Semiclassical Scattering in a Circular Semiconductor Microstructure

The conductance of a microscopic junction shows fluctuations caused by quantum interference of waves that follow different paths between the leads. We give a semiclassical formula for these fluctuations. The theory utilizes trajectories which travel between the centers of the lead apertures; it also incorporates diffraction at these apertures. We extend the theory to include ‘‘ghost paths,’’ which scatter diffractively off the lead mouths. Semiclassical S-matrix elements are computed for a circular junction over a range of Fermi wave numbers, and the large-scale structure of these matrix elements shows good agreement with quantum results. Finally, we propose a hypothesis about the effect of the quantum coherence length on the S matrix and on the semiclassical sum. © 1996 The American Physical Society

Excitation of weakly bound Rydberg electrons by half-cycle pulses

The interaction of a weakly bound Rydberg electron with an electromagnetic half-cycle pulse (HCP) is described with the help of a multidimensional semiclassical treatment. This approach relates the quantum evolution of the electron to its underlying classical dynamics. The method is nonperturbative and is valid for arbitrary spatial and temporal shapes of the applied HCP. On the basis of this approach angle- and energy-resolved spectra resulting from the ionization of Rydberg atoms by HCPs are analyzed. The different types of spectra obtainable in the sudden-impact approximation are characterized in terms of the appearing semiclassical scattering phenomena. Typical modifications of the spectra originating from finite pulse effects are discussed.Comment: Submitted to Phys. Rev.

Negative length orbits in normal-superconductor billiard systems

The Path-Length Spectra of mesoscopic systems including diffractive scatterers and connected to superconductor is studied theoretically. We show that the spectra differs fundamentally from that of normal systems due to the presence of Andreev reflection. It is shown that negative path-lengths should arise in the spectra as opposed to normal system. To highlight this effect we carried out both quantum mechanical and semiclassical calculations for the simplest possible diffractive scatterer. The most pronounced peaks in the Path-Length Spectra of the reflection amplitude are identified by the routes that the electron and/or hole travels.Comment: 4 pages, 4 figures include

Quantum control and the Strocchi map

Identifying the real and imaginary parts of wave functions with coordinates and momenta, quantum evolution may be mapped onto a classical Hamiltonian system. In addition to the symplectic form, quantum mechanics also has a positive-definite real inner product which provides a geometrical interpretation of the measurement process. Together they endow the quantum Hilbert space with the structure of a K\"{a}ller manifold. Quantum control is discussed in this setting. Quantum time-evolution corresponds to smooth Hamiltonian dynamics and measurements to jumps in the phase space. This adds additional power to quantum control, non unitarily controllable systems becoming controllable by ``measurement plus evolution''. A picture of quantum evolution as Hamiltonian dynamics in a classical-like phase-space is the appropriate setting to carry over techniques from classical to quantum control. This is illustrated by a discussion of optimal control and sliding mode techniques.Comment: 16 pages Late

Structure calculation, refinement and validation using CcpNmr Analysis

CcpNmr Analysis provides a streamlined pipeline for both NMR chemical shift assignment and structure determination of biological macromolecules. In addition, it encompasses tools to analyse the many additional experiments that make NMR such a pivotal technique for research into complex biological questions. This report describes how CcpNmr Analysis can seamlessly link together all of the tasks in the NMR structure-determination process. It details each of the stages from generating NMR restraints [distance, dihedral,hydrogen bonds and residual dipolar couplings (RDCs)],exporting these to and subsequently re-importing them from structure-calculation software (such as the programs CYANA or ARIA) and analysing and validating the results obtained from the structure calculation to, ultimately, the streamlined deposition of the completed assignments and the refined ensemble of structures into the PDBe repository. Until recently, such solution-structure determination by NMR has been quite a laborious task, requiring multiple stages and programs. However, with the new enhancements to CcpNmr Analysis described here, this process is now much more intuitive and efficient and less error-prone

Diffraction and boundary conditions in semi-classical open billiards

The conductance through open quantum dots or quantum billiards shows fluctuations, that can be explained as interference between waves following different paths between the leads of the billiard. We examine such systems by the use of a semi-classical Green's functions. In this paper we examine how the choice of boundary conditions at the lead mouths affect the diffraction. We derive a new formula for the S-matrix element. Finally we compare semi-classical simulations to quantum mechanical ones, and show that this new formula yield superior results.Comment: 7 pages, 4 figure

Estimation of interdomain flexibility of N-terminus of factor H using residual dipolar couplings

Characterization of segmental flexibility is needed to understand the biological mechanisms of the very large category of functionally diverse proteins, exemplified by the regulators of complement activation, that consist of numerous compact modules or domains linked by short, potentially flexible, sequences of amino acid residues. The use of NMR-derived residual dipolar couplings (RDCs), in magnetically aligned media, to evaluate interdomain motion is established but only for two-domain proteins. We focused on the three N-terminal domains (called CCPs or SCRs) of the important complement regulator, human factor H (i.e. FH1-3). These domains cooperate to facilitate cleavage of the key complement activation-specific protein fragment, C3b, forming iC3b that no longer participates in the complement cascade. We refined a three-dimensional solution structure of recombinant FH1-3 based on nuclear Overhauser effects and RDCs. We then employed a rudimentary series of RDC datasets, collected in media containing magnetically aligned bicelles (disk-like particles formed from phospholipids) under three different conditions, to estimate interdomain motions. This circumvents a requirement of previous approaches for technically difficult collection of five independent RDC datasets. More than 80% of conformers of this predominantly extended three-domain molecule exhibit flexions of < 40 °. Such segmental flexibility (together with the local dynamics of the hypervariable loop within domain 3), could facilitate recognition of C3b via initial anchoring and eventual reorganization of modules to the conformation captured in the previously solved crystal structure of a C3b:FH1-4 complex

Mapping the encounter state of a transient protein complex by PRE NMR spectroscopy

Many biomolecular interactions proceed via a short-lived encounter state, consisting of multiple, lowly-populated species invisible to most experimental techniques. Recent development of paramagnetic relaxation enhancement (PRE) nuclear magnetic resonance (NMR) spectroscopy has allowed to directly visualize such transient intermediates in a number of protein-protein and protein-DNA complexes. Here we present an analysis of the recently published PRE NMR data for a protein complex of yeast cytochrome c (Cc) and cytochrome c peroxidase (CcP). First, we describe a simple, general method to map out the spatial and temporal distributions of binding geometries constituting the Cc-CcP encounter state. We show that the spatiotemporal mapping provides a reliable estimate of the experimental coverage and, at higher coverage levels, allows to delineate the conformational space sampled by the minor species. To further refine the encounter state, we performed PRE-based ensemble simulations. The generated solutions reproduce well the experimental data and lie within the allowed regions of the encounter maps, confirming the validity of the mapping approach. The refined encounter ensembles are distributed predominantly in a region encompassing the dominant form of the complex, providing experimental proof for the results of classical theoretical simulations

Geometry-dependent scattering through quantum billiards: Experiment and theory

We present experimental studies of the geometry-specific quantum scattering in microwave billiards of a given shape. We perform full quantum mechanical scattering calculations and find an excellent agreement with the experimental results. We also carry out the semiclassical calculations where the conductance is given as a sum of all classical trajectories between the leads, each of them carrying the quantum-mechanical phase. We unambiguously demonstrate that the characteristic frequencies of the oscillations in the transmission and reflection amplitudes are related to the length distribution of the classical trajectories between the leads, whereas the frequencies of the probabilities can be understood in terms of the length difference distribution in the pairs of classical trajectories. We also discuss the effect of non-classical "ghost" trajectories that include classically forbidden reflection off the lead mouths.Comment: 4 pages, 4 figure

Optical creation of vibrational intrinsic localized modes in anharmonic lattices with realistic interatomic potentials

Using an efficient optimal control scheme to determine the exciting fields, we theoretically demonstrate the optical creation of vibrational intrinsic localized modes (ILMs) in anharmonic perfect lattices with realistic interatomic potentials. For systems with finite size, we show that ILMs can be excited directly by applying a sequence of femtosecond visible laser pulses at THz repetition rates. For periodic lattices, ILMs can be created indirectly via decay of an unstable extended lattice mode which is excited optically either by a sequence of pulses as described above or by a single picosecond far-infrared laser pulse with linearly chirped frequency. In light of recent advances in experimental laser pulse shaping capabilities, the approach is experimentally promising.Comment: 20 pages, 7 eps figures. Accepted, Phys. Rev.