Large Box Size Research Articles

On the Cosmic Variance of the Merger Rate Density of Binary Neutron Stars

The cosmic variance on the star formation history may lead to bias in the merger rate density estimation of binary neutron star (BNS) mergers by compact binary population synthesis. In this paper, we take advantage of the large box size of the Millennium Simulation combined with the semianalytic galaxy formation model GABE and the parameterized population binary star evolution model to examine how much effect the cosmic variance will introduce on the estimation of the merger rate density of BNS mergers. We find that for subbox sizes of 100 and 200 Mpc, the variance of merger rate density σ R /R at different redshifts is about 23%–35% and 13%–20%, respectively. On the one hand, as for the variance of the detection rate on BNS mergers with the current LIGO–Virgo–KAGRA (LVK) detector network, this value is very small at ≲10%, which indicates ignoring the cosmic variance is reasonable for estimating the merger rate density from current LVK observations. On the other hand, with next-generation gravitational wave detectors, it is possible to localize BNS mergers within subboxes possessing a length of 40 Mpc for a source redshift z s < 0.2. In such a small box, the cosmic variance of the merger rate density is significant, i.e., the value of σ R /R is about ∼55%. This hints that estimating the merger rate density of BNS in different sky areas may provide useful information on the cosmic variance.

Relative baryon-dark matter velocities in cosmological zoom simulations

ABSTRACT Supersonic relative motion between baryons and dark matter due to the decoupling of baryons from the primordial plasma after recombination affects the growth of the first small-scale structures. Large box sizes (greater than a few hundred Mpc) are required to sample the full range of scales pertinent to the relative velocity, while the effect of the relative velocity is strongest on small scales (less than a few hundred kpc). This separation of scales naturally lends itself to the use of ‘zoom’ simulations, and here we present our methodology to self-consistently incorporate the relative velocity in zoom simulations, including its cumulative effect from recombination through to the start time of the simulation. We apply our methodology to a large-scale cosmological zoom simulation, finding that the inclusion of relative velocities suppresses the halo baryon fraction by 46–23 per cent between z = 13.6 and 11.2, in qualitative agreement with previous works. In addition, we find that including the relative velocity delays the formation of star particles by ∼20 Myr on average (of the order of the lifetime of a ∼9 M⊙ Population III star) and suppresses the final stellar mass by as much as 79 per cent at z = 11.2.

Structural modeling of ZnFe2O4 systems using Buckingham potentials with static molecular dynamics

Using Buckingham potentials we study zinc spinel ferrites ZnFe2O4 mechanical properties such as elastic constants, bulk moduli and vacancy formation energies EV at zero temperature. These properties are analyzed as a function of the lattice parameter, the pressure and the inversion degree parameter. The potentials predict the geometry of normal and partial inverse spinels in good agreement with reported experimental data. Statistical randomness of the octahedral sites in partial inverse spinels is implemented to investigate its effects in energies, the lattice parameter, the elastic constants and bulk moduli. The results show that deformations of up to ±6% are associated with pressures of up to 50 GPa, and that the normal spinel at zero pressure is in the limit between brittle and ductile, (B/G = 1.77). Besides, positive pressures make the normal spinel brittle while negative ones transform it into ductile. However, the partial inverse spinels are ductile materials whose ductility increases with the inversion degree. It is also found that EV(O)≤EV(Zn)≤EV(Fe) and that these computations require a large box size. Our results show that fluctuations due to randomness of Ze and Fe play an important role in the formation of vacancies in the inverse spinel and their stability, but they can be safely ignored for elastic constants. The results are compared to experimental data found in the literature.

P‐23: Image Adaptation to Human Vision (Eyeglasses Free): Full Visual‐Corrected Function in Light‐Field Near‐to‐Eye Displays

Many design factors are highly demanded in developing optimum near‐to‐eye display, such as higher resolution and wider FOV for vivid image quality, embedded vision correction for visual comfort, and light, compact and large eye box size for wearing comfort and stylish. Several optical approaches could achieve the visual correction, such as time‐multiplexed light field, space‐multiplexed light field, holographic display, multi‐focal planes, etc. In this study, based on the space‐multiplexed light field, the authors propose a special method that can adapt the variable pupil distance and deliver several virtual image planes at the same time by an algorithm of image processing. LFNEDs utilize this method which can adapt to the diversified facial shape and avoid wearing prescription glasses in using AR/VR glasses, no matter users have myopia, hyperopia, and astigmatism.

The Distribution and Evolution of Quasar Proximity Zone Sizes

Abstract In this paper, we study the sizes of quasar proximity zones with synthetic quasar absorption spectra obtained by postprocessing a Cosmic Reionization On Computers (CROC) simulation. CROC simulations have both relatively large box sizes and high spatial resolution, allowing us to resolve Lyman limit systems (LLSs), which are crucial for modeling the quasar absorption spectra. We find that before reionization, most quasar proximity zone sizes grow steadily for ∼10 Myr, while after reionization, they grow rapidly but only for ∼0.1 Myr. We also find a slow growth of R obs with decreasing turn-on redshift. In addition, we find that ∼1%–2% of old quasars (30 Myr old) display extremely small proximity zone sizes (&lt;1 proper Mpc), the vast majority of which are due to the occurrence of a damped Lyα absorber (DLA) or an LLS along the line of sight. These DLAs and LLSs are contaminated with metal, which offers a way to distinguish them from the normal proximity zones of young quasars.

The Completed SDSS-IV Extended Baryon Oscillation Spectroscopic Survey: N-body Mock Challenge for Galaxy Clustering Measurements

Abstract We develop a series of N-body data challenges, functional to the final analysis of the extended Baryon Oscillation Spectroscopic Survey (eBOSS) Data Release 16 (DR16) galaxy sample. The challenges are primarily based on high-fidelity catalogs constructed from the Outer Rim simulation – a large box size realization (3h−1Gpc) characterized by an unprecedented combination of volume and mass resolution, down to 1.85 · 109h−1M⊙. We generate synthetic galaxy mocks by populating Outer Rim halos with a variety of halo occupation distribution (HOD) schemes of increasing complexity, spanning different redshift intervals. We then assess the performance of three complementary redshift space distortion (RSD) models in configuration and Fourier space, adopted for the analysis of the complete DR16 eBOSS sample of Luminous Red Galaxies (LRGs). We find all the methods mutually consistent, with comparable systematic errors on the Alcock-Paczynski parameters and the growth of structure, and robust to different HOD prescriptions – thus validating the robustness of the models and the pipelines used for the baryon acoustic oscillation (BAO) and full shape clustering analysis. In particular, all the techniques are able to recover α∥ and α⊥ to within $0.9\%$, and fσ8 to within $1.5\%$. As a by-product of our work, we are also able to gain interesting insights on the galaxy-halo connection. Our study is relevant for the final eBOSS DR16 ‘consensus cosmology’, as the systematic error budget is informed by testing the results of analyses against these high-resolution mocks. In addition, it is also useful for future large-volume surveys, since similar mock-making techniques and systematic corrections can be readily extended to model for instance the Dark Energy Spectroscopic Instrument (DESI) galaxy sample.

Critical transition in fast-rotating turbulence within highly elongated domains

Abstract

Large effect of lateral box size in molecular dynamics simulations of liquid-solid friction.

Molecular dynamics simulations are a powerful tool to characterize liquid-solid friction. A slab configuration with periodic boundary conditions in the lateral dimensions is commonly used, where the measured friction coefficient could be affected by the finite lateral size of the simulation box. Here we show that for a very wetting liquid close to its melting temperature, strong finite size effects can persist up to large box sizes along the flow direction, typically ∼30 particle diameters. We relate the observed decrease of friction in small boxes to changes in the structure of the first adsorbed layer, which becomes less commensurable with the wall structure. Although these effects disappear for lower wetting cases or at higher temperatures, we suggest that the possible effect of the finite lateral box size on the friction coefficient should not be automatically set aside when exploring unknown systems.

Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'.

A recent molecular dynamics investigation into the stability of hemoglobin concluded that the unliganded protein is only stable in the T state when a solvent box is used in the simulations that is ten times larger than what is usually employed (El Hage et al., 2018). Here, we express three main concerns about that study. In addition, we find that with an order of magnitude more statistics, the reported box size dependence is not reproducible. Overall, no significant effects on the kinetics or thermodynamics of conformational transitions were observed.

Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'

Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'

Response to comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'.

We recently reported that molecular dynamics simulations for hemoglobin require a surprisingly large box size to stabilize the T(0) state relative to R(0), as observed in experiments (El Hage et al., 2018). Gapsys and de Groot have commented on this work but do not provide convincing evidence that the conclusions of El Hage et al., 2018 are incorrect. Here we respond to these concerns, argue that our original conclusions remain valid, and raise our own concerns about some of the results reported in the comment by Gapsys and de Groot that require clarification.

Kinetic simulations of mildly relativistic shocks – I. Particle acceleration in high Mach number shocks

Abstract We use fully kinetic particle-in-cell simulations with unprecedentedly large transverse box sizes to study particle acceleration in weakly magnetized mildly relativistic shocks travelling at a velocity ≈ 0.75c and a Mach number of 15. We examine both subluminal (quasi-parallel) and superluminal (quasi-perpendicular) magnetic field orientations. We find that quasi-parallel shocks are mediated by a filamentary non-resonant (Bell) instability driven by returning ions, producing magnetic fluctuations on scales comparable to the ion gyroradius. In quasi-parallel shocks, both electrons and ions are accelerated into non-thermal power laws whose maximum energy grows linearly with time. The upstream heating of electrons is small, and the two species enter the shock front in rough thermal equilibrium. The shock’s structure is complex; the current of returning non-thermal ions evacuates cavities in the upstream that form filaments of amplified magnetic fields once advected downstream. At late times, 10 per cent of the shock’s energy goes into non-thermal protons and ${\gtrsim }10{{\ \rm per\ cent}}$ into magnetic fields. We find that properly capturing the magnetic turbulence driven by the non-thermal ions is important for properly measuring the energy fraction of non-thermal electrons, εe. We find εe ∼ 5 × 10−4 for quasi-parallel shocks with v = 0.75c, slightly larger than what was measured in simulations of non-relativistic shocks. In quasi-perpendicular shocks, no non-thermal power-law develops in ions or electrons. The ion acceleration efficiency in quasi-parallel shocks suggests that astrophysical objects that could host mildly relativistic quasi-parallel shocks – for example, the jets of active galactic nuclei or microquasars – may be important sources of cosmic rays and their secondaries, such as gamma-rays and neutrinos.

Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size.

Recent molecular dynamics (MD) simulations of human hemoglobin (Hb) give results in disagreement with experiment. Although it is known that the unliganded (T[Formula: see text]) and liganded (R[Formula: see text]) tetramers are stable in solution, the published MD simulations of T[Formula: see text] undergo a rapid quaternary transition to an R-like structure. We show that T[Formula: see text] is stable only when the periodic solvent box contains ten times more water molecules than the standard size for such simulations. The results suggest that such a large box is required for the hydrophobic effect, which stabilizes the T[Formula: see text] tetramer, to be manifested. Even in the largest box, T[Formula: see text] is not stable unless His146 is protonated, providing an atomistic validation of the Perutz model. The possibility that extra large boxes are required to obtain meaningful results will have to be considered in evaluating existing and future simulations of a wide range of systems.

Fast generation of weak lensing maps by the inverse-Gaussianization method

To take full advantage of the unprecedented power of upcoming weak lensing surveys, understanding the noise, such as cosmic variance and geometry/mask effects, is as important as understanding the signal itself. Accurately quantifying the noise requires a large number of statistically independent mocks for a variety of cosmologies. This is impractical for weak lensing simulations, which are costly for simultaneous requirements of large box size (to cover a significant fraction of the past light cone) and high resolution (to robustly probe the small scale where most lensing signal resides). Therefore fast mock generation methods are desired and are under intensive investigation. We propose a new fast weak lensing map generation method, named the inverse-Gaussianization method, based on the finding that a lensing convergence field can be Gaussianized to excellent accuracy by a local transformation [Yu et al, Phys. Rev. D 84, 023523 (2011)]. Given a simulation, it enables us to produce as many as infinite statistically independent lensing maps as fast as producing the simulation initial conditions. The proposed method is tested against simulations for each tomography bin centered at lens redshift $z \sim 0.5$, 1, and 2, with various statistics. We find that the lensing maps generated by our method have reasonably accurate power spectra, bispectra, and power spectrum covariance matrix. Therefore, it will be useful for weak lensing surveys to generate realistic mocks. As an example of application, we measure the probability distribution function of the lensing power spectrum, from 16384 lensing maps produced by the inverse-Gaussianization method.

SMBH growth parameters in the early Universe of Millennium and Millennium-II simulations

We make black hole (BH) merger trees from Millennium and Millennium-II simulations to find under what conditions 10^9Msun SMBH can form by redshift z=7. In order to exploit both: large box size in the Millennium simulation; and large mass resolution in the Millennium-II simulation, we develop a method to combine these two simulations together, and use the Millennium-II merger trees to predict the BH seeds to be used in the Millennium merger trees. We run multiple semi-analytical simulations where SMBHs grow through mergers and episodes of gas accretion triggered by major mergers. As a constraint, we use observed BH mass function at redshift z=6. We find that in the light of the recent observations of moderate super-Eddington accretion, low-mass seeds (100Msun) could be the progenitors of high-redshift SMBHs (z~7), as long as the accretion during the accretion episodes is moderately super-Eddington, where f_Edd=3.7 is the effective Eddington ratio averaged over 50 Myr.

Cosmological perturbation theory as a tool for estimating box-scale effects inN-body simulations

In performing cosmological N-body simulations, it is widely appreciated that the growth of structure on the largest scales within a simulation box will be inhibited by the finite size of the simulation volume. Following ideas set forth in Seto (1999), this paper shows that standard (a.k.a. 1-loop) cosmological perturbation theory (SPT) can be used to predict, in an approximate way, the deleterious effect of the box scale on the power spectrum of density fluctuations in simulation volumes. Alternatively, this approach can be used to quickly estimate post facto the effect of the box scale on power spectrum results from existing simulations. In this way SPT can help determine whether larger box sizes or other more-sophisticated methods are needed to achieve a particular level of precision for a given application (e.g. simulations to measure the non-linear evolution of baryon acoustic oscillations). I focus on SPT in this note and show that its predictions differ only by about a factor of two or less from the measured suppression inferred from both powerlaw and $\Lambda$CDM $N$-body simulations. It should be possible to improve the accuracy of these predictions through using more-sophisticated perturbation theory models. An appendix compares power spectrum measurements from the powerlaw simulations at outputs where box-scale effects are minimal to perturbation theory models and previously-published fitting functions. These power spectrum measurements are included with this paper to aid efforts to develop new perturbation theory models.

QCD thermodynamics with continuum extrapolated Wilson fermions I

QCD thermodynamics is considered using Wilson fermions in the fixed scale approach. The temperature dependence of the renormalized chiral condensate, quark number susceptibility and Polyakov loop is measured at four lattice spacings allowing for a controlled continuum limit. The light quark masses are fixed to heavier than physical values in this first study. Finite volume effects are ensured to be negligible by using approriately large box sizes. The final continuum results are compared with staggered fermion simulations performed in the fixed N_t approach. The same continuum renormalization conditions are used in both approaches and the final results agree perfectly.

Modulo-2pi phase determination from individual ESPI images

A family of correlation methods is presented that enables a modulo-2π phase map to be evaluated from a single ESPI fringe image and at least two phase-stepped reference images. The requirement for only a single fringe image is useful when making ESPI measurements on moving surfaces, where the time interval between the acquisition of multiple phase-stepped fringe images is not acceptable. The phase computation method involves correlating an image area within a small box around each pixel of the fringe image to the corresponding areas within the reference images. With careful arrangement of the computation sequence and the storage of some intermediate results it is possible to achieve computation times only double that of the classical 4+4 stepped image method, independent of correlation box size. The performance of the proposed phase calculation scheme is demonstrated using experimentally measured speckle images acquired from a Mach–Zehnder interferometer. It is also shown that the phase map evaluation quality can be enhanced by subtracting the mostly uncorrelated phase-average component of the incident light. The correlation box size provides a simple means of controlling spatial filtering, with a small box size giving good spatial resolution with high noise, and a large box size giving smoother results but with slightly reduced spatial resolution.

Optimization of the imaginary time step evolution for the Dirac equation

Taking the single neutron levels of 12C in the Fermi sea as examples, the optimization of the imaginary time step (ITS) evolution with the box size and mesh size for the Dirac equation is investigated. For the weakly bound states, in order to reproduce the exact single-particle energies and wave functions, a relatively large box size is required. As long as the exact results can be reproduced, the ITS evolution with a smaller box size converges faster, while for both the weakly and deeply bound states, the ITS evolutions are less sensitive to the mesh size. Moreover, one can find a parabola relationship between the mesh size and the corresponding critical time step, i.e., the largest time step to guarantee the convergence, which suggests that the ITS evolution with a larger mesh size allows larger critical time step, and thus can converge faster to the exact result. These conclusions are very helpful for optimizing the evolution procedure in the future self-consistent calculations.

Cosmic evolution of the C iv in high-resolution hydrodynamic simulations

We investigate the properties of triply ionized carbon (C iv) in the intergalactic medium (IGM) using a set of high resolution and large box size cosmological hydrodynamic simulations of a Lambda cold dark matter (ΛCDM) model. We rely on a modification of the publicly available TreeSPH code gadget-2 that self-consistently follows the metal enrichment mechanism by means of a detailed chemical evolution model. We focus on several numerical implementations of galactic feedback: galactic winds in the energy-driven and momentum-driven prescriptions, galactic winds hydrodynamically coupled to the surrounding gas and active galactic nuclei (AGNs) powered by gas accretion on to massive black holes. Furthermore, our results are compared to a run in which galactic feedback is not present and we also explore different initial stellar mass function. After having addressed some global properties of the simulated volume like the impact on the star formation rate and the content in carbon and C iv, we extract mock IGM transmission spectra in neutral hydrogen (H i) and C iv and perform Voigt profile fitting. The results are then compared with high-resolution quasar (QSO) spectra obtained with the Ultraviolet Echelle Spectrograph (UVES) at the Very Large Telescope (VLT) and the High Resolution Echelle Spectrograph (HIRES) at Keck. We find that feedback has little impact on statistics related to the neutral hydrogen, while C iv is more affected by galactic winds and/or AGN feedback. The feedback schemes investigated have a different strength and redshift evolution with a general tendency for AGN feedback to be more effective at lower redshift than galactic winds. When the same analysis is performed over observed and simulated C iv lines, we find a reasonably good agreement between data and simulations over the column density range NC IV= 1012.5-15 cm−2. Also the C iv linewidth distribution appears to be in agreement with the observed values, while the H i Doppler parameters, bH I, are in general too large, showing that the diffuse cosmic web is heated more than what is inferred by observations. The simulation without feedback fails in reproducing the C iv systems at high column densities at all redshift, while the AGN feedback case agrees with observations only at z < 3, when this form of feedback is particularly effective. We also present scatter plots in the b–N and in the NC IV–NH I planes, showing that there is rough agreement between observations and simulations only when feedback is taken into account. Although it seems difficult to constrain the nature and the strength of galactic feedback using the present framework and find a unique model that fits all the observations, these simulations offer the perspective of understanding the galaxy–IGM interplay and how metals produced by stars can reach the low-density IGM.