Three-dimensional finite element modelling of stack pollutant emissions

In this paper we propose a finite element method approach formodelling the air quality in a local scale over complex terrain. The area of interest is up to tens of kilometres and it includes pollutant sources. The proposed methodology involves the generation of an adaptive tetrahedral mesh, the computation of an ambient wind field, the inclusion of the plume rise effect in the wind field, and the simulation of transport and reaction of pollutants. The methodology is used to simulate a fictitious pollution episode in La Palma island (Canary Island, Spain).Peer ReviewedPostprint (published version

Chaste: a test-driven approach to software development for biological modelling

Chaste (‘Cancer, heart and soft-tissue environment’) is a software library and a set of test suites for computational simulations in the domain of biology. Current functionality has arisen from modelling in the fields of cancer, cardiac physiology and soft-tissue mechanics. It is released under the LGPL 2.1 licence.\ud \ud Chaste has been developed using agile programming methods. The project began in 2005 when it was reasoned that the modelling of a variety of physiological phenomena required both a generic mathematical modelling framework, and a generic computational/simulation framework. The Chaste project evolved from the Integrative Biology (IB) e-Science Project, an inter-institutional project aimed at developing a suitable IT infrastructure to support physiome-level computational modelling, with a primary focus on cardiac and cancer modelling

Mapping energy transport networks in proteins

The response of proteins to chemical reactions or impulsive excitation that occurs within the molecule has fascinated chemists for decades. In recent years ultrafast X-ray studies have provided ever more detailed information about the evolution of protein structural change following ligand photolysis, and time-resolved IR and Raman techniques, e.g., have provided detailed pictures of the nature and rate of energy transport in peptides and proteins, including recent advances in identifying transport through individual amino acids of several heme proteins. Computational tools to locate energy transport pathways in proteins have also been advancing. Energy transport pathways in proteins have since some time been identified by molecular dynamics (MD) simulations, and more recent efforts have focused on the development of coarse graining approaches, some of which have exploited analogies to thermal transport in other molecular materials. With the identification of pathways in proteins and protein complexes, network analysis has been applied to locate residues that control protein dynamics and possibly allostery, where chemical reactions at one binding site mediate reactions at distance sites of the protein. In this chapter we review approaches for locating computationally energy transport networks in proteins. We present background into energy and thermal transport in condensed phase and macromolecules that underlies the approaches we discuss before turning to a description of the approaches themselves. We also illustrate the application of the computational methods for locating energy transport networks and simulating energy dynamics in proteins with several examples

A modeling framework for contact, adhesion and mechano-transduction between excitable deformable cells

Cardiac myocytes are the fundamental cells composing the heart muscle. The propagation of electric signals and chemical quantities through them is responsible for their nonlinear contraction and dilatation. In this study, a theoretical model and a finite element formulation are proposed for the simulation of adhesive contact interactions between myocytes across the so-called gap junctions. A multi-field interface constitutive law is proposed for their description, integrating the adhesive and contact mechanical response with their electrophysiological behavior. From the computational point of view, the initial and boundary value problem is formulated as a structure-structure interaction problem, which leads to a straightforward implementation amenable for parallel computations. Numerical tests are conducted on different couples of myocytes, characterized by different shapes related to their stages of growth, capturing the experimental response. The proposed framework is expected to have impact on the understanding how imperfect mechano-transduction could lead to emergent pathological responses.Comment: 31 pages, 17 figure

Experimental effects on dynamics and thermodynamics in nuclear reactions on the symmetry energy as seen by the CHIMERA 4π\pi detector

Heavy ion collisions have been widely used in the last decade to constraint the parameterizations of the symmetry energy term of nuclear equation of state (EOS) for asymmetric nuclear matter as a function of baryonic density. In the Fermi energy domain one is faced with variations of the density within a narrow range of values around the saturation density $\rho_0$=0.16 fm$^{-3}$ down towards sub-saturation densities. The experimental observables which are sensitive to the symmetry energy are constructed starting from the detected light particles, clusters and heavy fragments that, in heavy ion collisions, are generally produced by different emission mechanisms at different stages and time scales of the reaction. In this review the effects of dynamics and thermodynamics on the symmetry energy in nuclear reactions are discussed and characterized using an overview of the data taken so far with the CHIMERA multi-detector array.Comment: 21 pages, 25 figures. Review to appear in EPJA special volume on nuclear symmetry energ

Draping of Cluster Magnetic Fields over Bullets and Bubbles -- Morphology and Dynamic Effects

High-resolution X-ray observations have revealed cavities and `cold fronts' with sharp edges in temperature, density, and metallicity within galaxy clusters. Their presence poses a puzzle since these features are not expected to be hydrodynamically stable, or to remain sharp in the presence of diffusion. However, a moving core or bubble in even a very weakly magnetized plasma necessarily sweeps up enough magnetic field to build up a dynamically important sheath around the object; the layer's strength is set by a competition between `plowing up' of field and field lines slipping around the core. We show that a two-dimensional approach to the problem is quite generally not possible. In three dimensions, we show with analytic arguments and in numerical experiments, that this magnetic layer modifies the dynamics of a plunging core, greatly modifies the effects of hydrodynamic instabilities on the core, modifies the geometry of stripped material, and even slows the fall of the core through magnetic tension. We derive an expression for the maximum magnetic field strength, the thickness of the layer, and the opening angle of the magnetic wake. The morphology of the magnetic draping layer implies the suppression of thermal conduction across the layer, thus conserving strong temperature gradients over the contact surface. The intermittent amplification of the magnetic field as well as the injection of MHD turbulence in the wake of the core is identified to be due to vorticity generation within the magnetic draping layer. These results have important consequences for understanding the physical properties and the complex gasdynamical processes of the intra-cluster medium, and apply quite generally to motions through other magnetized environments, e.g., the ISM.Comment: For version of this paper with interactive 3D graphics and full-resolution figures, see http://www.cita.utoronto.ca/~ljdursi/draping/ . 19p, 26 figures, emulateapj format. Version accepted by ApJ - new references, improved figure

Population III star formation in a Lambda CDM universe, I: The effect of formation redshift and environment on protostellar accretion rate

(abridged) We perform 12 extremely high resolution adaptive mesh refinement cosmological hydrodynamic simulations of Population III star formation in a Lambda CDM universe, varying the box size and large-scale structure, to understand systematic effects in the formation of primordial protostellar cores. We find results that are qualitatively similar to those observed previously. We observe that the threshold halo mass for formation of a Population III protostar does not evolve significantly with time in the redshift range studied (33 > z > 19) but exhibits substantial scatter due to different halo assembly histories: Halos which assembled more slowly develop cooling cores at lower mass than those that assemble more rapidly, in agreement with Yoshida et al. (2003). We do, however, observe significant evolution in the accretion rates of Population III protostars with redshift, with objects that form later having higher maximum accretion rates, with a variation of two orders of magnitude (10^-4 - 10^-2 Msolar/year). This can be explained by considering the evolving virial properties of the halos with redshift and the physics of molecular hydrogen formation at low densities. Our result implies that the mass distribution of Population III stars inferred from their accretion rates may be broader than previously thought, and may evolve with redshift. Finally, we observe that our collapsing protostellar cloud cores do not fragment, consistent with previous results, which suggests that Population III stars which form in halos of mass 10^5 - 10^6 Msun always form in isolation.Comment: Accepted by The Astrophysical Journal. Some minor changes. 65 pages, 3 tables, 21 figures (3 color). To appear in January 1, 2007 issu