112,389 research outputs found
Calculating Biological Behaviors of Epigenetic States in Phage lambda Life Cycle
Gene regulatory network of lambda phage is one the best studied model systems
in molecular biology. More 50 years of experimental study has provided a
tremendous amount of data at all levels: physics, chemistry, DNA, protein, and
function. However, its stability and robustness for both wild type and mutants
has been a notorious theoretical/mathematical problem. In this paper we report
our successful calculation on the properties of this gene regulatory network.
We believe it is of its first kind. Our success is of course built upon
numerous previous theoretical attempts, but following 3 features make our
modeling uniqu:
1) A new modeling method particular suitable for stability and robustness
study;
2) Paying a close attention to the well-known difference of in vivo and in
vitro;
3) Allowing more important role for noise and stochastic effect to play.
The last two points have been discussed by two of us (Ao and Yin,
cond-mat/0307747), which we believe would be enough to make some of previous
theoretical attempts successful, too. We hope the present work would stimulate
a further interest in the emerging field of gene regulatory network.Comment: 16 pages, 3 figures, 1 tabl
Trapped ion quantum computation with transverse phonon modes
We propose a scheme to implement quantum gates on any pair of trapped ions
immersed in a large linear crystal, using interaction mediated by the
transverse phonon modes. Compared with the conventional approaches based on the
longitudinal phonon modes, this scheme is much less sensitive to ion heating
and thermal motion outside of the Lamb-Dicke limit thanks to the stronger
confinement in the transverse direction. The cost for such a gain is only a
moderate increase of the laser power to achieve the same gate speed. We also
show how to realize arbitrary-speed quantum gates with transverse phonon modes
based on simple shaping of the laser pulses.Comment: 5 page
Geometric quantum gates robust against stochastic control errors
We analyze a scheme for quantum computation where quantum gates can be
continuously changed from standard dynamic gates to purely geometric ones.
These gates are enacted by controlling a set of parameters that are subject to
unwanted stochastic fluctuations. This kind of noise results in a departure
from the ideal case that can be quantified by a gate fidelity. We find that the
maximum of this fidelity corresponds to quantum gates with a vanishing
dynamical phase.Comment: 4 pager
Dynamic microscopic structures and dielectric response in the cubic-to-tetragonal phase transition for BaTiO3 studied by first-principles molecular dynamics simulation
The dynamic structures of the cubic and tetragonal phase in BaTiO3 and its
dielectric response above the cubic-to-tetragonal phase transition temperature
(Tp) are studied by first-principles molecular dynamics (MD) simulation. It's
shown that the phase transition is due to the condensation of one of the
transverse correlations. Calculation of the phonon properties for both the
cubic and tetragonal phase shows a saturation of the soft mode frequency near
60 cm-1 near Tp and advocates its order-disorder nature. Our first-principles
calculation leads directly to a two modes feature of the dielectric function
above Tp [Phys. Rev. B 28, 6097 (1983)], which well explains the long time
controversies between experiments and theories
Implementation of universal quantum gates based on nonadiabatic geometric phases
We propose an experimentally feasible scheme to achieve quantum computation
based on nonadiabatic geometric phase shifts, in which a cyclic geometric phase
is used to realize a set of universal quantum gates. Physical implementation of
this set of gates is designed for Josephson junctions and for NMR systems.
Interestingly, we find that the nonadiabatic phase shift may be independent of
the operation time under appropriate controllable conditions. A remarkable
feature of the present nonadiabatic geometric gates is that there is no
intrinsic limitation on the operation time, unlike adiabatic geometric gates.
Besides fundamental interest, our results may simplify the implementation of
geometric quantum computation based on solid state systems, where the
decoherence time may be very short.Comment: 5 pages, 2 figures; the version published in Phys. Rev. Let
Arbitrary-speed quantum gates within large ion crystals through minimum control of laser beams
We propose a scheme to implement arbitrary-speed quantum entangling gates on
two trapped ions immersed in a large linear crystal of ions, with minimal
control of laser beams. For gate speeds slower than the oscillation frequencies
in the trap, a single appropriately-detuned laser pulse is sufficient for
high-fidelity gates. For gate speeds comparable to or faster than the local ion
oscillation frequency, we discover a five-pulse protocol that exploits only the
local phonon modes. This points to a method for efficiently scaling the ion
trap quantum computer without shuttling ions.Comment: 4 page
Elastic forward scattering in the cuprate superconducting state
We investigate the effect of elastic forward scattering on the ARPES spectrum
of the cuprate superconductors. In the normal state, small angle scattering
from out-of-plane impurities is thought to broaden the ARPES spectral response
with minimal effect on the resistivity or the superconducting transition
temperature . Here we explore how such forward scattering affects the
ARPES spectrum in the d-wave superconducting state. Away from the nodal
direction, the one-electron impurity scattering rate is found to be suppressed
as approaches the gap edge by a cancellation between normal and
anomalous scattering processes, leading to a square-root-like feature in the
spectral weight as approaches -\Delta_\k from below. For momenta
away from the Fermi surface, our analysis suggests that a dirty optimally or
overdoped system will still display a sharp but nondispersive peak which could
be confused with a quasiparticle spectral feature. Only in cleaner samples
should the true dispersing quasiparticle peak become visible. At the nodal
point on the Fermi surface, the contribution of the anomalous scattering
vanishes and the spectral weight exhibits a Lorentzian quasiparticle peak in
both energy and momentum.
Our analysis, including a treatment of unitary scatterers and inelastic spin
fluctuation scattering, suggests explanations for the sometimes mysterious
lineshapes and temperature dependences of the peak structures observed in the
\BSCCO system.Comment: 12 pages, 14 figure
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