Constraint optimization and landscapes

We describe an effective landscape introduced in [1] for the analysis of Constraint Satisfaction problems, such as Sphere Packing, K-SAT and Graph Coloring. This geometric construction reexpresses these problems in the more familiar terms of optimization in rugged energy landscapes. In particular, it allows one to understand the puzzling fact that unsophisticated programs are successful well beyond what was considered to be the `hard' transition, and suggests an algorithm defining a new, higher, easy-hard frontier.Comment: Contribution to STATPHYS2

A New Simulated Annealing Algorithm for the Multiple Sequence Alignment Problem: The approach of Polymers in a Random Media

We proposed a probabilistic algorithm to solve the Multiple Sequence Alignment problem. The algorithm is a Simulated Annealing (SA) that exploits the representation of the Multiple Alignment between $D$ sequences as a directed polymer in $D$ dimensions. Within this representation we can easily track the evolution in the configuration space of the alignment through local moves of low computational cost. At variance with other probabilistic algorithms proposed to solve this problem, our approach allows for the creation and deletion of gaps without extra computational cost. The algorithm was tested aligning proteins from the kinases family. When D=3 the results are consistent with those obtained using a complete algorithm. For $D>3$ where the complete algorithm fails, we show that our algorithm still converges to reasonable alignments. Moreover, we study the space of solutions obtained and show that depending on the number of sequences aligned the solutions are organized in different ways, suggesting a possible source of errors for progressive algorithms.Comment: 7 pages and 11 figure

A very fast inference algorithm for finite-dimensional spin glasses: Belief Propagation on the dual lattice

Starting from a Cluster Variational Method, and inspired by the correctness of the paramagnetic Ansatz (at high temperatures in general, and at any temperature in the 2D Edwards-Anderson model) we propose a novel message passing algorithm --- the Dual algorithm --- to estimate the marginal probabilities of spin glasses on finite dimensional lattices. We show that in a wide range of temperatures our algorithm compares very well with Monte Carlo simulations, with the Double Loop algorithm and with exact calculation of the ground state of 2D systems with bimodal and Gaussian interactions. Moreover it is usually 100 times faster than other provably convergent methods, as the Double Loop algorithm.Comment: 23 pages, 12 figures. v2: improved introductio

Zero temperature solutions of the Edwards-Anderson model in random Husimi Lattices

We solve the Edwards-Anderson model (EA) in different Husimi lattices. We show that, at T=0, the structure of the solution space depends on the parity of the loop sizes. Husimi lattices with odd loop sizes have always a trivial paramagnetic solution stable under 1RSB perturbations while, in Husimi lattices with even loop sizes, this solution is absent. The range of stability under 1RSB perturbations of this and other RS solutions is computed analytically (when possible) or numerically. We compute the free-energy, the complexity and the ground state energy of different Husimi lattices at the level of the 1RSB approximation. We also show, when the fraction of ferromagnetic couplings increases, the existence, first, of a discontinuous transition from a paramagnetic to a spin glass phase and latter of a continuous transition from a spin glass to a ferromagnetic phase.Comment: 20 pages, 10 figures (v3: Corrected analysis of transitions. Appendix proof fixed

Mutual antagonism of target of rapamycin and calcineurin signaling

Growth and stress are generally incompatible states. Stressed cells adapt to an insult by restraining growth, and conversely, growing cells keep stress responses at bay. This is evident in many physiological settings, including for example, the effect of stress on the immune or nervous system, but the underlying signaling mechanisms mediating such mutual antagonism are poorly understood. In eukaryotes, a central activator of cell growth is the protein kinase target of rapamycin (TOR) and its namesake signaling network. Calcineurin is a conserved, Ca(2+)/calmodulin-dependent protein phosphatase and target of the immunosuppressant FK506 (tacrolimus) that is activated in yeast during stress to promote cell survival. Here we show yeast mutants defective for TOR complex 2 (TORC2) or the essential homologous TORC2 effectors, SLM1 and SLM2, exhibited constitutive activation of calcineurin-dependent transcription and actin depolarization. Conversely, cells defective in calcineurin exhibited SLM1 hyperphosphorylation and enhanced interaction between TORC2 and SLM1. Furthermore, a mutant SLM1 protein (SLM1(DeltaC14)) lacking a sequence related to the consensus calcineurin docking site (PxIxIT) was insensitive to calcineurin, and SLM1(Delta)(C14) slm2 mutant cells were hypersensitive to oxidative stress. Thus, TORC2-SLM signaling negatively regulates calcineurin, and calcineurin negatively regulates TORC2-SLM. These findings provide a molecular basis for the mutual antagonism of growth and stress

Mutual optical injection in coupled DBR laser pairs

We report an experimental study of nonlinear effects, characteristic of mutual optical coupling, in an ultra-short coupling regime observed in a distributed Bragg reflector laser pair fabricated on the same chip. Optical feedback is amplified via a double pass through a common onchip optical amplifier, which introduces further nonlinear phenomena. Optical coupling has been introduced via back reflection from a cleaveended fibre. The coupling may be varied in strength by varying the distance of the fibre from the output of the chip, without significantly affecting the coupling time. © 2008 Optical. Society of America

Bacterial membrane injuries induced by lactacin F and nisin

The combined action of nisin and lactacin F, two bacteriocins produced by lactic acid bacteria, is additive. In this report, the basis of this effect is examined. Channels formed by lactacin F were studied by experiments using planar lipid bilayers, and bactericidal effects were analyzed by flow cytometry. Lactacin F produced pores with a conductance of 1 ns in black lipid bilayers in 1 mM KClat 10 mV at 20°C. Pore formation was strongly dependent on voltage. Although lactacin F formed pores at very low potential (10 mV), the dependence was exponentialabov e 40 mV. The injuries induced by nisin and lactacin F in the membranes of Lactobacillus helveticus produced different flow cytometric profiles. Probably, when both bacteriocins are present, each acts separately; their cooperation may be due to an increase in the number of single membrane injuries

Coloring random graphs

We study the graph coloring problem over random graphs of finite average connectivity $c$. Given a number $q$ of available colors, we find that graphs with low connectivity admit almost always a proper coloring whereas graphs with high connectivity are uncolorable. Depending on $q$, we find the precise value of the critical average connectivity $c_q$. Moreover, we show that below $c_q$ there exist a clustering phase $c\in [c_d,c_q]$ in which ground states spontaneously divide into an exponential number of clusters and where the proliferation of metastable states is responsible for the onset of complexity in local search algorithms.Comment: 4 pages, 1 figure, version to app. in PR

Two-frequency emission and polarization dynamics at lasing threshold in vertical-cavity surface-emitting lasers

11 pages, 16 figures.-- PACS nrs.: 42.55.Px, 42.60.Mi, 42.65.Sf.We investigate experimentally and theoretically the polarization dynamics in vertical-cavity surface-emitting lasers in the vicinity of the lasing threshold. If the net gain anisotropy between the two orthogonally polarized modes is close to zero, the laser operates in a partially polarized state. This state occurs at and slightly above the lasing threshold. It is characterized by anticorrelated dynamics of the two modes which result from completely anticorrelated dynamics at low frequencies and correlated dynamics on the time scale of the relaxation oscillations. If the net anisotropy is changed by a change of the detuning between the cavity resonance and the gain maximum, one of the two linear polarization states is selected depending on the sign of the net gain. For one sign the well-known phenomenon of polarization switching is recovered at higher currents. The experimental results show very good agreement with simulations based on a model that takes into account nonlinear spin dynamics and linear temperature-dependent detuning effects.M.S., M.W., and T.A. gratefully acknowledge financial support by the Deutsche Forschungsgemeinschaft and the Deutsche Akademische Austauschdienst and thank W. Lange for his support and stimulating discussions. S.B. and J.M. gratefully acknowledge financial support by VISTA HCTMR BFM-2000-1108 and TIC 99-0645-C05-02.Peer reviewe