Gradual sub-lattice reduction and a new complexity for factoring polynomials

We present a lattice algorithm specifically designed for some classical applications of lattice reduction. The applications are for lattice bases with a generalized knapsack-type structure, where the target vectors are boundably short. For such applications, the complexity of the algorithm improves traditional lattice reduction by replacing some dependence on the bit-length of the input vectors by some dependence on the bound for the output vectors. If the bit-length of the target vectors is unrelated to the bit-length of the input, then our algorithm is only linear in the bit-length of the input entries, which is an improvement over the quadratic complexity floating-point LLL algorithms. To illustrate the usefulness of this algorithm we show that a direct application to factoring univariate polynomials over the integers leads to the first complexity bound improvement since 1984. A second application is algebraic number reconstruction, where a new complexity bound is obtained as well

An Exact Algorithm for Side-Chain Placement in Protein Design

Computational protein design aims at constructing novel or improved functions on the structure of a given protein backbone and has important applications in the pharmaceutical and biotechnical industry. The underlying combinatorial side-chain placement problem consists of choosing a side-chain placement for each residue position such that the resulting overall energy is minimum. The choice of the side-chain then also determines the amino acid for this position. Many algorithms for this NP-hard problem have been proposed in the context of homology modeling, which, however, reach their limits when faced with large protein design instances. In this paper, we propose a new exact method for the side-chain placement problem that works well even for large instance sizes as they appear in protein design. Our main contribution is a dedicated branch-and-bound algorithm that combines tight upper and lower bounds resulting from a novel Lagrangian relaxation approach for side-chain placement. Our experimental results show that our method outperforms alternative state-of-the art exact approaches and makes it possible to optimally solve large protein design instances routinely

On the consistency of de Sitter vacua

In this paper the consistency of the de Sitter invariant $\alpha$-vacua, which have been introduced as simple tools to study the effects of transplanckian physics, is investigated. In particular possible non renormalization problems are discussed, as well as non standard properties of Greens functions. We also discuss the non thermal properties of the $\alpha$-vacua and the necessity of $\alpha$ to change. The conclusion is that non of these problems necessarily exclude an application of the $\alpha$-vacua to inflation.Comment: 12 pages, v2: minor clarifications and corrections to reference

Squeezed States in the de Sitter Vacuum

We discuss the treatment of squeezed states as excitations in the Euclidean vacuum of de Sitter space. A comparison with the treatment of these states as candidate no-particle states, or alpha-vacua, shows important differences already in the free theory. At the interacting level alpha-vacua are inconsistent, but squeezed state excitations seem perfectly acceptable. Indeed, matrix elements can be renormalized in the excited states using precisely the standard local counterterms of the Euclidean vacuum. Implications for inflationary scenarios in cosmology are discussed.Comment: 15 pages, no figures. One new citation in version 3; no other change

Quantum Search with Two-atom Collisions in Cavity QED

We propose a scheme to implement two-qubit Grover's quantum search algorithm using Cavity Quantum Electrodynamics. Circular Rydberg atoms are used as quantum bits (qubits). They interact with the electromagnetic field of a non-resonant cavity . The quantum gate dynamics is provided by a cavity-assisted collision, robust against decoherence processes. We present the detailed procedure and analyze the experimental feasibility.Comment: 4 pages, 2 figure

On Thermalization in de Sitter Space

We discuss thermalization in de Sitter space and argue, from two different points of view, that the typical time needed for thermalization is of order $R^{3}/l_{pl}^{2}$, where $R$ is the radius of the de Sitter space in question. This time scale gives plenty of room for non-thermal deviations to survive during long periods of inflation. We also speculate in more general terms on the meaning of the time scale for finite quantum systems inside isolated boxes, and comment on the relation to the Poincar\'{e} recurrence time.Comment: 14 pages, 2 figures, latex, references added. Improved discussion in section 3 adde

Modification to the power spectrum in the brane world inflation driven by the bulk inflaton

We compute the cosmological perturbations generated in the brane world inflation driven by the bulk inflaton. Different from the model that the inflation is a brane effect, we exhibit the modification of the power spectrum of scalar perturbations due to the existence of the fifth dimension. With the change of the initial vacuum, we investigate the dependence of the correction of the power spectrum on the choice of the vacuum.Comment: replaced with the revised version, accepted for publication in PR

Primeval Corrections to the CMB Anisotropies

We show that deviations of the quantum state of the inflaton from the thermal vacuum of inflation may leave an imprint in the CMB anisotropies. The quantum dynamics of the inflaton in such a state produces corrections to the inflationary fluctuations, which may be observable. Because these effects originate from IR physics below the Planck scale, they will dominate over any trans-Planckian imprints in any theory which obeys decoupling. Inflation sweeps away these initial deviations and forces its quantum state closer to the thermal vacuum. We view this as the quantum version of the cosmic no-hair theorem. Such imprints in the CMB may be a useful, independent test of the duration of inflation, or of significant features in the inflaton potential about 60 e-folds before inflation ended, instead of an unlikely discovery of the signatures of quantum gravity. The absence of any such substructure would suggest that inflation lasted uninterrupted much longer than ${\cal O}(100)$ e-folds.Comment: 17 pages, latex, no figures; v3: added references and comments, final version to appear in Phys. Rev.

A comment on multiple vacua, particle production and the time dependent AdS/CFT correspondence

We give an explicit formulation of the time dependent AdS/CFT correspondence when there are multiple vacua present in Lorentzian signature. By computing sample two point functions we show how different amplitudes are related by cosmological particle production. We illustrate our methods in two example spacetimes: (a) a ``bubble of nothing'' in AdS space, and (b) an asymptotically locally AdS spacetime with a bubble of nothing on the boundary. In both cases the alpha vacua of de Sitter space make an interesting appearance.Comment: 9 page

The long-time dynamics of two hydrodynamically-coupled swimming cells

Swimming micro-organisms such as bacteria or spermatozoa are typically found in dense suspensions, and exhibit collective modes of locomotion qualitatively different from that displayed by isolated cells. In the dilute limit where fluid-mediated interactions can be treated rigorously, the long-time hydrodynamics of a collection of cells result from interactions with many other cells, and as such typically eludes an analytical approach. Here we consider the only case where such problem can be treated rigorously analytically, namely when the cells have spatially confined trajectories, such as the spermatozoa of some marine invertebrates. We consider two spherical cells swimming, when isolated, with arbitrary circular trajectories, and derive the long-time kinematics of their relative locomotion. We show that in the dilute limit where the cells are much further away than their size, and the size of their circular motion, a separation of time scale occurs between a fast (intrinsic) swimming time, and a slow time where hydrodynamic interactions lead to change in the relative position and orientation of the swimmers. We perform a multiple-scale analysis and derive the effective dynamical system - of dimension two - describing the long-time behavior of the pair of cells. We show that the system displays one type of equilibrium, and two types of rotational equilibrium, all of which are found to be unstable. A detailed mathematical analysis of the dynamical systems further allows us to show that only two cell-cell behaviors are possible in the limit of $t\to\infty$, either the cells are attracted to each other (possibly monotonically), or they are repelled (possibly monotonically as well), which we confirm with numerical computations