Molecular-Dynamics Simulation of a Glassy Polymer Melt: Incoherent Scattering Function

We present simulation results for a model polymer melt, consisting of short, nonentangled chains, in the supercooled state. The analysis focuses on the monomer dynamics, which is monitored by the incoherent intermediate scattering function. The scattering function is recorded over six decades in time and for many different wave-vectors. The lowest temperatures studied are slightly above the critical temperature of mode-coupling theory (MCT), which was determined from a quantitative analysis of the beta- and alpha-relaxations. We find evidence for the space-time factorization theorem in the beta-relaxation regime, and for the time-temperature superposition principle in the alpha-regime, if the temperature is not too close to the critical temperature. The wave-vector dependence of the nonergodicity parameter, of the critical amplitude, and the alpha-relaxation time are in qualitative agreement with calculations for hard spheres. For wave-vectors larger than the maximum of the structure factor the alpha-relaxation time already agrees fairly well with the asymptotic MCT-prediction. The behavior of the relaxation time at small wave-vectors can be rationalized by the validity of the Gaussian approximation and the value of the Kohlrausch stretching exponent.Comment: 23 pages of REVTeX, 13 PostScript figures, submitted to Phys. Rev.

Understanding the physics of oligonucleotide microarrays: the Affymetrix spike-in data reanalysed

The Affymetrix U95 and U133 Latin Square spike-in datasets are reanalysed, together with a dataset from a version of the U95 spike-in experiment without a complex non-specific background. The approach uses a physico-chemical model which includes the effects the specific and non-specific hybridisation and probe folding at the microarray surface, target folding and hybridisation in the bulk RNA target solution, and duplex dissociation during the post-hybridisatoin washing phase. The model predicts a three parameter hyperbolic response function that fits well with fluorescence intensity data from all three datasets. The importance of the various hybridisation and washing effects in determining each of the three parameters is examined, and some guidance is given as to how a practical algorithm for determining specific target concentrations might be developed.Comment: 32 pages, 13 figures, minor amendment

Binary mixture of hard disks as a model glass former: Caging and uncaging

I have proposed a measure for the cage effect in glass forming systems. A binary mixture of hard disks is numerically studied as a model glass former. A network is constructed on the basis of the colliding pairs of disks. A rigidity matrix is formed from the isostatic (rigid) sub--network, corresponding to a cage. The determinant of the matrix changes its sign when an uncaging event occurs. Time evolution of the number of the uncaging events is determined numerically. I have found that there is a gap in the uncaging timescales between the cages involving different numbers of disks. Caging of one disk by two neighboring disks sustains for a longer time as compared with other cages involving more than one disk. This gap causes two--step relaxation of this system

Properties of iterative Monte Carlo single histogram reweighting

We present iterative Monte Carlo algorithm for which the temperature variable is attracted by a critical point. The algorithm combines techniques of single histogram reweighting and linear filtering. The 2d Ising model of ferromagnet is studied numerically as an illustration. In that case, the iterations uncovered stationary regime with invariant probability distribution function of temperature which is peaked nearly the pseudocritical temperature of specific heat. The sequence of generated temperatures is analyzed in terms of stochastic autoregressive model. The error of histogram reweighting can be better understood within the suggested model. The presented model yields a simple relation, connecting variance of pseudocritical temperature and parameter of linear filtering.Comment: 3 figure

Coupled Fluctuations near Critical Wetting

Recent work on the complete wetting transition has emphasized the role played by the coupling of fluctuations of the order parameter at the wall and at the depinning fluid interface. Extending this approach to the wetting transition itself we predict a novel crossover effect associated with the decoupling of fluctuations as the temperature is lowered towards the transition temperature T_W. Using this we are able to reanalyse recent Monte-Carlo simulation studies and extract a value \omega(T_W)=0.8 at T_W=0.9T_C in very good agreement with long standing theoretical predictions.Comment: 4 pages, LaTex, 1 postscript figur

Optimal stochastic modelling with unitary quantum dynamics

Identifying and extracting the past information relevant to the future behaviour of stochastic processes is a central task in the quantitative sciences. Quantum models offer a promising approach to this, allowing for accurate simulation of future trajectories whilst using less past information than any classical counterpart. Here we introduce a class of phase-enhanced quantum models, representing the most general means of causal simulation with a unitary quantum circuit. We show that the resulting constructions can display advantages over previous state-of-art methods - both in the amount of information they need to store about the past, and in the minimal memory dimension they require to store this information. Moreover, we find that these two features are generally competing factors in optimisation - leading to an ambiguity in what constitutes the optimal model - a phenomenon that does not manifest classically. Our results thus simultaneously offer new quantum advantages for stochastic simulation, and illustrate further qualitative differences in behaviour between classical and quantum notions of complexity.Comment: 9 pages, 5 figure

Critical behavior of colloid-polymer mixtures in random porous media

We show that the critical behavior of a colloid-polymer mixture inside a random porous matrix of quenched hard spheres belongs to the universality class of the random-field Ising model. We also demonstrate that random-field effects in colloid-polymer mixtures are surprisingly strong. This makes these systems attractive candidates to study random-field behavior experimentally.Comment: 4 pages, 3 figures, to appear in Phys. Rev. Let