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

Involvement of the nuclear cap-binding protein complex in alternative splicing in Arabidopsis thaliana

The nuclear cap-binding protein complex (CBC) participates in 5′ splice site selection of introns that are proximal to the mRNA cap. However, it is not known whether CBC has a role in alternative splicing. Using an RT–PCR alternative splicing panel, we analysed 435 alternative splicing events in Arabidopsis thaliana genes, encoding mainly transcription factors, splicing factors and stress-related proteins. Splicing profiles were determined in wild type plants, the cbp20 and cbp80(abh1) single mutants and the cbp20/80 double mutant. The alternative splicing events included alternative 5′ and 3′ splice site selection, exon skipping and intron retention. Significant changes in the ratios of alternative splicing isoforms were found in 101 genes. Of these, 41% were common to all three CBC mutants and 15% were observed only in the double mutant. The cbp80(abh1) and cbp20/80 mutants had many more changes in alternative splicing in common than did cbp20 and cbp20/80 suggesting that CBP80 plays a more significant role in alternative splicing than CBP20, probably being a platform for interactions with other splicing factors. Cap-binding proteins and the CBC are therefore directly involved in alternative splicing of some Arabidopsis genes and in most cases influenced alternative splicing of the first intron, particularly at the 5′ splice site

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