QmeQ 1.0: An open-source Python package for calculations of transport through quantum dot devices

QmeQ is an open-source Python package for numerical modeling of transport through quantum dot devices with strong electron-electron interactions using various approximate master equation approaches. The package provides a framework for calculating stationary particle or energy currents driven by differences in chemical potentials or temperatures between the leads which are tunnel coupled to the quantum dots. The electronic structures of the quantum dots are described by their single-particle states and the Coulomb matrix elements between the states. When transport is treated perturbatively to lowest order in the tunneling couplings, the possible approaches are Pauli (classical), first-order Redfield, and first-order von Neumann master equations, and a particular form of the Lindblad equation. When all processes involving two-particle excitations in the leads are of interest, the second-order von Neumann approach can be applied. All these approaches are implemented in QmeQ. We here give an overview of the basic structure of the package, give examples of transport calculations, and outline the range of applicability of the different approximate approaches.Comment: 34 pages, 10 figure

Estimation of motility parameters from trajectory data:A condensate of our recent results

International audienceGiven a theoretical model for a self-propelled particle or micro-organism, how does one optimally determine the parameters of the model from experimental data in the form of a time-lapse recorded trajectory? For very long trajectories, one has very good statistics, and optimality may matter little. However, for biological micro-organisms, one may not control the duration of recordings, and then optimality can matter. This is especially the case if one is interested in individuality and hence cannot improve statistics by taking population averages over many trajectories. One can learn much about this problem by studying its simplest case, pure diffusion with no self-propagation. This is an interesting problem also in its own right for the very same reasons: interest in individuality and short trajectories. We summarize our recent results on this latter issue here and speculate about the extent to which similar results may be obtained also for self-propelled particles

Concentrating and labeling genomic DNA in a nanofluidic array

Genomic DNA is concentrated in a dense nanofluidic array and labeled by a polymerase ϕ29 reaction where neither the DNA nor the enzyme is attached to a solid support.</p

Classification of DNA nucleotides with transverse tunneling currents

It has been theoretically suggested and experimentally demonstrated that fast and low-cost sequencing of DNA, RNA, and peptide molecules might be achieved by passing such molecules between electrodes embedded in a nanochannel. The experimental realization of this scheme faces major challenges, however. In realistic liquid environments, typical currents in tunnelling devices are of the order of picoamps. This corresponds to only six electrons per microsecond, and this number affects the integration time required to do current measurements in real experiments. This limits the speed of sequencing, though current fluctuations due to Brownian motion of the molecule average out during the required integration time. Moreover, data acquisition equipment introduces noise, and electronic filters create correlations in time-series data. We discuss how these effects must be included in the analysis of, e.g., the assignment of specific nucleobases to current signals. As the signals from different molecules overlap, unambiguous classification is impossible with a single measurement. We argue that the assignment of molecules to a signal is a standard pattern classification problem and calculation of the error rates is straightforward. The ideas presented here can be extended to other sequencing approaches of current interest

Coherent Transport through an interacting double quantum dot: Beyond sequential tunneling

Various causes for negative differential conductance in transport through an interacting double quantum dot are investigated. Particular focus is given to the interplay between the renormalization of the energy levels due to the coupling to the leads and the decoherence of the states. The calculations are performed within a basis of many-particle eigenstates and we consider the dynamics given by the von Neumann-equation taking into account also processes beyond sequential tunneling. A systematic comparison between the levels of approximation and also with different formalisms is performed. It is found that the current is qualitatively well described by sequential processes as long as the temperature is larger than the level broadening induced by the contacts.Comment: 11 pages, 5 figures included in tex