Pattern matching and pattern discovery algorithms for protein topologies

We describe algorithms for pattern matching and pattern learning in TOPS diagrams (formal descriptions of protein topologies). These problems can be reduced to checking for subgraph isomorphism and finding maximal common subgraphs in a restricted class of ordered graphs. We have developed a subgraph isomorphism algorithm for ordered graphs, which performs well on the given set of data. The maximal common subgraph problem then is solved by repeated subgraph extension and checking for isomorphisms. Despite the apparent inefficiency such approach gives an algorithm with time complexity proportional to the number of graphs in the input set and is still practical on the given set of data. As a result we obtain fast methods which can be used for building a database of protein topological motifs, and for the comparison of a given protein of known secondary structure against a motif database

Quantum computation in a Ising spin chain taking into account second neighbor couplings

We consider the realization of a quantum computer in a chain of nuclear spins coupled by an Ising interaction. Quantum algorithms can be performed with the help of appropriate radio-frequency pulses. In addition to the standard nearest-neighbor Ising coupling, we also allow for a second neighbor coupling. It is shown, how to apply the 2\pi k method in this more general setting, where the additional coupling eventually allows to save a few pulses. We illustrate our results with two numerical simulations: the Shor prime factorization of the number 4 and the teleportation of a qubit along a chain of 3 qubits. In both cases, the optimal Rabi frequency (to suppress non-resonant effects) depends primarily on the strength of the second neighbor interaction.Comment: 19 pages, 6 figure

Szeg\"o kernel asymptotics and Morse inequalities on CR manifolds

We consider an abstract compact orientable Cauchy-Riemann manifold endowed with a Cauchy-Riemann complex line bundle. We assume that the manifold satisfies condition Y(q) everywhere. In this paper we obtain a scaling upper-bound for the Szeg\"o kernel on (0, q)-forms with values in the high tensor powers of the line bundle. This gives after integration weak Morse inequalities, analogues of the holomorphic Morse inequalities of Demailly. By a refined spectral analysis we obtain also strong Morse inequalities which we apply to the embedding of some convex-concave manifolds.Comment: 40 pages, the constants in Theorems 1.1-1.8 have been modified by a multiplicative constant 1/2 ; v.2 is a final updat

Atom focusing by far-detuned and resonant standing wave fields: Thin lens regime

The focusing of atoms interacting with both far-detuned and resonant standing wave fields in the thin lens regime is considered. The thin lens approximation is discussed quantitatively from a quantum perspective. Exact quantum expressions for the Fourier components of the density (that include all spherical aberration) are used to study the focusing numerically. The following lens parameters and density profiles are calculated as functions of the pulsed field area $\theta$: the position of the focal plane, peak atomic density, atomic density pattern at the focus, focal spot size, depth of focus, and background density. The lens parameters are compared to asymptotic, analytical results derived from a scalar diffraction theory for which spherical aberration is small but non-negligible ($\theta \gg 1$). Within the diffraction theory analytical expressions show that the focused atoms in the far detuned case have an approximately constant background density $0.5(1-0.635\theta ^{- 1/2})$ while the peak density behaves as $$, the focal distance or time as $\theta ^{-1}(1+1.27\theta ^{- 1/2})$, the focal spot size as $0.744\theta ^{-3/4}$, and the depth of focus as $1.91\theta ^{- 3/2}$. Focusing by the resonant standing wave field leads to a new effect, a Rabi- like oscillation of the atom density. For the far-detuned lens, chromatic aberration is studied with the exact Fourier results. Similarly, the degradation of the focus that results from angular divergence in beams or thermal velocity distributions in traps is studied quantitatively with the exact Fourier method and understood analytically using the asymptotic results. Overall, we show that strong thin lens focusing is possible with modest laser powers and with currently achievable atomic beam characteristics.Comment: 21 pages, 11 figure

Characteristics of Quantum-Classical Correspondence for Two Interacting Spins

The conditions of quantum-classical correspondence for a system of two interacting spins are investigated. Differences between quantum expectation values and classical Liouville averages are examined for both regular and chaotic dynamics well beyond the short-time regime of narrow states. We find that quantum-classical differences initially grow exponentially with a characteristic exponent consistently larger than the largest Lyapunov exponent. We provide numerical evidence that the time of the break between the quantum and classical predictions scales as log(${\cal J}/ \hbar$), where ${\cal J}$ is a characteristic system action. However, this log break-time rule applies only while the quantum-classical deviations are smaller than order hbar. We find that the quantum observables remain well approximated by classical Liouville averages over long times even for the chaotic motions of a few degree-of-freedom system. To obtain this correspondence it is not necessary to introduce the decoherence effects of a many degree-of-freedom environment.Comment: New introduction, accepted in Phys Rev A (May 2001 issue), 12 latex figures, 3 ps figure

Hard Photodisintegration of a Proton Pair

We present a study of high energy photodisintegration of proton-pairs through the gamma + 3He -> p+p+n channel. Photon energies from 0.8 to 4.7 GeV were used in kinematics corresponding to a proton pair with high relative momentum and a neutron nearly at rest. The s-11 scaling of the cross section, as predicted by the constituent counting rule for two nucleon photodisintegration, was observed for the first time. The onset of the scaling is at a higher energy and the cross section is significantly lower than for deuteron (pn pair) photodisintegration. For photon energies below the scaling region, the scaled cross section was found to present a strong energy-dependent structure not observed in deuteron photodisintegration.Comment: 7 pages, 3 figures, for submission to Phys. Lett.

Environment-Induced Decoherence and the Transition From Quantum to Classical

We study dynamics of quantum open systems, paying special attention to those aspects of their evolution which are relevant to the transition from quantum to classical. We begin with a discussion of the conditional dynamics of simple systems. The resulting models are straightforward but suffice to illustrate basic physical ideas behind quantum measurements and decoherence. To discuss decoherence and environment-induced superselection einselection in a more general setting, we sketch perturbative as well as exact derivations of several master equations valid for various systems. Using these equations we study einselection employing the general strategy of the predictability sieve. Assumptions that are usually made in the discussion of decoherence are critically reexamined along with the ``standard lore'' to which they lead. Restoration of quantum-classical correspondence in systems that are classically chaotic is discussed. The dynamical second law -it is shown- can be traced to the same phenomena that allow for the restoration of the correspondence principle in decohering chaotic systems (where it is otherwise lost on a very short time-scale). Quantum error correction is discussed as an example of an anti-decoherence strategy. Implications of decoherence and einselection for the interpretation of quantum theory are briefly pointed out.Comment: 80 pages, 7 figures included, Lectures given by both authors at the 72nd Les Houches Summer School on "Coherent Matter Waves", July-August 199

Complete measurement of three-body photodisintegration of 3He for photon energies between 0.35 and 1.55 GeV

The three-body photodisintegration of 3He has been measured with the CLAS detector at Jefferson Lab, using tagged photons of energies between 0.35 GeV and 1.55 GeV. The large acceptance of the spectrometer allowed us for the first time to cover a wide momentum and angular range for the two outgoing protons. Three kinematic regions dominated by either two- or three-body contributions have been distinguished and analyzed. The measured cross sections have been compared with results of a theoretical model, which, in certain kinematic ranges, have been found to be in reasonable agreement with the data.Comment: 22 pages, 25 eps figures, 2 tables, submitted to PRC. Modifications: removed 2 figures, improvements on others, a few minor modifications to the tex