33 research outputs found
Parallel Performance for a Real Time Lattice Boltzmann Code
The paper will present the details of a Lattice Boltzmann solver running in real time for unsteady
wake computations. In addition to algorithmic implementation, computational results, single
core and parallel optimization of the methods are also discussed
Coupled atomistic–continuum simulations of nucleate boiling
Boiling is a striking example of a multiscale process, where the dynamics of bubbles is governed by the interplay between the molecular interactions responsible for nucleation, and the macroscale hydrodynamic and thermal boundary layers. A complete description of this phenomenon requires coupling molecular- and continuum-scale fluid mechanics into a single modelling framework. This article presents a hybrid atomistic–continuum computational model for coupled simulations of nucleate boiling. A domain decomposition coupling method is utilised, where the near-wall region is solved by a Molecular Dynamics description, which handles nucleation and the moving contact lines, while the bulk flow region is solved by a continuum-scale description based on the Navier–Stokes equations. The latter employs a Volume Of Fluid method to track the evolution of the liquid–vapour interface and the interphase mass transfer is computed via the Hertz–Knudsen–Schrage relationship. Boiling of a Lennard-Jones fluid over a heated wall is simulated and the hybrid solution is validated against a fully molecular solution. The results obtained with the coupled framework in terms of time-dependent bubble volume, phase-change rates, bubble dynamics and evolution of the temperature field agree quantitatively with those achieved by a MD-only simulation. The coupled framework reproduces the bubble growth rate over time from nucleation until a bubble diameter of about 70 nm, demonstrating the accuracy and robustness of the coupling architecture. This also demonstrates that the fluid dynamics description based on the Navier–Stokes equations is capable of correctly capturing the main heat and mass transfer mechanisms responsible for bubble growth at the nanoscale. The proposed modelling framework paves the way towards multiscale simulations of boiling, where the necessary molecular-level physics is retained in a computational fluid dynamics solver
A Systematic Analysis of Cell Cycle Regulators in Yeast Reveals That Most Factors Act Independently of Cell Size to Control Initiation of Division
Upstream events that trigger initiation of cell division, at a point called START in yeast, determine the overall rates of cell proliferation. The identity and complete sequence of those events remain unknown. Previous studies relied mainly on cell size changes to identify systematically genes required for the timely completion of START. Here, we evaluated panels of non-essential single gene deletion strains for altered DNA content by flow cytometry. This analysis revealed that most gene deletions that altered cell cycle progression did not change cell size. Our results highlight a strong requirement for ribosomal biogenesis and protein synthesis for initiation of cell division. We also identified numerous factors that have not been previously implicated in cell cycle control mechanisms. We found that CBS, which catalyzes the synthesis of cystathionine from serine and homocysteine, advances START in two ways: by promoting cell growth, which requires CBS's catalytic activity, and by a separate function, which does not require CBS's catalytic activity. CBS defects cause disease in humans, and in animals CBS has vital, non-catalytic, unknown roles. Hence, our results may be relevant for human biology. Taken together, these findings significantly expand the range of factors required for the timely initiation of cell division. The systematic identification of non-essential regulators of cell division we describe will be a valuable resource for analysis of cell cycle progression in yeast and other organisms
A spatial overview of the global importance of Indigenous lands for conservation
Understanding the scale, location and nature conservation values of the lands over which Indigenous Peoples exercise tradi- tional rights is central to implementation of several global conservation and climate agreements. However, spatial information on Indigenous lands has never been aggregated globally. Here, using publicly available geospatial resources, we show that Indigenous Peoples manage or have tenure rights over at least ~38 million km2 in 87 countries or politically distinct areas on all inhabited continents. This represents over a quarter of the world’s land surface, and intersects about 40% of all terrestrial protected areas and ecologically intact landscapes (for example, boreal and tropical primary forests, savannas and marshes). Our results add to growing evidence that recognizing Indigenous Peoples’ rights to land, benefit sharing and institutions is essential to meeting local and global conservation goals. The geospatial analysis presented here indicates that collaborative partnerships involving conservation practitioners, Indigenous Peoples and governments would yield significant benefits for conservation of ecologically valuable landscapes, ecosystems and genes for future generations
Planetary Migration in Protoplanetary Disks
The known exoplanet population displays a great diversity of orbital architectures, and explaining the origin of this is a major challenge for planet formation theories. The gravitational interaction between young planets and their protoplanetary disks provides one way in which planetary orbits can be shaped during the formation epoch. Disk-planet interactions are strongly influenced by the structure and physical processes that drive the evolution of the protoplanetary disk. In this review we focus on how disk-planet interactions drive the migration of planets when different assumptions are made about the physics of angular momentum transport, and how it drives accretion flows in protoplanetary disk models. In particular, we consider migration in discs where: (i) accretion flows arise because turbulence diffusively transports angular momentum; (ii) laminar accretion flows are confined to thin, ionised layers near disk surfaces and are driven by the launching of magneto-centrifugal winds, with the midplane being completely inert; (iii) laminar accretion flows pervade the full column density of the disc, and are driven by a combination of large scale horizontal and vertical magnetic fields
Numerical Study of Three-Dimensional Flow using Fast Parallel Particle Algorithms.
Numerical studies of turbulent flows have always been prone to crude approximations due to the limitations in computing power. With the advent of supercomputers, new turbulence models and fast particle algorithms, more highly resolved models can now be computed. Vortex Methods are grid-free and so avoid a number of shortcomings of gridbased methods for solving turbulent fluid flow equations; these include such problems as poor resolution and numerical diffusion. In these methods, the continuum vorticity field is discretised into a collection of Lagrangian elements, known as vortex elements, which are free to move in the flow field they collectively induce. The vortex element interaction constitutes an N-body problem, which may be calculated by a direct pairwise summation method, in a time proportional to N 2 . This time complexity may be reduced by use of fast particle algorithms. The most common algorithms are known as the N-body Treecodes and have a hierarchical structure. An in-de..
3D FFTs on HPCx (IBM vs FFTW)
Fast Fourier Transforms (FFTs) are an essential part of many scientific codes: from Molecular Dynamics to Climate Modelling. It is, therefore, evident that HPCx requires efficient methods for performing FFTs and related calculations. This study compares the performance of the two main FFT libraries on HPCx: IBM’s ESSL/PESSL and FFTW. Both serial and parallel (distributedmemory only) 3D complex-to-complex FFT routines are investigated, and the performance of the two different libraries is discussed. In general, the ESSL and FFTW serial 3D FFT routines are comparable. For parallel FFTs, the PESSL library is, in general, slightly faster, however, FFTW has better parallel efficiency. Some further comments are made about the overall performance of HPCx, and its impact of the use of FFT library routines.