic conductance increases. Our considerations open the way towards a realistic theory of dissipation in closed mesoscopic ballistic devices.Comment: 18 pages, 5 figures, published version with updated ref

Accurate Reaction-Diffusion Operator Splitting on Tetrahedral Meshes for Parallel Stochastic Molecular Simulations

Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, meaning that the serial limit has already been reached in sub-cellular models. This calls for parallel simulations that can take advantage of the power of modern supercomputers; however exact methods are known to be inherently serial. We introduce an operator splitting implementation for irregular grids with a novel method to improve accuracy, and demonstrate potential for scalable parallel simulations in an initial MPI version. We foresee that this groundwork will enable larger scale, whole-cell stochastic simulations in the near future.Comment: 33 pages, 10 figure

Automatic annotation of bioinformatics workflows with biomedical ontologies

Legacy scientific workflows, and the services within them, often present scarce and unstructured (i.e. textual) descriptions. This makes it difficult to find, share and reuse them, thus dramatically reducing their value to the community. This paper presents an approach to annotating workflows and their subcomponents with ontology terms, in an attempt to describe these artifacts in a structured way. Despite a dearth of even textual descriptions, we automatically annotated 530 myExperiment bioinformatics-related workflows, including more than 2600 workflow-associated services, with relevant ontological terms. Quantitative evaluation of the Information Content of these terms suggests that, in cases where annotation was possible at all, the annotation quality was comparable to manually curated bioinformatics resources.Comment: 6th International Symposium on Leveraging Applications (ISoLA 2014 conference), 15 pages, 4 figure

Lattice Model of Sweeping Interface for Drying Process in Water-Granule Mixture

Based on the invasion percolation model, a lattice model for the sweeping interface dynamics is constructed to describe the pattern forming process by a sweeping interface upon drying the water-granule mixture. The model is shown to produce labyrinthine patterns similar to those found in the experiment[Yamazaki and Mizuguchi, J. Phys. Soc. Jpn. \textbf{69} (2000) 2387]. Upon changing the initial granular density, resulting patterns undergo the percolation transition, but estimated critical exponents are different from those of the conventional percolation. Loopless structure of clusters in the patterns produced by the sweeping dynamics seems to influence the nature of the transition.Comment: 6 pages, 7 figure