Half-Cycle Pulse Acting on a One-Dimensional Rydberg Atom: Semiclassical Transition Amplitudes in Action and Angle Variables

In this paper we derive the expression for the transition coefficient used in the preceding paper [C. D. Schwieters and J. B. Delos, Phys. Rev. A 51, 1023 (1995)] for principal-quantum-number transitions in one-dimensional hydrogen caused by half-cycle pulses. We briefly review the methods of Miller [Adv. Chem. Phys. 25, 69 (1974)] and Marcus [Chem. Phys. Lett. 7, 525 (1970); J. Chem. Phys. 54, 3965 (1971)], and then derive the result using the methods of Maslov and Fedoriuk [Semi-Classical Approximation in Quantum Mechanics, (Reidel, Dordrecht, 1981)]. Also, we examine the approximate reduction of hydrogen from three to one dimension and we find a hitherto unknown correction due to the residual motion of one of the ignored degrees of freedom. We discuss the regime of validity of this one-dimensional approximation

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

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.

Microwave study of quantum n-disk scattering

We describe a wave-mechanical implementation of classically chaotic n-disk scattering based on thin 2-D microwave cavities. Two, three, and four-disk scattering are investigated in detail. The experiments, which are able to probe the stationary Green's function of the system, yield both frequencies and widths of the low-lying quantum resonances. The observed spectra are found to be in good agreement with calculations based on semiclassical periodic orbit theory. Wave-vector autocorrelation functions are analyzed for various scattering geometries, the small wave-vector behavior allowing one to extract the escape rate from the quantum repeller. Quantitative agreement is found with the value predicted from classical scattering theory. For intermediate energies, non-universal oscillations are detected in the autocorrelation function, reflecting the presence of periodic orbits.Comment: 13 pages, 8 eps figures include

Conductance of Open Quantum Billiards and Classical Trajectories

We analyse the transport phenomena of 2D quantum billiards with convex boundary of different shape. The quantum mechanical analysis is performed by means of the poles of the S-matrix while the classical analysis is based on the motion of a free particle inside the cavity along trajectories with a different number of bounces at the boundary. The value of the conductance depends on the manner the leads are attached to the cavity. The Fourier transform of the transmission amplitudes is compared with the length of the classical paths. There is good agreement between classical and quantum mechanical results when the conductance is achieved mainly by special short-lived states such as whispering gallery modes (WGM) and bouncing ball modes (BBM). In these cases, also the localization of the wave functions agrees with the picture of the classical paths. The S-matrix is calculated classically and compared with the transmission coefficients of the quantum mechanical calculations for five modes in each lead. The number of modes coupled to the special states is effectively reduced.Comment: 19 pages, 6 figures (jpg), 2 table

Practical computational toolkits for dendrimers and dendrons structure design

Dendrimers and dendrons offer an excellent platform for developing novel drug delivery systems and medicines. The rational design and further development of these repetitively branched systems are restricted by difficulties in scalable synthesis and structural determination, which can be overcome by judicious use of molecular modelling and molecular simulations. A major difficulty to utilise in silico studies to design dendrimers lies in the laborious generation of their structures. Current modelling tools utilise automated assembly of simpler dendrimers or the inefficient manual assembly of monomer precursors to generate more complicated dendrimer structures. Herein we describe two novel graphical user interface (GUI) toolkits written in Python that provide an improved degree of automation for rapid assembly of dendrimers and generation of their 2D and 3D structures. Our first toolkit uses the RDkit library, SMILES nomenclature of monomers and SMARTS reaction nomenclature to generate SMILES and mol files of dendrimers without 3D coordinates. These files are used for simple graphical representations and storing their structures in databases. The second toolkit assembles complex topology dendrimers from monomers to construct 3D dendrimer structures to be used as starting points for simulation using existing and widely available software and force fields. Both tools were validated for ease-of-use to prototype dendrimer structure and the second toolkit was especially relevant for dendrimers of high complexity and size.Peer reviewe

Solution structure and dynamic analysis of chicken MBD2 methyl binding domain bound to a target-methylated DNA sequence

The epigenetic code of DNA methylation is interpreted chiefly by methyl cytosine binding domain (MBD) proteins which in turn recruit multiprotein co-repressor complexes. We previously isolated one such complex, MBD2-NuRD, from primary erythroid cells and have shown it contributes to embryonic/fetal β-type globin gene silencing during development. This complex has been implicated in silencing tumor suppressor genes in a variety of human tumor cell types. Here we present structural details of chicken MBD2 bound to a methylated DNA sequence from the ρ-globin promoter to which it binds in vivo and mediates developmental transcriptional silencing in normal erythroid cells. While previous studies have failed to show sequence specificity for MBD2 outside of the symmetric mCpG, we find that this domain binds in a single orientation on the ρ-globin target DNA sequence. Further, we show that the orientation and affinity depends on guanine immediately following the mCpG dinucleotide. Dynamic analyses show that DNA binding stabilizes the central β-sheet, while the N- and C-terminal regions of the protein maintain mobility. Taken together, these data lead to a model in which DNA binding stabilizes the MBD2 structure and that binding orientation and affinity is influenced by the DNA sequence surrounding the central mCpG