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 $T_c$. 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 $\omega$ 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 $\omega$ 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