Goodness-of-fit criteria for survival data

The definition of an appropriate measure for goodness-of-fit in case of survival data comparable to R^2 in linear regression is difficult due to censored observations. In this paper, a variety of answers based on different residuals and variance of survival curves are presented together with a newly introduced criterion. In univariate simulation studies, the presented criteria are examined with respect to their dependence on the value of the coefficient associated with the covariate; underlying covariate distribution and censoring percentage in the data. Investigation of the relations between the values of the different criteria indicates strong dependencies, although the absolute values show high discrepancies and the criteria building processes differ substantially

Symmetric Diblock Copolymers in Thin Films (I): Phase stability in Self-Consistent Field Calculations and Monte Carlo Simulations

We investigate the phase behavior of symmetric AB diblock copolymers confined into a thin film. The film boundaries are parallel, impenetrable and attract the A component of the diblock copolymer. Using a self-consistent field technique [M.W. Matsen, J.Chem.Phys. {\bf 106}, 7781 (1997)], we study the ordered phases as a function of incompatibility $\chi$ and film thickness in the framework of the Gaussian chain model. For large film thickness and small incompatibility, we find first order transitions between phases with different number of lamellae which are parallel oriented to the film boundaries. At high incompatibility or small film thickness, transitions between parallel oriented and perpendicular oriented lamellae occur. We compare the self-consistent field calculations to Monte Carlo simulations of the bond fluctuation model for chain length N=32. In the simulations we quench several systems from $\chi N=0$ to $\chi N=30$ and monitor the morphology into which the diblock copolymers assemble. Three film thicknesses are investigated, corresponding to parallel oriented lamellae with 2 and 4 interfaces and a perpendicular oriented morphology. Good agreement between self-consistent field calculations and Monte Carlo simulations is found.Comment: to appear in J.Chem.Phy

Monte Carlo simulations of copolymers at homopolymer interfaces: Interfacial structure as a function of the copolymer density

By means of extensive Monte Carlo simulations of the bond fluctuation model, we study the effect of adding AB diblock copolymers on the properties of an interface between demixed homopolymer phases. The parameters are chosen such that the homopolymers are strongly segregated, and the whole range of copolymer concentrations in the two phase coexistence region is scanned. We compare the ``mushroom'' regime, in which copolymers are diluted and do not interact with each other, with the ``wet brush'' regime, where copolymers overlap and stretch, but are still swollen by the homopolymers. A ``dry brush'' regime is never entered for our choice of chain lengths. ``Intrinsic'' profiles are calculated using a block analysis method introduced by us in earlier work. We discuss density profiles, orientational profiles and contact number profiles. In general, the features of the profiles are similar at all copolymer concentrations, however, the profiles in the concentrated regime are much broader than in the dilute regime. The results compare well with self-consistent field calculations.Comment: to appear in J. Chem. Phy

Implementation of complex interactions in a Cox regression framework

The standard Cox proportional hazards model has been extended by functionally describable interaction terms. The first of which are related to neural networks by adopting the idea of transforming sums of weighted covariables by means of a logistic function. A class of reasonable weight combinations within the logistic transformation is described. Apart from the standard covariable product interaction, a product of logistically transformed covariables has also been included in the analysis of performance of the new terms. An algorithm combining likelihood ratio tests and AIC criterion has been defined for model choice. The critical values of the likelihood ratio test statistics had to be corrected in order to guarantee a maximum type I error of 5% for each interaction term. The new class of interaction terms allows interpretation of functional relationships between covariables with more flexibility and can easily be implemented in standard software packages

ReDecay: A novel approach to speed up the simulation at LHCb

With the steady increase in the precision of flavour physics measurements collected during LHC Run 2, the LHCb experiment requires simulated data samples of larger and larger sizes to study the detector response in detail. The simulation of the detector response is the main contribution to the time needed to simulate full events. This time scales linearly with the particle multiplicity. Of the dozens of particles present in the simulation only the few participating in the signal decay under study are of interest, while all remaining particles mainly affect the resolutions and efficiencies of the detector. This paper presents a novel development for the LHCb simulation software which re-uses the rest of the event from previously simulated events. This approach achieves an order of magnitude increase in speed and the same quality compared to the nominal simulation

Equilibrium properties and force-driven unfolding pathways of RNA molecules

The mechanical unfolding of a simple RNA hairpin and of a 236--bases portion of the Tetrahymena thermophila ribozyme is studied by means of an Ising--like model. Phase diagrams and free energy landscapes are computed exactly and suggest a simple two--state behaviour for the hairpin and the presence of intermediate states for the ribozyme. Nonequilibrium simulations give the possible unfolding pathways for the ribozyme, and the dominant pathway corresponds to the experimentally observed one.Comment: Main text + appendix, to appear in Phys. Rev. Let

Dephasing-assisted Gain and Loss in Mesoscopic Quantum Systems

Motivated by recent experiments, we analyse the phonon-assisted steady-state gain of a microwave field driving a double quantum-dot in a resonator. We apply the results of our companion paper, which derives the complete set of fourth-order Lindblad dissipators using Keldysh methods, to show that resonator gain and loss are substantially affected by dephasing-assisted dissipative processes in the quantum-dot system. These additional processes, which go beyond recently proposed polaronic theories, are in good quantitative agreement with experimental observationsComment: 5 pages, 3 Figures, published together with arXiv:1608.0416

Visual adaptation to convexity in macaque area V4

Aftereffects are perceptual illusions caused by visual adaptation to one or more stimulus attribute, such as orientation, motion, or shape. Neurophysiological studies seeking to understand the basis of visual adaptation have observed firing rate reduction and changes in tuning of stimulus-selective neurons following periods of prolonged visual stimulation. In the domain of shape, recent psychophysical work has shown that adaptation to a convex pattern induces a subsequently seen rectangle to appear slightly concave. In the present study, we investigate the possible contribution of V4 neurons of rhesus monkeys, which are thought to be involved in the coding of convexity, to shape-specific adaptation. Visually responsive neurons were monitored during the brief presentation of simple shapes varying in their convexity level. Each test presentation was preceded by either a blank period or several seconds of adaptation to a convex or concave stimulus, presented in two different sizes. Adaptation consistently shifted the tuning of neurons away from the convex or concave adapter, including shifting response to the neutral rectangle in the direction of the opposite convexity. This repulsive shift resembled the known perceptual distortion associated with adaptation to such stimuli. In addition, adaptation caused a nonspecific response decrease, as well as a specific decrease for repeated stimuli. The latter effects were observed whether or not the adapting and test stimuli matched closely in their size. Taken together, these results provide evidence for shape-specific adaptation of neurons in area V4, which may contribute to the perception of the convexity aftereffect