Is protein folding problem really a NP-complete one ? First investigations

To determine the 3D conformation of proteins is a necessity to understand their functions or interactions with other molecules. It is commonly admitted that, when proteins fold from their primary linear structures to their final 3D conformations, they tend to choose the ones that minimize their free energy. To find the 3D conformation of a protein knowing its amino acid sequence, bioinformaticians use various models of different resolutions and artificial intelligence tools, as the protein folding prediction problem is a NP complete one. More precisely, to determine the backbone structure of the protein using the low resolution models (2D HP square and 3D HP cubic), by finding the conformation that minimize free energy, is intractable exactly. Both the proof of NP-completeness and the 2D prediction consider that acceptable conformations have to satisfy a self-avoiding walk (SAW) requirement, as two different amino acids cannot occupy a same position in the lattice. It is shown in this document that the SAW requirement considered when proving NP-completeness is different from the SAW requirement used in various prediction programs, and that they are different from the real biological requirement. Indeed, the proof of NP completeness and the predictions in silico consider conformations that are not possible in practice. Consequences of this fact are investigated in this research work.Comment: Submitted to Journal of Bioinformatics and Computational Biology, under revie

Influence of Rough and Smooth Walls on Macroscale Flows in Tumblers

Walls in discrete element method simulations of granular flows are sometimes modeled as a closely packed monolayer of fixed particles, resulting in a rough wall rather than a geometrically smooth wall. An implicit assumption is that the resulting rough wall differs from a smooth wall only locally at the particle scale. Here we test this assumption by considering the impact of the wall roughness at the periphery of the flowing layer on the flow of monodisperse particles in a rotating spherical tumbler. We find that varying the wall roughness significantly alters average particle trajectories even far from the wall. Rough walls induce greater poleward axial drift of particles near the flowing layer surface, but decrease the curvature of the trajectories. Increasing the volume fill level in the tumbler has little effect on the axial drift for rough walls, but increases the drift while reducing curvature of the particle trajectories for smooth walls. The mechanism for these effects is related to the degree of local slip at the bounding wall, which alters the flowing layer thickness near the walls, affecting the particle trajectories even far from the walls near the equator of the tumbler. Thus, the proper choice of wall conditions is important in the accurate simulation of granular flows, even far from the bounding wall.Comment: 32 pages, 19 figures, regular article, accepted for publication in Physical Review E 200

Simulation of the elementary evolution operator with the motional states of an ion in an anharmonic trap

Following a recent proposal of L. Wang and D. Babikov, J. Chem. Phys. 137, 064301 (2012), we theoretically illustrate the possibility of using the motional states of a $Cd^+$ ion trapped in a slightly anharmonic potential to simulate the single-particle time-dependent Schr\"odinger equation. The simulated wave packet is discretized on a spatial grid and the grid points are mapped on the ion motional states which define the qubit network. The localization probability at each grid point is obtained from the population in the corresponding motional state. The quantum gate is the elementary evolution operator corresponding to the time-dependent Schr\"odinger equation of the simulated system. The corresponding matrix can be estimated by any numerical algorithm. The radio-frequency field able to drive this unitary transformation among the qubit states of the ion is obtained by multi-target optimal control theory. The ion is assumed to be cooled in the ground motional state and the preliminary step consists in initializing the qubits with the amplitudes of the initial simulated wave packet. The time evolution of the localization probability at the grids points is then obtained by successive applications of the gate and reading out the motional state population. The gate field is always identical for a given simulated potential, only the field preparing the initial wave packet has to be optimized for different simulations. We check the stability of the simulation against decoherence due to fluctuating electric fields in the trap electrodes by applying dissipative Lindblad dynamics.Comment: 31 pages, 8 figures. Revised version. New title, new figure and new reference

Cooling of the crust in the neutron star low-mass X-ray binary MXB 1659-29

In quasi-persistent neutron star transients, long outbursts cause the neutron star crust to be heated out of thermal equilibrium with the rest of the star. During quiescence, the crust then cools back down. Such crustal cooling has been observed in two quasi-persistent sources: KS 1731-260 and MXB 1659-29. Here we present an additional Chandra observation of MXB 1659-29 in quiescence, which extends the baseline of monitoring to 6.6 yr after the end of the outburst. This new observation strongly suggests that the crust has thermally relaxed, with the temperature remaining consistent over 1000 days. Fitting the temperature cooling curve with an exponential plus constant model we determine an e-folding timescale of 465 +/- 25 days, with the crust cooling to a constant surface temperature of kT = 54 +/- 2 eV (assuming D=10 kpc). From this, we infer a core temperature in the range 3.5E7-8.3E7 K (assuming D=10 kpc), with the uncertainty due to the surface composition. Importantly, we tested two neutron star atmosphere models as well as a blackbody model, and found that the thermal relaxation time of the crust is independent of the chosen model and the assumed distance.Comment: accepted for publication in ApJL, 4 pages, 1 figure

The Quiescent X-ray Spectrum of Accreting Black Holes

The quiescent state is the dominant accretion mode for black holes on all mass scales. Our knowledge of the X-ray spectrum is limited due to the characteristic low luminosity in this state. Herein, we present an analysis of the sample of dynamically-confirmed stellar-mass black holes observed in quiescence in the \textit{Chandra/XMM-Newton/Suzaku} era resulting in a sample of 8 black holes with $\sim$ 570 ks of observations. In contrast to the majority of AGN where observations are limited by contamination from diffuse gas, the stellar-mass systems allow for a clean study of the X-ray spectrum resulting from the accretion flow alone. The data are characterized using simple models. We find a model consisting of a power-law or thermal bremsstrahlung to both provide excellent descriptions of the data, where we measure $\rm \Gamma = 2.06 \pm 0.03$ and $\rm kT = 5.03^{+0.33}_{-0.31} keV$ respectively in the 0.3 -- 10 keV bandpass, at a median luminosity of $\rm L_x \sim 5.5\times10^{-7} L_{Edd}$. This result in discussed in the context of our understanding of the accretion flow onto stellar and supermassive black holes at low luminosities.Comment: 12 pages, 5 figures, 2 tables, MNRAS accepte

The Effects of ITQ Management on Fishermen’s Welfare When the Processing Sector is Imperfectly Competitive

In this paper we use a general model of imperfect competition to predict welfare changes within an open-access fishery transitioning to individual transferable quota (ITQ) management. Although related research has explored the effects of market power in the harvesting sector on ITQ performance, none have considered the implications of an imperfectly competitive processing sector. This study addresses this question specifically in the context of the Atlantic herring fishery, although its implications are relevant to all fisheries with similar industry structure. Our results show that ITQs could have a negative impact on fishermen’s welfare when processors have market power and the cap on aggregate harvest is binding or becomes binding with the implementation of ITQs.ITQ, imperfect competition, welfare analysis, fisheries

Fibrillar Elastomeric Micropatterns Create Tunable Adhesion Even to Rough Surfaces

Acknowledgements V.B., N.K.G., and E.A. contributed with conception and experimental design. V.B. performed the experiments. V.B., R.H., A.G., and R.M.M. carried out analysis and interpretation of data. V.B., R.H., A.G., and E.A. wrote the manuscript. V.B. and R.H. contributed equally to this work. V.B. acknowledges funding by SPP 1420 of the German Science Foundation DFG. E.A., N.K.G., and R.H. acknowledge funding from the European Research Council under the European Union/ERC Advanced Grant “Switch2Stick,” Agreement No. 340929.Peer reviewedPublisher PD