PROTEINS IN VACUO. A MORE EFFICIENT MEANS OF CALCULATING ORIENTATIONALLY-AVERAGED COLLISION CROSS SECTIONS OF PROTEIN IONS

With the aim of understanding solvent effects in protein folding, unfolding, stability and dynamic behavior, studies of protein ions in vacuo have become popular in recent years. One experimental descriptor which gives a general overview of ionic structure is the orientationally-averaged collision cross section , which is obtained from ion drift mobility (IDM) and other kinds of measurements. In modelling protein structures in vacuo with molecular dynamics simulations, it is necessary to calculate for a plurality of model structures for comparison with experiments. The collision cross section is sensitive to the roughness (concavity) of the protein surface because of the possibility of multiple collisions during an encounter between a given bath gas particle and the protein. Calculations of , though in principle straightforward, are time consuming. In the work presented below, it was investigated whether a more efficient calculation scheme can be employed without sacrificing too much accuracy. In the new scheme, atomic-scale protein surface granularity is smoothed out by a collected-atoms approach, while large-scale concavity of the protein is essentially preserved. (Received August 31, 2001; revised December 26, 2001) Bull.Chem.Soc.Ethiop. 2001, 15(2), 157-16

Size distribution of sputtered particles from Au nanoislands due to MeV self-ion bombardment

Nanoisland gold films, deposited by vacuum evaporation of gold onto Si(100) substrates, were irradiated with 1.5 MeV Au$^{2+}$ ions up to a fluence of $5\times 10^{14}$ ions cm$^{-2}$ and at incidence angles up to $60^{\circ}$ with respect to the surface normal. The sputtered particles were collected on carbon coated grids (catcher grid) during ion irradiation and were analyzed with transmission electron microscopy and Rutherford backscattering spectrometry. The average sputtered particle size and the areal coverage are determined from transmission electron microscopy measurements, whereas the amount of gold on the substrate is found by Rutherford backscattering spectrometry. The size distributions of larger particles (number of atoms/particle, $n$ $\ge$ 1,000) show an inverse power-law with an exponent of $\sim$ -1 in broad agreement with a molecular dynamics simulation of ion impact on cluster targets.Comment: 13 pages, 8 figures, Submitted for publication in JA

Mixtures of Bose gases confined in concentrically coupled annular traps

A two-component Bose-Einstein condensate confined in an axially-symmetric potential with two local minima, resembling two concentric annular traps, is investigated. The system shows a number of quantum phase transitions that result from the competition between phase coexistence, and radial/azimuthal phase separation. The ground-state phase diagram, as well as the rotational properties, including the (meta)stability of currents in this system, are analysed.Comment: 6 pages, 5 figures, minor revision

Phase transitions in optimal unsupervised learning

We determine the optimal performance of learning the orientation of the symmetry axis of a set of P = alpha N points that are uniformly distributed in all the directions but one on the N-dimensional sphere. The components along the symmetry breaking direction, of unitary vector B, are sampled from a mixture of two gaussians of variable separation and width. The typical optimal performance is measured through the overlap Ropt=B.J* where J* is the optimal guess of the symmetry breaking direction. Within this general scenario, the learning curves Ropt(alpha) may present first order transitions if the clusters are narrow enough. Close to these transitions, high performance states can be obtained through the minimization of the corresponding optimal potential, although these solutions are metastable, and therefore not learnable, within the usual bayesian scenario.Comment: 9 pages, 8 figures, submitted to PRE, This new version of the paper contains one new section, Bayesian versus optimal solutions, where we explain in detail the results supporting our claim that bayesian learning may not be optimal. Figures 4 of the first submission was difficult to understand. We replaced it by two new figures (Figs. 4 and 5 in this new version) containing more detail

A Quantum Analogue of the Jarzynski Equality

A quantum analogue of the Jarzynski equality is constructed. This equality connects an ensemble average of exponentiated work with the Helmholtz free-energy difference in a nonequilibrium switching process subject to a thermal heat bath. To confirm its validity in a practical situation, we also investigate an open quantum system that is a spin 1/2 system with a scanning magnetic field interacting with a thermal heat bath. As a result, we find that the quantum analogue functions well.Comment: 7 pages, 1 figure; to appear in J. Phys. Soc. Jpn. 69 (2000

Ultrafast spatio-temporal dynamics of terahertz generation by ionizing two-color femtosecond pulses in gases

We present a combined theoretical and experimental study of spatio-temporal propagation effects in terahertz (THz) generation in gases using two-color ionizing laser pulses. The observed strong broadening of the THz spectra with increasing gas pressure reveals the prominent role of spatio-temporal reshaping and of a plasma-induced blue-shift of the pump pulses in the generation process. Results obtained from (3+1)-dimensional simulations are in good agreement with experimental findings and clarify the mechanisms responsible for THz emission

Symmetry Constraints and the Electronic Structures of a Quantum Dot with Thirteen Electrons

The symmetry constraints imposing on the quantum states of a dot with 13 electrons has been investigated. Based on this study, the favorable structures (FSs) of each state has been identified. Numerical calculations have been performed to inspect the role played by the FSs. It was found that, if a first-state has a remarkably competitive FS, this FS would be pursued and the state would be crystal-like and have a specific core-ring structure associated with the FS. The magic numbers are found to be closely related to the FSs.Comment: 13 pages, 5 figure

Three and four current reversals versus temperature in correlation ratchets with a simple sawtooh potential

Transport of Brownian particles on a simple sawtooth potential subjected to both unbiased thermal and nonequilibrium symmetric three-level Markovian noise is considered. The new effects of three and four current reversals as a function of temperature are established in such correlation ratchets. The parameter space coordinates of the fixed points associated with these current reversals and the necessary and sufficient conditions for the existence of the novel current reversals are found.Comment: 4 pages, 5 figures; some changes introduced; accepted for publication in Physical Review

Rotational and vibrational spectra of quantum rings

One can confine the two-dimensional electron gas in semiconductor heterostructures electrostatically or by etching techniques such that a small electron island is formed. These man-made ``artificial atoms'' provide the experimental realization of a text-book example of many-particle physics: a finite number of quantum particles in a trap. Much effort was spent on making such "quantum dots" smaller and going from the mesoscopic to the quantum regime. Far-reaching analogies to the physics of atoms, nuclei or metal clusters were obvious from the very beginning: The concepts of shell structure and Hund's rules were found to apply -- just as in real atoms! In this Letter, we report the discovery that electrons confined in ring-shaped quantum dots form rather rigid molecules with antiferromagnetic order in the ground state. This can be seen best from an analysis of the rotational and vibrational excitations