A quasi-Newton approach to optimization problems with probability density constraints

A quasi-Newton method is presented for minimizing a nonlinear function while constraining the variables to be nonnegative and sum to one. The nonnegativity constraints were eliminated by working with the squares of the variables and the resulting problem was solved using Tapia's general theory of quasi-Newton methods for constrained optimization. A user's guide for a computer program implementing this algorithm is provided

Mechanical Unfolding of a Simple Model Protein Goes Beyond the Reach of One-Dimensional Descriptions

We study the mechanical unfolding of a simple model protein. The Langevin dynamics results are analyzed using Markov-model methods which allow to describe completely the configurational space of the system. Using transition path theory we also provide a quantitative description of the unfolding pathways followed by the system. Our study shows a complex dynamical scenario. In particular, we see that the usual one-dimensional picture: free-energy vs end-to-end distance representation, gives a misleading description of the process. Unfolding can occur following different pathways and configurations which seem to play a central role in one-dimensional pictures are not the intermediate states of the unfolding dynamics.Comment: 10 pages, 6 figure

Separable Measurement Estimation of Density Matrices and its Fidelity Gap with Collective Protocols

We show that there exists a gap between the performance of separable and collective measurements in qubit mixed-state estimation that persists in the large sample limit. We characterize such gap in terms of the corresponding bounds on the mean fidelity. We present an adaptive protocol that attains the separable-measurement bound. This (optimal separable) protocol uses von Neumann measurements and can be easily implemented with current technology.Comment: version published in PR

Optimal full estimation of qubit mixed states

We obtain the optimal scheme for estimating unknown qubit mixed states when an arbitrary number N of identically prepared copies is available. We discuss the case of states in the whole Bloch sphere as well as the restricted situation where these states are known to lie on the equatorial plane. For the former case we obtain that the optimal measurement does not depend on the prior probability distribution provided it is isotropic. Although the equatorial-plane case does not have this property for arbitrary N, we give a prior-independent scheme which becomes optimal in the asymptotic limit of large N. We compute the maximum mean fidelity in this asymptotic regime for the two cases. We show that within the pointwise estimation approach these limits can be obtained in a rather easy and rapid way. This derivation is based on heuristic arguments that are made rigorous by using van Trees inequalities. The interrelation between the estimation of the purity and the direction of the state is also discussed. In the general case we show that they correspond to independent estimations whereas for the equatorial-plane states this is only true asymptotically.Comment: 19 pages, no figure

Universal field equations for metric-affine theories of gravity

We show that almost all metric--affine theories of gravity yield Einstein equations with a non--null cosmological constant $\Lambda$. Under certain circumstances and for any dimension, it is also possible to incorporate a Weyl vector field $W_\mu$ and therefore the presence of an anisotropy. The viability of these field equations is discussed in view of recent astrophysical observations.Comment: 13 pages. This is a copy of the published paper. We are posting it here because of the increasing interest in f(R) theories of gravit

How to hide a secret direction

We present a procedure to share a secret spatial direction in the absence of a common reference frame using a multipartite quantum state. The procedure guarantees that the parties can determine the direction if they perform joint measurements on the state, but fail to do so if they restrict themselves to local operations and classical communication (LOCC). We calculate the fidelity for joint measurements, give bounds on the fidelity achievable by LOCC, and prove that there is a non-vanishing gap between the two of them, even in the limit of infinitely many copies. The robustness of the procedure under particle loss is also studied. As a by-product we find bounds on the probability of discriminating by LOCC between the invariant subspaces of total angular momentum N/2 and N/2-1 in a system of N elementary spins.Comment: 4 pages, 1 figur

Mesoscopic Model for Free Energy Landscape Analysis of DNA sequences

A mesoscopic model which allows us to identify and quantify the strength of binding sites in DNA sequences is proposed. The model is based on the Peyrard-Bishop-Dauxois model for the DNA chain coupled to a Brownian particle which explores the sequence interacting more importantly with open base pairs of the DNA chain. We apply the model to promoter sequences of different organisms. The free energy landscape obtained for these promoters shows a complex structure that is strongly connected to their biological behavior. The analysis method used is able to quantify free energy differences of sites within genome sequences.Comment: 7 pages, 5 figures, 1 tabl

Temporal evolution of short-lived penumbral microjets

Context. Penumbral microjets are elongated jet-like brightenings observed in the chromosphere above sunspot penumbrae. They are transient events that last from a few seconds to several minutes and are thought to originate from magnetic reconnection processes. Previous studies have mainly focused on their morphological and spectral characteristics, and more recently on their spectropolarimetric signals during the maximum brightness stage. Studies addressing the temporal evolution of PMJs have also been carried out, but they are based on spatial and spectral time variations only. Aims. Here we investigate the temporal evolution of the polarization signals produced by short-lived PMJs (lifetimes $<$ 2 minutes) to infer how the magnetic field vector evolves in the upper photosphere and mid-chromosphere. Methods. We use fast-cadence spectropolarimetric observations of the Ca II 854.2 nm line taken with the CRisp Imaging Spectropolarimeter at the Swedish 1-m Solar Telescope. The weak-field approximation (WFA) is used to estimate the strength and inclination of the magnetic field vector. Results. The WFA reveals larger magnetic field changes in the upper photosphere than in the chromosphere during the PMJ maximum brightness stage. In the photosphere, the magnetic field inclination and strength undergo a transient increase for most PMJs, but in 25$\%$ of the cases the field strength decreases during the brightening. In the chromosphere, the magnetic field tends to be slightly stronger during the PMJs. Conclusions. The propagation of compressive perturbation fronts followed by a rarefaction phase in the aftershock region may explain the observed behavior of the magnetic field vector. The fact that such behavior varies among the analyzed PMJs could be a consequence of the limited temporal resolution of the observations and the fast-evolving nature of the PMJs.Comment: Paper accepted for publication in section 9. The Sun and the Heliosphere of Astronomy and Astrophysics. 18 pages, 21 figure

On the geometry of four qubit invariants

The geometry of four-qubit entanglement is investigated. We replace some of the polynomial invariants for four-qubits introduced recently by new ones of direct geometrical meaning. It is shown that these invariants describe four points, six lines and four planes in complex projective space ${\bf CP}^3$. For the generic entanglement class of stochastic local operations and classical communication they take a very simple form related to the elementary symmetric polynomials in four complex variables. Moreover, their magnitudes are entanglement monotones that fit nicely into the geometric set of $n$-qubit ones related to Grassmannians of $l$-planes found recently. We also show that in terms of these invariants the hyperdeterminant of order 24 in the four-qubit amplitudes takes a more instructive form than the previously published expressions available in the literature. Finally in order to understand two, three and four-qubit entanglement in geometric terms we propose a unified setting based on ${\bf CP}^3$ furnished with a fixed quadric.Comment: 19 page