410 research outputs found
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 : 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 (). Within the diffraction theory
analytical expressions show that the focused atoms in the far detuned case have
an approximately constant background density
while the peak density behaves as , the focal distance or
time as , the focal spot size as
, and the depth of focus as .
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(), where 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.
The Trauma Risk Management Approach to Post-Traumatic Stress Disorder in the British Military: Masculinity, Biopolitics and Depoliticisation
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
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