Multidimensional simulations of radiative transfer in Type Ia supernovae

A three-dimensional Monte Carlo code for modelling radiation transport in Type Ia supernovae is described. In addition to tracking Monte Carlo quanta to follow the emission, scattering and deposition of radiative energy, a scheme involving volume-based Monte Carlo estimators is used to allow properties of the emergent radiation field to be extracted for specific viewing angles in a multidimensional structure. This eliminates the need to compute spectra or light curves by angular binning of emergent quanta. The code is applied to two test problems to illustrate consequences of multidimensional structure on the modelling of light curves. First, elliptical models are used to quantify how large-scale asphericity can introduce angular dependence to light curves. Secondly, a model which incorporates complex structural inhomogeneity, as predicted by modern explosion models, is used to investigate how such structure may affect light-curve properties. © 2006 RAS.

3D deflagration simulations leaving bound remnants:A model for 2002cx-like Type Ia supernovae

2002cx-like supernovae are a sub-class of sub-luminous Type Ia supernovae (SNe). Their light curves and spectra are characterized by distinct features that indicate strong mixing of the explosion ejecta. Pure turbulent deflagrations have been shown to produce such mixed ejecta. Here, we present hydrodynamics, nucleosynthesis and radiative-transfer calculations for a 3D full-star deflagration of a Chandrasekhar-mass white dwarf. Our model is able to reproduce the characteristic observational features of SN 2005hk (a prototypical 2002cx-like supernova), not only in the optical, but also in the near-infrared. For that purpose we present, for the first time, five near-infrared spectra of SN 2005hk from -0.2 to 26.6 d with respect to B-band maximum. Since our model burns only small parts of the initial white dwarf, it fails to completely unbind the white dwarf and leaves behind a bound remnant of ~1.03Mconsisting mainly of unburned carbon and oxygen, but also enriched by some amount of intermediate-mass and iron-group elements from the explosion products that fall back on the remnant.We discuss possibilities for detecting this bound remnant and how it might influence the late-time observables of 2002cx-like SNe. © 2013 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.

Synthetic X-ray spectra for simulations of the dynamics of an accretion flow irradiated by a quasar

Ultraviolet and X-ray observations show evidence of outflowing gas around many active galactic nuclei. It has been proposed that some of these outflows are driven off gas infalling towards the central supermassive black hole. We perform radiative transfer calculations to compute the gas ionization state and the emergent X-ray spectra for both two- and three-dimensional (3D) hydrodynamical simulations of this outflow-from-inflow scenario. By comparison with observations, our results can be used to test the theoretical models and guide future numerical simulations. We predict both absorption and emission features, most of which are formed in a polar funnel of relatively dense (10 -10 g cm ) outflowing gas. This outflow causes strong absorption for observer orientation angles of ?35°. Particularly in 3D, the strength of this absorption varies significantly for different lines of sight owing to the fragmentary structure of the gas flow. Although infalling material occupies a large fraction of the simulation volume, we do not find that it imprints strong absorption features in the X-ray spectra since the ionization state is predicted to be very high. Thus, an absence of observed inflow absorption features does not exclude the models. The main spectroscopic consequence of the infalling gas is a Compton-scattered continuum component that partially re-fills the absorption features caused by the outflowing polar funnel. Fluorescence and scattering in the outflow are predicted to give rise to several emission features including a multicomponent Fe Ka emission complex for all observer orientations. For the hydrodynamical simulations considered, we predict both ionization states and column densities for the outflowing gas that are too high to be quantitatively consistent with well-observed X-ray absorption systems. Nevertheless, our results are qualitatively encouraging and further exploration of the model parameter space is warranted. Higher resolution hydrodynamic simulations are needed to determine whether the outflows fragment on scales unresolved in our current study, which may yield the denser lower ionization material that could reconcile the models and the observations. © 2012 The Authors Monthly Notices of the Royal Astronomical Society © 2012 RAS.

Using sketch-map coordinates to analyze and bias molecular dynamics simulations

When examining complex problems, such as the folding of proteins, coarse grained descriptions of the system drive our investigation and help us to rationalize the results. Oftentimes collective variables (CVs), derived through some chemical intuition about the process of interest, serve this purpose. Because finding these CVs is the most difficult part of any investigation, we recently developed a dimensionality reduction algorithm, sketch-map, that can be used to build a low-dimensional map of a phase space of high-dimensionality. In this paper we discuss how these machine-generated CVs can be used to accelerate the exploration of phase space and to reconstruct free-energy landscapes. To do so, we develop a formalism in which high-dimensional configurations are no longer represented by low-dimensional position vectors. Instead, for each configuration we calculate a probability distribution, which has a domain that encompasses the entirety of the low-dimensional space. To construct a biasing potential, we exploit an analogy with metadynamics and use the trajectory to adaptively construct a repulsive, history-dependent bias from the distributions that correspond to the previously visited configurations. This potential forces the system to explore more of phase space by making it desirable to adopt configurations whose distributions do not overlap with the bias. We apply this algorithm to a small model protein and succeed in reproducing the free-energy surface that we obtain from a parallel tempering calculation.

Assessment of rolling resistance models in discrete element simulations

Particulate systems are of interest in many disciplines. They are often investigated using the discrete element method because of its capability to investigate particulate systems at the individual particle scale. To model the interaction between two particles and between a particle and a boundary, conventional discrete element models use springs and dampers in both the normal and tangential directions. The significance of particle rotation has been highlighted in both numerical studies and physical experiments. Several researchers have attempted to incorporate a rotational torque to account for the rolling resistance or rolling friction by developing different models. This paper presents a review of the commonly used models for rolling resistance and proposes a more general model. These models are classified into four categories according to their key characteristics. The robustness of these models in reproducing rolling resistance effects arising from different physical situations was assessed by using several benchmarking test cases. The proposed model can be seen to be more general and suitable for modelling problems involving both dynamic and pseudo-static regimes. An example simulation of the formation of a 2D sandpile is also shown. For simplicity, all formulations and examples are presented in 2D form, though the general conclusions are also applicable to 3D systems.

COMPUTATION OF SYNTHETIC SPECTRA FROM SIMULATIONS OF RELATIVISTIC SHOCKS

Particle-in-cell (PIC) simulations of relativistic shocks are in principle capable of predicting the spectra of photons that are radiated incoherently by the accelerated particles. The most direct method evaluates the spectrum using the fields given by the Lienard-Wiechart potentials. However, for relativistic particles this procedure is computationally expensive. Here we present an alternative method that uses the concept of the photon formation length. The algorithm is suitable for evaluating spectra both from particles moving in a specific realization of a turbulent electromagnetic field or from trajectories given as a finite, discrete time series by a PIC simulation. The main advantage of the method is that it identifies the intrinsic spectral features and filters out those that are artifacts of the limited time resolution and finite duration of input trajectories.

TWO-DIMENSIONAL PARTICLE-IN-CELL SIMULATIONS OF THE NONRESONANT, COSMIC-RAY-DRIVEN INSTABILITY IN SUPERNOVA REMNANT SHOCKS

In supernova remnants, the nonlinear amplification of magnetic fields upstream of collisionless shocks is essential for the acceleration of cosmic rays to the energy of the "knee" at 10(15.5) eV. A nonresonant instability driven by the cosmic ray current is thought to be responsible for this effect. We perform two-dimensional, particle-in-cell simulations of this instability. We observe an initial growth of circularly polarized nonpropagating magnetic waves as predicted in linear theory. It is demonstrated that in some cases the magnetic energy density in the growing waves can grow to at least 10 times its initial value. We find no evidence of competing modes, nor of significant modification by thermal effects. At late times, we observe saturation of the instability in the simulation, but the mechanism responsible is an artifact of the periodic boundary conditions and has no counterpart in the supernova-shock scenario.

Simulations of Biased Agonists in the β2 Adrenergic Receptor with Accelerated Molecular Dynamics

The biased agonism of the G protein-coupled receptors (GPCRs), where in addition to a traditional G protein-signalling pathway a GPCR promotes intracellular signals though ß-arrestin, is a novel paradigm in pharmacology. Biochemical and biophysical studies have suggested that a GPCR forms a distinct ensemble of conformations signalling through the G protein and ß-arrestin. Here we report on the dynamics of the ß2 adrenergic receptor bound to the ß-arrestin and G protein biased agonists and the empty receptor to further characterize the receptor conformational changes caused by biased agonists. We use conventional and accelerated molecular dynamics (aMD) simulations to explore the conformational transitions of the GPCR from the active state to the inactive state. We found that aMD simulations enable monitoring the transition within the nanosecond timescale while capturing the known microscopic characteristics of the inactive states, such as the ionic lock, the inward position of F6.44, and water clusters. Distinct conformational states are shown to be stabilized by each biased agonist. In particular, in simulations of the receptor with the ß-arrestin biased agonist, N-cyclopentylbutanepherine we observe a different pattern of motions in helix 7 when compared to simulations with the G protein biased agonist, Salbutamol that involves perturbations of the network of interactions within the NPxxY motif. Understanding the network of interactions induced by biased ligands and the subsequent receptor conformational shifts will lead to development of more efficient drugs. © 2013 American Chemical Society

MALTS: A Tool to Simulate Lorentz Transmission Electron Microscopy From Micromagnetic Simulations

Here we describe the development of the MALTS software which is a generalized tool that simulates Lorentz Transmission Electron Microscopy (LTEM) contrast of magnetic nanostructures. Complex magnetic nanostructures typically have multiple stable domain structures. MALTS works in conjunction with the open access micromagnetic software Object Oriented Micromagnetic Framework or MuMax. Magnetically stable trial magnetization states of the object of interest are input into MALTS and simulated LTEM images are output. MALTS computes the magnetic and electric phases accrued by the transmitted electrons via the Aharonov-Bohm expressions. Transfer and envelope functions are used to simulate the progression of the electron wave through the microscope lenses. The final contrast image due to these effects is determined by Fourier Optics. Similar approaches have been used previously for simulations of specific cases of LTEM contrast. The novelty here is the integration with micromagnetic codes via a simple user interface enabling the computation of the contrast from any structure. The output from MALTS is in good agreement with both experimental data and published LTEM simulations. A widely-available generalized code for the analysis of Lorentz contrast is a much needed step towards the use of LTEM as a standardized laboratory technique.

Comparison of lagrangian and eulerian simulations of slurry flows in a sudden expansion

From a review of technical literature, it was not apparent if the Lagrangian or the Eulerian dispersed phase modeling approach was more valid to simulate dilute erosive slurry flow. In this study, both modeling approaches were employed and a comparative analysis of performances and accuracy between the two models was carried out. Due to an impossibility to define, for the Eulerian model already implemented in FLUENT, a set of boundary conditions consistent with the Lagrangian impulsive equations, an Eulerian dispersed phase model was integrated in the FLUENT code using subroutines and user-defined scalar equations. Numerical predictions obtained from the two different approaches for two-phase flow in a sudden expansion were compared with the measured data. Excellent agreement was attained between the predicted and observed fluid and particle velocity in the axial direction and for the kinetic energy. Erosion profiles in a sudden expansion computed using the Lagrangian scheme yielded good qualitative agreement with measured data and predicted a maximum impact angle of 29 deg at the fluid reattachment point. The Eulerian model was adversely affected by the reattachment of the fluid phase to the wall and the simulated erosion profiles were not in agreement with the Lagrangian or measured data. Furthermore, the Eulerian model under-predicted the Lagrangian impact angle at all locations except the reattachment point. © 2010 American Society of Mechanical Engineers.

Discriminating Taxonomic Categories and Domains in Mental Simulations of Concepts of Varying Concreteness

Most studies of conceptual knowledge in the brain focus on a narrow range of concrete conceptual categories, rely on the researchers' intuitions about which object belongs to these categories, and assume a broadly taxonomic organization of knowledge. In this fMRI study, we focus on concepts with a variety of concreteness levels; we use a state of the art lexical resource (WordNet 3.1) as the source for a relatively large number of category distinctions and compare a taxonomic style of organization with a domain-based model (associating concepts with scenarios). Participants mentally simulated situations associated with concepts when cued by text stimuli. Using multivariate pattern analysis, we find evidence that all Taxonomic categories and Domains can be distinguished from fMRI data and also observe a clear concreteness effect: Tools and Locations can be reliably predicted for unseen participants, but less concrete categories (e.g., Attributes, Communications, Events, Social Roles) can only be reliably discriminated within participants. A second concreteness effect relates to the interaction of Domain and Taxonomic category membership: Domain (e.g., relation to Law vs. Music) can be better predicted for less concrete categories. We repeated the analysis within anatomical regions, observing discrimination between all/most categories in the left middle occipital and temporal gyri, and more specialized discrimination for concrete categories Tool and Location in the left precentral and fusiform gyri, respectively. Highly concrete/abstract Taxonomic categories and Domain were segregated in frontal regions. We conclude that both Taxonomic and Domain class distinctions are relevant for interpreting neural structuring of concrete and abstract concepts.

Atomistic investigation on the structure-property relationship during thermal spray nanoparticle impact

During thermal spraying, hot particles impact on a colder substrate. This interaction of crystalline copper nanoparticles and copper substrate is modelled, using MD simulation. The quantitative results of the impacts at different velocities and temperatures are evaluated using a newly defined flattening aspect ratio. This ratio between the maximum diameter after the impact and the height of the splat increases with increasing Reynolds numbers until a critical value is reached. At higher Reynolds numbers the flattening aspect ratio decreases again, as the kinetic energy of the particle leads to increasing substrate temperature and, therefore, decreases the substrate resistance. Thus, the particle penetrates into the substrate and deforms less.