Theory of scanning gate microscopy

A systematic theory of the conductance measurements of non-invasive (weak probe) scanning gate microscopy is presented that provides an interpretation of what precisely is being measured. A scattering approach is used to derive explicit expressions for the first and second order conductance changes due to the perturbation by the tip potential in terms of the scattering states of the unperturbed structure. In the case of a quantum point contact, the first order correction dominates at the conductance steps and vanishes on the plateaus where the second order term dominates. Both corrections are non-local for a generic structure. Only in special cases, such as that of a centrally symmetric quantum point contact in the conductance quantization regime, can the second order correction be unambiguously related with the local current density. In the case of an abrupt quantum point contact we are able to obtain analytic expressions for the scattering eigenfunctions and thus evaluate the resulting conductance corrections.Comment: 19 pages, 7 figure

Phase Space Tomography of Matter-Wave Diffraction in the Talbot Regime

We report on the theoretical investigation of Wigner distribution function (WDF) reconstruction of the motional quantum state of large molecules in de Broglie interference. De Broglie interference of fullerenes and as the like already proves the wavelike behaviour of these heavy particles, while we aim to extract more quantitative information about the superposition quantum state in motion. We simulate the reconstruction of the WDF numerically based on an analytic probability distribution and investigate its properties by variation of parameters, which are relevant for the experiment. Even though the WDF described in the near-field experiment cannot be reconstructed completely, we observe negativity even in the partially reconstructed WDF. We further consider incoherent factors to simulate the experimental situation such as a finite number of slits, collimation, and particle-slit van der Waals interaction. From this we find experimental conditions to reconstruct the WDF from Talbot interference fringes in molecule Talbot-Lau interferometry.Comment: 16 pages, 9 figures, accepted at New Journal of Physic

The Buffer Gas Beam: An Intense, Cold, and Slow Source for Atoms and Molecules

Beams of atoms and molecules are stalwart tools for spectroscopy and studies of collisional processes. The supersonic expansion technique can create cold beams of many species of atoms and molecules. However, the resulting beam is typically moving at a speed of 300-600 m/s in the lab frame, and for a large class of species has insufficient flux (i.e. brightness) for important applications. In contrast, buffer gas beams can be a superior method in many cases, producing cold and relatively slow molecules in the lab frame with high brightness and great versatility. There are basic differences between supersonic and buffer gas cooled beams regarding particular technological advantages and constraints. At present, it is clear that not all of the possible variations on the buffer gas method have been studied. In this review, we will present a survey of the current state of the art in buffer gas beams, and explore some of the possible future directions that these new methods might take

Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa

Background The Multinational Brassica rapa Genome Sequencing Project (BrGSP) has developed valuable genomic resources, including BAC libraries, BAC-end sequences, genetic and physical maps, and seed BAC sequences for Brassica rapa. An integrated linkage map between the amphidiploid B. napus and diploid B. rapa will facilitate the rapid transfer of these valuable resources from B. rapa to B. napus (Oilseed rape, Canola). Results In this study, we identified over 23,000 simple sequence repeats (SSRs) from 536 sequenced BACs. 890 SSR markers (designated as BrGMS) were developed and used for the construction of an integrated linkage map for the A genome in B. rapa and B. napus. Two hundred and nineteen BrGMS markers were integrated to an existing B. napus linkage map (BnaNZDH). Among these mapped BrGMS markers, 168 were only distributed on the A genome linkage groups (LGs), 18 distrubuted both on the A and C genome LGs, and 33 only distributed on the C genome LGs. Most of the A genome LGs in B. napus were collinear with the homoeologous LGs in B. rapa, although minor inversions or rearrangements occurred on A2 and A9. The mapping of these BAC-specific SSR markers enabled assignment of 161 sequenced B. rapa BACs, as well as the associated BAC contigs to the A genome LGs of B. napus. Conclusion The genetic mapping of SSR markers derived from sequenced BACs in B. rapa enabled direct links to be established between the B. napus linkage map and a B. rapa physical map, and thus the assignment of B. rapa BACs and the associated BAC contigs to the B. napus linkage map. This integrated genetic linkage map will facilitate exploitation of the B. rapa annotated genomic resources for gene tagging and map-based cloning in B. napus, and for comparative analysis of the A genome within Brassica species

Ontologies of design frameworks as a tool for supporting decisions on steering committees

Celem artykułu jest wykazanie przydatności ontologii jako narzędzia wspomagającego decyzje prac komitetów sterujących. Budowa ontologii jako narzędzia wspomagającego decyzje była konsekwencją pojawienia się problemu oceny wniosków projektowych zgłaszanych do projektu Inteligentnych Specjalizacji Pomorza Smart Port & City. W artykule przedstawiono etapy budowy ontologii oraz jej zastosowanie do analizy zgodności dokumentów z przyjętymi ramami projektu.The aim of this article is to present usefulness of an ontology as a tool to support decisions of steering committees. Construction of the ontology as a decisions’ supporting tool was a consequence of a problem with assessment of project proposals submitted to the Inteligentne Specjalizacje Smart Port & City project. The article presents stages of the construction of the ontology and its use for the analysis of compatibility with the accepted frames of the project

High-speed quantum dot lasers and amplifiers for optical data communication

Quantum dot based 1.3 m fiber-coupled laser and amplifier modules show 10 Gb/s and 40 Gb/s operation, respectively, with bit error rates below 10 -11. Amplifier chip gain up to 26 dB has been demonstrated. Mode-locked quantum dot lasers show optical pulses with widths below 1 ps and repetition frequencies up to 80 GHz. 710 fs pulses were amplified with 10 dB net gain and without pulse broadening

Comparing the Ability of Enhanced Sampling Molecular Dynamics Methods to Reproduce the Behavior of Fluorescent Labels on Proteins

Adequately sampling the large number of conformations accessible to proteins and other macromolecules is one of the central challenges in molecular dynamics (MD) simulations; this activity can be difficult, even for relatively simple systems. An example where this problem arises is in the simulation of dye-labeled proteins, which are now being widely used in the design and interpretation of Förster resonance energy transfer (FRET) experiments. In this study, MD simulations are used to characterize the motion of two commonly used FRET dyes attached to an immobilized chain of polyproline. Even in this simple system, the dyes exhibit complex behavior that is a mixture of fast and slow motions. Consequently, very long MD simulations are required to sufficiently sample the entire range of dye motion. Here, we compare the ability of enhanced sampling methods to reproduce the behavior of fluorescent labels on proteins. In particular, we compared Accelerated Molecular Dynamics (AMD), metadynamics, Replica Exchange Molecular Dynamics (REMD), and High Temperature Molecular Dynamics (HTMD) to equilibrium MD simulations. We find that, in our system, all of these methods improve the sampling of the dye motion, but the most significant improvement is achieved using REMD