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

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

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

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

Driving steady-state visual evoked potentials at arbitrary frequencies using temporal interpolation of stimulus presentation

Date of Acceptance: 29/10/2015 We thank Renate Zahn for help with data collection. This work was supported by Deutsche Forschungsgemeinschaft (AN 841/1-1, MU 972/20-1). We would like to thank A. Trujillo-Ortiz, R. Hernandez-Walls, A. Castro-Perez and K. BarbaRojo (Universidad Autonoma de Baja California) for making Matlab code for non-sphericity corrections freely available.Peer reviewedPublisher PD

Equation of state and critical behavior of polymer models: A quantitative comparison between Wertheim's thermodynamic perturbation theory and computer simulations

We present an application of Wertheim's Thermodynamic Perturbation Theory (TPT1) to a simple coarse grained model made of flexibly bonded Lennard-Jones monomers. We use both the Reference Hyper-Netted-Chain (RHNC) and Mean Spherical approximation (MSA) integral equation theories to describe the properties of the reference fluid. The equation of state, the density dependence of the excess chemical potential, and the critical points of the liquid--vapor transition are compared with simulation results and good agreement is found. The RHNC version is somewhat more accurate, while the MSA version has the advantage of being almost analytic. We analyze the scaling behavior of the critical point of chain fluids according to TPT1 and find it to reproduce the mean field exponents: The critical monomer density is predicted to vanish as $n^{-1/2}$ upon increasing the chain length $n$ while the critical temperature is predicted to reach an asymptotic finite temperature that is attained as $n^{-1/2}$. The predicted asymptotic finite critical temperature obtained from the RHNC and MSA versions of TPT1 is found to be in good agreement with the $\Theta$ point of our polymer model as obtained from the temperature dependence of the single chain conformations.Comment: to appear in J.Chem.Phy

New mechanism of membrane fusion

We have carried out Monte Carlo simulation of the fusion of bilayers of single chain amphiphiles which show phase behavior similar to that of biological lipids. The fusion mechanism we observe is very different from the ``stalk'' hypothesis. Stalks do form on the first stage of fusion, but they do not grow radially to form a hemifused state. Instead, stalk formation destabilizes the membranes and results in hole formation in the vicinity of the stalks. When holes in each bilayer nucleate spontaneously next to the same stalk, an incomplete fusion pore is formed. The fusion process is completed by propagation of the initial connection, the stalk, along the edges of the aligned holes.Comment: 4 pages, 3 figure

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