A simple two-module problem to exemplify building-block assembly under crossover

Theoretically and empirically it is clear that a genetic algorithm with crossover will outperform a genetic algorithm without crossover in some fitness landscapes, and vice versa in other landscapes. Despite an extensive literature on the subject, and recent proofs of a principled distinction in the abilities of crossover and non-crossover algorithms for a particular theoretical landscape, building general intuitions about when and why crossover performs well when it does is a different matter. In particular, the proposal that crossover might enable the assembly of good building-blocks has been difficult to verify despite many attempts at idealized building-block landscapes. Here we show the first example of a two-module problem that shows a principled advantage for cross-over. This allows us to understand building-block assembly under crossover quite straightforwardly and build intuition about more general landscape classes favoring crossover or disfavoring it

Effects of a nanoscopic filler on the structure and dynamics of a simulated polymer melt and the relationship to ultra-thin films

We perform molecular dynamics simulations of an idealized polymer melt surrounding a nanoscopic filler particle to probe the effects of a filler on the local melt structure and dynamics. We show that the glass transition temperature $T_g$ of the melt can be shifted to either higher or lower temperatures by appropriately tuning the interactions between polymer and filler. A gradual change of the polymer dynamics approaching the filler surface causes the change in the glass transition. We also find that while the bulk structure of the polymers changes little, the polymers close to the surface tend to be elongated and flattened, independent of the type of interaction we study. Consequently, the dynamics appear strongly influenced by the interactions, while the melt structure is only altered by the geometric constraints imposed by the presence of the filler. Our findings show a strong similarity to those obtained for ultra-thin polymer films (thickness $\lesssim 100$ nm) suggesting that both ultra-thin films and filled-polymer systems might be understood in the same context

Effect of rhenium irradiations on the mechanical properties of tungsten for nuclear fusion applications

As-received and annealed tungsten samples were irradiated at a temperature of 400 °C with Re and W ions to peak concentrations of 1600 appm (atomic parts per million) and damage levels of 40 dpa (displacements per atom). Mechanical properties were investigated using nanoindentation, and the orientation and depth dependence of irradiation damage was investigated using Electron Back Scatter Diffraction (EBSD). Following irradiation there was a 13% increase in hardness in the as received sheet and a 23% increase in the annealed material for both tungsten and rhenium irradiation. The difference between the tungsten and rhenium irradiated samples was negligible, suggesting that for the concentrations and damage levels employed, the presence of rhenium does not have a significant effect on the hardening mechanism. Energy dependent EBSD of annealed samples provided information about the depth distribution of the radiation damage in individual tungsten grains and confirmed that the radiation damage is orientation dependant

Simultaneous alignment and folding of protein sequences

Accurate comparative analysis tools for low-homology proteins remains a difficult challenge in computational biology, especially sequence alignment and consensus folding problems. We presentpartiFold-Align, the first algorithm for simultaneous alignment and consensus folding of unaligned protein sequences; the algorithm’s complexity is polynomial in time and space. Algorithmically,partiFold-Align exploits sparsity in the set of super-secondary structure pairings and alignment candidates to achieve an effectively cubic running time for simultaneous pairwise alignment and folding. We demonstrate the efficacy of these techniques on transmembrane β-barrel proteins, an important yet difficult class of proteins with few known three-dimensional structures. Testing against structurally derived sequence alignments,partiFold-Align significantly outperforms state-of-the-art pairwise sequence alignment tools in the most difficult low sequence homology case and improves secondary structure prediction where current approaches fail. Importantly, partiFold-Align requires no prior training. These general techniques are widely applicable to many more protein families. partiFold-Align is available at http://partiFold.csail.mit.edu

Measurement of (anti)deuteron and (anti)proton production in DIS at HERA

The first observation of (anti)deuterons in deep inelastic scattering at HERA has been made with the ZEUS detector at a centre-of-mass energy of 300--318 GeV using an integrated luminosity of 120 pb-1. The measurement was performed in the central rapidity region for transverse momentum per unit of mass in the range 0.3<p_T/M<0.7. The particle rates have been extracted and interpreted in terms of the coalescence model. The (anti)deuteron production yield is smaller than the (anti)proton yield by approximately three orders of magnitude, consistent with the world measurements.Comment: 26 pages, 9 figures, 5 tables, submitted to Nucl. Phys.

Measurement of dijet photoproduction for events with a leading neutron at HERA

Differential cross sections for dijet photoproduction and this process in association with a leading neutron, e+ + p -> e+ + jet + jet + X (+ n), have been measured with the ZEUS detector at HERA using an integrated luminosity of 40 pb-1. The fraction of dijet events with a leading neutron was studied as a function of different jet and event variables. Single- and double-differential cross sections are presented as a function of the longitudinal fraction of the proton momentum carried by the leading neutron, xL, and of its transverse momentum squared, pT^2. The dijet data are compared to inclusive DIS and photoproduction results; they are all consistent with a simple pion-exchange model. The neutron yield as a function of xL was found to depend only on the fraction of the proton beam energy going into the forward region, independent of the hard process. No firm conclusion can be drawn on the presence of rescattering effects.Comment: 40 pages, 18 figure

Deep inelastic inclusive and diffractive scattering at Q2Q^2 values from 25 to 320 GeV2^2 with the ZEUS forward plug calorimeter

Deep inelastic scattering and its diffractive component, $ep \to e^{\prime}\gamma^* p \to e^{\prime}XN$, have been studied at HERA with the ZEUS detector using an integrated luminosity of 52.4 pb$^{-1}$. The $M_X$ method has been used to extract the diffractive contribution. A wide range in the centre-of-mass energy $W$ (37 -- 245 GeV), photon virtuality $Q^2$ (20 -- 450 GeV$^2$) and mass $M_X$ (0.28 -- 35 GeV) is covered. The diffractive cross section for $2 < M_X < 15$ GeV rises strongly with $W$, the rise becoming steeper as $Q^2$ increases. The data are also presented in terms of the diffractive structure function, $F^{\rm D(3)}_2$, of the proton. For fixed $Q^2$ and fixed $M_X$, \xpom F^{\rm D(3)}_2 shows a strong rise as \xpom \to 0, where \xpom is the fraction of the proton momentum carried by the Pomeron. For Bjorken-$x < 1 \cdot 10^{-3}$, \xpom F^{\rm D(3)}_2 shows positive $\log Q^2$ scaling violations, while for $x \ge 5 \cdot 10^{-3}$ negative scaling violations are observed. The diffractive structure function is compatible with being leading twist. The data show that Regge factorisation is broken.Comment: 89 pages, 27 figure