Berry phase for a spin 1/2 in a classical fluctuating field

The effect of fluctuations in the classical control parameters on the Berry phase of a spin 1/2 interacting with a adiabatically cyclically varying magnetic field is analyzed. It is explicitly shown that in the adiabatic limit dephasing is due to fluctuations of the dynamical phase.Comment: 4 pages, 1 figure, published versio

Observations Outside the Light-Cone: Algorithms for Non-Equilibrium and Thermal States

We apply algorithms based on Lieb-Robinson bounds to simulate time-dependent and thermal quantities in quantum systems. For time-dependent systems, we modify a previous mapping to quantum circuits to significantly reduce the computer resources required. This modification is based on a principle of "observing" the system outside the light-cone. We apply this method to study spin relaxation in systems started out of equilibrium with initial conditions that give rise to very rapid entanglement growth. We also show that it is possible to approximate time evolution under a local Hamiltonian by a quantum circuit whose light-cone naturally matches the Lieb-Robinson velocity. Asymptotically, these modified methods allow a doubling of the system size that one can obtain compared to direct simulation. We then consider a different problem of thermal properties of disordered spin chains and use quantum belief propagation to average over different configurations. We test this algorithm on one dimensional systems with mixed ferromagnetic and anti-ferromagnetic bonds, where we can compare to quantum Monte Carlo, and then we apply it to the study of disordered, frustrated spin systems.Comment: 19 pages, 12 figure

Entanglement production by quantum error correction in the presence of correlated environment

We analyze the effect of a quantum error correcting code on the entanglement of encoded logical qubits in the presence of a dephasing interaction with a correlated environment. Such correlated reservoir introduces entanglement between physical qubits. We show that for short times the quantum error correction interprets such entanglement as errors and suppresses it. However for longer time, although quantum error correction is no longer able to correct errors, it enhances the rate of entanglement production due to the interaction with the environment.Comment: 7 pages, 3 figures, published versio

Improved Core Genes Prediction for Constructing well-supported Phylogenetic Trees in large sets of Plant Species

The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies, many similarity based algorithms, mainly dependent on calculating sequence alignment matrices, have been proposed to find them. In these kinds of approaches, a significantly high similarity score between two coding sequences extracted from a given annotation tool means that one has the same genes. In a previous work article, we presented a quality test approach (QTA) that improves the core genes quality by combining two annotation tools (namely NCBI, a partially human-curated database, and DOGMA, an efficient annotation algorithm for chloroplasts). This method takes the advantages from both sequence similarity and gene features to guarantee that the core genome contains correct and well-clustered coding sequences (\emph{i.e.}, genes). We then show in this article how useful are such well-defined core genes for biomolecular phylogenetic reconstructions, by investigating various subsets of core genes at various family or genus levels, leading to subtrees with strong bootstraps that are finally merged in a well-supported supertree.Comment: 12 pages, 7 figures, IWBBIO 2015 (3rd International Work-Conference on Bioinformatics and Biomedical Engineering

Genotype influence on shelf life behaviour of minimal processed loquat (Eriobotrya japonica (Thunb.) Lindl.) fruit: the role of sugar, acid organics and phenolic compounds

Background: Loquat cultivars cultivated in Southern Italy are very appreciated by consumers for their sensorial characteristics, such as persistent aroma and taste. Apposite maturity indexes for peeling and processing loquat fruit were investigated to increase diffusion of minimally processed loquat. The genotype’s effect on the minimally processed loquat fruit shelf life and quality harvested at commercial maturity (80% yellow color) was investigated on peeled fruit stored at 5 °C for 10 days. The role of sugars, organic acids and phenols composition was observed through in depth qualitative analysis. In addition, several qualitative analyses were carried out to determine the quality of minimal processed fruit. Results: Loquat fruits harvested at commercial ripening stage performed very good palatability and flesh color persistency. Late ripening fruits genotypes shown a low rate of pulp oxidation and quality decay, while early ripening fruits were not suitable for fresh-cut. Genotype had a great influence on weight loss, β-carotene content, fruit respiration, ascorbic acid and total phenols content during the shelf life. Conclusions: This work shows how the amount of the composition of sugars and organic acids as an intrinsic characteristic of genotype influences the quality of loquat fruits minimal processed. The higher values of glucose, sorbitol and ascorbic acid accumulated in the cv ‘Nespolone Trabia’ contributed to a reduction in chilling injury and oxidative stress after cutting. Graphical Abstract: [Figure not available: see fulltext.

A scheme for entanglement extraction from a solid

Some thermodynamical properties of solids, such as heat capacity and magnetic susceptibility, have recently been shown to be linked to the amount of entanglement in a solid. However this entanglement may appear a mere mathematical artifact of the typical symmetrization procedure of many-body wave function in solid state physics. Here we show that this entanglement is physical demonstrating the principles of its extraction from a typical solid state system by scattering two particles off the system. Moreover we show how to simulate this process using present-day optical lattices technology. This demonstrates not only that entanglement exists in solids but also that it can be used for quantum information processing or for test of Bell's inequalities.Comment: 10 pages, 3 figures, published versio

Experiences with Mesh-like computations using Prediction Binary Trees

In this paper we aim at exploiting the temporal coherence among successive phases of a computation, in order to implement a load-balancing technique in mesh-like computations to be mapped on a cluster of processors. A key concept, on which the load balancing schema is built on, is the use of a Predictor component that is in charge of providing an estimation of the unbalancing between successive phases. By using this information, our method partitions the computation in balanced tasks through the Prediction Binary Tree (PBT). At each new phase, current PBT is updated by using previous phase computing time for each task as next phase's cost estimate. The PBT is designed so that it balances the load across the tasks as well as reduces {\em dependency} among processors for higher performances. Reducing dependency is obtained by using rectangular tiles of the mesh, of almost-square shape (i. e. one dimension is at most twice the other). By reducing dependency, one can reduce inter-processors communication or exploit local dependencies among tasks (such as data locality). Furthermore, we also provide two heuristics which take advantage of data-locality. Our strategy has been assessed on a significant problem, Parallel Ray Tracing. Our implementation shows a good scalability, and improves performance in both cheaper commodity cluster and high performance clusters with low latency networks. We report different measurements showing that tasks granularity is a key point for the performances of our decomposition/mapping strategy

Entanglement evolution after connecting finite to infinite quantum chains

We study zero-temperature XX chains and transverse Ising chains and join an initially separate finite piece on one or on both sides to an infinite remainder. In both critical and non-critical systems we find a typical increase of the entanglement entropy after the quench, followed by a slow decay towards the value of the homogeneous chain. In the critical case, the predictions of conformal field theory are verified for the first phase of the evolution, while at late times a step structure can be observed.Comment: 15 pages, 11 figure

Optimal control of atom transport for quantum gates in optical lattices

By means of optimal control techniques we model and optimize the manipulation of the external quantum state (center-of-mass motion) of atoms trapped in adjustable optical potentials. We consider in detail the cases of both non interacting and interacting atoms moving between neighboring sites in a lattice of a double-well optical potentials. Such a lattice can perform interaction-mediated entanglement of atom pairs and can realize two-qubit quantum gates. The optimized control sequences for the optical potential allow transport faster and with significantly larger fidelity than is possible with processes based on adiabatic transport.Comment: revised version: minor changes, 2 references added, published versio

Targeting cytosolic proliferating cell nuclear antigen in neutrophil-dominated inflammation.

New therapeutic approaches that can accelerate neutrophil apoptosis under inflammatory conditions to enhance the resolution of inflammation are now under study. Neutrophils are deprived of proliferative capacity and have a tightly controlled lifespan to avoid their persistence at the site of injury. We have recently described that the proliferating cell nuclear antigen (PCNA), a nuclear factor involved in DNA replication and repair of proliferating cells is a key regulator of neutrophil survival. The nuclear-to-cytoplasmic relocalization occurred during granulocytic differentiation and is dependent on a nuclear export sequence thus strongly suggesting that PCNA has physiologic cytoplasmic functions. In this review, we will try to put into perspective the physiologic relevance of PCNA in neutrophils. We will discuss key issues such as molecular structure, post-translational modifications, based on our knowledge of nuclear PCNA, assuming that similar principles governing its function are conserved between nuclear and cytosolic PCNA. The example of cystic fibrosis that features one of the most intense neutrophil-dominated pulmonary inflammation will be discussed. We believe that through an intimate comprehension of the cytosolic PCNA scaffold based on nuclear PCNA knowledge, novel pathways regulating neutrophil survival can be unraveled and innovative agents can be developed to dampen inflammation where it proves detrimental