Pattern matching and pattern discovery algorithms for protein topologies

We describe algorithms for pattern matching and pattern learning in TOPS diagrams (formal descriptions of protein topologies). These problems can be reduced to checking for subgraph isomorphism and finding maximal common subgraphs in a restricted class of ordered graphs. We have developed a subgraph isomorphism algorithm for ordered graphs, which performs well on the given set of data. The maximal common subgraph problem then is solved by repeated subgraph extension and checking for isomorphisms. Despite the apparent inefficiency such approach gives an algorithm with time complexity proportional to the number of graphs in the input set and is still practical on the given set of data. As a result we obtain fast methods which can be used for building a database of protein topological motifs, and for the comparison of a given protein of known secondary structure against a motif database

Enhanced Fusion-Evaporation Cross Sections in Neutron-Rich 132^{132}Sn on 64^{64}Ni

Evaporation residue cross sections have been measured with neutron-rich radioactive $^{132}$Sn beams on $^{64}$Ni in the vicinity of the Coulomb barrier. The average beam intensity was $2\times 10^{4}$ particles per second and the smallest cross section measured was less than 5 mb. Large subbarrier fusion enhancement was observed. Coupled-channels calculations taking into account inelastic excitation and neutron transfer underpredict the measured cross sections below the barrier.Comment: 4 pages including 1 table and 3 figure

Peculiarities of sub-barrier fusion with quantum diffusion approach

With the quantum diffusion approach the unexpected behavior of fusion cross section, angular momentum, and astrophysical S-factor at sub-barrier energies has been revealed. Out of the region of short-range nuclear interaction and action of friction at turning point the decrease rate of the cross section under the barrier becomes smaller. The calculated results for the reactions with spherical nuclei are in a good agreement with the existing experimental data.Comment: 11 pages, 5 figure

Scale-free memory model for multiagent reinforcement learning. Mean field approximation and rock-paper-scissors dynamics

A continuous time model for multiagent systems governed by reinforcement learning with scale-free memory is developed. The agents are assumed to act independently of one another in optimizing their choice of possible actions via trial-and-error search. To gain awareness about the action value the agents accumulate in their memory the rewards obtained from taking a specific action at each moment of time. The contribution of the rewards in the past to the agent current perception of action value is described by an integral operator with a power-law kernel. Finally a fractional differential equation governing the system dynamics is obtained. The agents are considered to interact with one another implicitly via the reward of one agent depending on the choice of the other agents. The pairwise interaction model is adopted to describe this effect. As a specific example of systems with non-transitive interactions, a two agent and three agent systems of the rock-paper-scissors type are analyzed in detail, including the stability analysis and numerical simulation. Scale-free memory is demonstrated to cause complex dynamics of the systems at hand. In particular, it is shown that there can be simultaneously two modes of the system instability undergoing subcritical and supercritical bifurcation, with the latter one exhibiting anomalous oscillations with the amplitude and period growing with time. Besides, the instability onset via this supercritical mode may be regarded as "altruism self-organization". For the three agent system the instability dynamics is found to be rather irregular and can be composed of alternate fragments of oscillations different in their properties.Comment: 17 pages, 7 figur

Dynamical mean-field approach to materials with strong electronic correlations

We review recent results on the properties of materials with correlated electrons obtained within the LDA+DMFT approach, a combination of a conventional band structure approach based on the local density approximation (LDA) and the dynamical mean-field theory (DMFT). The application to four outstanding problems in this field is discussed: (i) we compute the full valence band structure of the charge-transfer insulator NiO by explicitly including the p-d hybridization, (ii) we explain the origin for the simultaneously occuring metal-insulator transition and collapse of the magnetic moment in MnO and Fe2O3, (iii) we describe a novel GGA+DMFT scheme in terms of plane-wave pseudopotentials which allows us to compute the orbital order and cooperative Jahn-Teller distortion in KCuF3 and LaMnO3, and (iv) we provide a general explanation for the appearance of kinks in the effective dispersion of correlated electrons in systems with a pronounced three-peak spectral function without having to resort to the coupling of electrons to bosonic excitations. These results provide a considerable progress in the fully microscopic investigations of correlated electron materials.Comment: 24 pages, 14 figures, final version, submitted to Eur. Phys. J. for publication in the Special Topics volume "Cooperative Phenomena in Solids: Metal-Insulator Transitions and Ordering of Microscopic Degrees of Freedom

Effect of halo modelling on WIMP exclusion limits

WIMP direct detection experiments are just reaching the sensitivity required to detect galactic dark matter in the form of neutralinos. Data from these experiments are usually analysed under the simplifying assumption that the Milky Way halo is an isothermal sphere with maxwellian velocity distribution. Observations and numerical simulations indicate that galaxy halos are in fact triaxial and anisotropic. Furthermore, in the cold dark matter paradigm galactic halos form via the merger of smaller subhalos, and at least some residual substructure survives. We examine the effect of halo modelling on WIMP exclusion limits, taking into account the detector response. Triaxial and anisotropic halo models, with parameters motivated by observations and numerical simulations, lead to significant changes which are different for different experiments, while if the local WIMP distribution is dominated by small scale clumps then the exclusion limits are changed dramatically.Comment: 9 pages, 9 figures, version to appear in Phys. Rev. D, minor change

Recent experimental results in sub- and near-barrier heavy ion fusion reactions

Recent advances obtained in the field of near and sub-barrier heavy-ion fusion reactions are reviewed. Emphasis is given to the results obtained in the last decade, and focus will be mainly on the experimental work performed concerning the influence of transfer channels on fusion cross sections and the hindrance phenomenon far below the barrier. Indeed, early data of sub-barrier fusion taught us that cross sections may strongly depend on the low-energy collective modes of the colliding nuclei, and, possibly, on couplings to transfer channels. The coupled-channels (CC) model has been quite successful in the interpretation of the experimental evidences. Fusion barrier distributions often yield the fingerprint of the relevant coupled channels. Recent results obtained by using radioactive beams are reported. At deep sub-barrier energies, the slope of the excitation function in a semi-logarithmic plot keeps increasing in many cases and standard CC calculations over-predict the cross sections. This was named a hindrance phenomenon, and its physical origin is still a matter of debate. Recent theoretical developments suggest that this effect, at least partially, may be a consequence of the Pauli exclusion principle. The hindrance may have far-reaching consequences in astrophysics where fusion of light systems determines stellar evolution during the carbon and oxygen burning stages, and yields important information for exotic reactions that take place in the inner crust of accreting neutron stars.Comment: 40 pages, 63 figures, review paper accepted for EPJ

Search for W′→tb→qqbb decays in pp collisions at √s=8 TeV with the ATLAS detector

A search for a massive W′ gauge boson decaying to a top quark and a bottom quark is performed with the ATLAS detector in pp collisions at the LHC. The dataset was taken at a centre-of-mass energy of √s=8 TeV and corresponds to 20.3 fb−1 of integrated luminosity. This analysis is done in the hadronic decay mode of the top quark, where novel jet substructure techniques are used to identify jets from high-momentum top quarks. This allows for a search for high-mass W′ bosons in the range 1.5–3.0 TeV. b-tagging is used to identify jets originating from b-quarks. The data are consistent with Standard Model background-only expectations, and upper limits at 95 % confidence level are set on the W′→tb cross section times branching ratio ranging from 0.16pb to 0.33pb for left-handed W′ bosons, and ranging from 0.10pb to 0.21pb for W′ bosons with purely right-handed couplings. Upper limits at 95 % confidence level are set on the W′-boson coupling to tb as a function of the W′ mass using an effective field theory approach, which is independent of details of particular models predicting a W′boson