Second-order cosmological perturbation theory and initial conditions for N-body simulations

We use gauge-invariant cosmological perturbation theory to calculate the displacement field that sets the initial conditions for $N$-body simulations. Using first and second-order fully relativistic perturbation theory in the synchronous-comoving gauge, allows us to go beyond the Newtonian predictions and to calculate relativistic corrections to it. We use an Einstein--de Sitter model, including both growing and decaying modes in our solutions. The impact of our results should be assessed through the implementation of the featured displacement in cosmological $N$-body simulations.Comment: V2: Second order density added and other expressions simplified. References updated. 15 page

Transitions of tethered polymer chains: A simulation study with the bond fluctuation lattice model

A polymer chain tethered to a surface may be compact or extended, adsorbed or desorbed, depending on interactions with the surface and the surrounding solvent. This leads to a rich phase diagram with a variety of transitions. To investigate these transitions we have performed Monte Carlo simulations of a bond-fluctuation model with Wang-Landau and umbrella sampling algorithms in a two-dimensional state space. The simulations' density of states results have been evaluated for interaction parameters spanning the range from good to poor solvent conditions and from repulsive to strongly attractive surfaces. In this work, we describe the simulation method and present results for the overall phase behavior and for some of the transitions. For adsorption in good solvent, we compare with Metropolis Monte Carlo data for the same model and find good agreement between the results. For the collapse transition, which occurs when the solvent quality changes from good to poor, we consider two situations corresponding to three-dimensional (hard surface) and two-dimensional (very attractive surface) chain conformations, respectively. For the hard surface, we compare tethered chains with free chains and find very similar behavior for both types of chains. For the very attractive surface, we find the two-dimensional chain collapse to be a two-step transition with the same sequence of transitions that is observed for three-dimensional chains: a coil-globule transition that changes the overall chain size is followed by a local rearrangement of chain segments.Comment: 17 pages, 12 figures, to appear in J. Chem. Phy

Cosmological parameters from large scale structure - geometric versus shape information

The matter power spectrum as derived from large scale structure (LSS) surveys contains two important and distinct pieces of information: an overall smooth shape and the imprint of baryon acoustic oscillations (BAO). We investigate the separate impact of these two types of information on cosmological parameter estimation, and show that for the simplest cosmological models, the broad-band shape information currently contained in the SDSS DR7 halo power spectrum (HPS) is by far superseded by geometric information derived from the baryonic features. An immediate corollary is that contrary to popular beliefs, the upper limit on the neutrino mass m_\nu presently derived from LSS combined with cosmic microwave background (CMB) data does not in fact arise from the possible small-scale power suppression due to neutrino free-streaming, if we limit the model framework to minimal LambdaCDM+m_\nu. However, in more complicated models, such as those extended with extra light degrees of freedom and a dark energy equation of state parameter w differing from -1, shape information becomes crucial for the resolution of parameter degeneracies. This conclusion will remain true even when data from the Planck surveyor become available. In the course of our analysis, we introduce a new dewiggling procedure that allows us to extend consistently the use of the SDSS HPS to models with an arbitrary sound horizon at decoupling. All the cases considered here are compatible with the conservative 95%-bounds \sum m_\nu < 1.16 eV, N_eff = 4.8 \pm 2.0.Comment: 18 pages, 4 figures; v2: references added, matches published versio

Conformational dynamics and internal friction in homopolymer globules: equilibrium vs. non-equilibrium simulations

We study the conformational dynamics within homopolymer globules by solvent-implicit Brownian dynamics simulations. A strong dependence of the internal chain dynamics on the Lennard-Jones cohesion strength ε and the globule size N [subscript G] is observed. We find two distinct dynamical regimes: a liquid-like regime (for ε ε[subscript s] with slow internal dynamics. The cohesion strength ε[subscript s] of this freezing transition depends on N G . Equilibrium simulations, where we investigate the diffusional chain dynamics within the globule, are compared with non-equilibrium simulations, where we unfold the globule by pulling the chain ends with prescribed velocity (encompassing low enough velocities so that the linear-response, viscous regime is reached). From both simulation protocols we derive the internal viscosity within the globule. In the liquid-like regime the internal friction increases continuously with ε and scales extensive in N [subscript G] . This suggests an internal friction scenario where the entire chain (or an extensive fraction thereof) takes part in conformational reorganization of the globular structure.American Society for Engineering Education. National Defense Science and Engineering Graduate Fellowshi

Cosmological N -body simulations including radiation perturbations

Cosmological N -body simulations are the standard tools to study the emergence of the observed large-scale structure of the Universe. Such simulations usually solve for the gravitational dynamics of matter within the Newtonian approximation, thus discarding general relativistic effects such as the coupling between matter and radiation ( ≡ photons and neutrinos). In this Letter, we investigate novel hybrid simulations that incorporate interactions between radiation and matter to the leading order in General Relativity, whilst evolving the matter dynamics in full non-linearity according to Newtonian theory. Our hybrid simulations come with a relativistic space–time and make it possible to investigate structure formation in a unified framework. In this work, we focus on simulations initialized at z = 99 and show that the extracted matter power spectrum receives up to 3 per cent corrections on very large scales through radiation. Our numerical findings compare favourably with linear analytical results from Fidler et al., from which we deduce that there cannot be any significant non-linear mode-coupling induced through linear radiation corrections