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Amsterdam, Netherlands

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Glebbeek E.,Radboud University Nijmegen | Gaburov E.,SURFsara | Zwart S.P.,Leiden University | Pols O.R.,Radboud University Nijmegen
Monthly Notices of the Royal Astronomical Society | Year: 2013

In young dense clusters repeated collisions between massive stars may lead to the formation of a very massive star (above 100M⊙). In the past, the study of the long-term evolution of merger remnants has mostly focused on collisions between low-mass stars (up to about 2M⊙) in the context of blue-straggler formation. The evolution of collision products of more massive stars has not been as thoroughly investigated. In this paper, we study the long-term evolution of a number of stellar mergers formed by the head-on collision of a primary star with a mass of 5-40M⊙with a lower mass star at three points in its evolution in order to better understand their evolution. We use smooth particle hydrodynamics calculations to model the collision between the stars. The outcome of this calculation is reduced to one dimension and imported into a stellar evolution code. We follow the subsequent evolution of the collision product through the main sequence at least until the onse of helium burning. We find that little hydrogen is mixed into the core of the collision products, in agreement with previous studies of collisions between low-mass stars. For collisions involving evolved stars, we find that during the merger the surface nitrogen abundance can be strongly enhanced. The evolution of most of the collision products proceeds analogously to that of normal stars with the same mass, but with a larger radius and luminosity. However, the evolution of collision products that form with a hydrogen-depleted core is markedly different from that of normal stars with the same mass. They undergo a long-lived period of hydrogen-shell burning close to the main-sequence band in the Hertzsprung-Russell diagram and spend the initial part of core-helium burning as compact blue supergiants. © 2013 The Authors Published by Oxford University Press on behalf of the Royal Astronomical Society.

Chertova M.V.,University Utrecht | Spakman W.,University Utrecht | Spakman W.,University of Oslo | Geenen T.,SURFsara | And 2 more authors.
Journal of Geophysical Research: Solid Earth | Year: 2014

No consensus exists on the tectonic evolution of the western Mediterranean since ~35 Ma. Three disparate tectonic evolution scenarios are identified, each portraying slab rollback as the driving mechanism but with rollback starting from strongly different subduction geometries. As a critical test for the validity of each tectonic scenario we employ thermomechanical modeling of the 3-D subduction evolution. From each tectonic scenario we configure an initial condition for numerical modeling that mimics the perceived subduction geometry at ~35 Ma. We seek to optimize the fit between observed and predicted slab morphology by varying the nonlinear viscoplastic rheology for mantle, slab, and continental margins. From a wide range of experiments we conclude that a tectonic scenario that starts from NW dipping subduction confined to the Balearic margin at ~35 Ma is successful in predicting present-day slab morphology. The other two scenarios (initial subduction from Gibraltar to the Baleares and initial subduction under the African margin) lead to mantle structure much different from what is tomographically imaged. The preferred model predicts slab rotation by more than 180°, east-west lithosphere tearing along the north African margin and a resulting steep east dipping slab under the Gibraltar Strait. The preferred subduction model also meets the first-order temporal constraints corresponding to Mid-Miocene (~16 Ma) thrusting of the Kabylides onto the African margin and nearly stalled subduction under the Rif-Gibraltar-Betic arc since the Tortonian (~8 Ma). Our modeling also provides constraints on the rheological properties of the mantle and slab, and of continental margins in the region. Key Points Three-dimensional numerical modeling of western Mediterranean subduction evolution since 35 Ma Modeled subduction evolution distinguishes between disparate tectonic scenarios Preferred model matches observed slab morphology and key temporal constraints © 2014. American Geophysical Union. All Rights Reserved.

Aznar J.I.,Distributed Applications and Networks Area DANA | Ruiter E.,SURFsara | Garcia-Espin J.A.,Distributed Applications and Networks Area DANA | Dijkstra F.,SURFsara
2014 IEEE 3rd International Conference on Cloud Networking, CloudNet 2014 | Year: 2014

The main target of the proposed solution has been to develop and implement a vendor independent overlay platform on datacenter network infrastructures to simplify the administration of operational functions of SURFsara and achieve a solution easy to deploy, easy to configure and easy to manage, with 'MUST BE' requirements and limited manpower resources. The solution proposes an OpenNaaS management framework powered implementation to provide data center administrators with a vendor independent overlay platform, which allows administration of the most crucial operational functions, and allows fixed administration permissions to users requesting for infrastructure resources. OpenNaaS platform constitutes an enabler for innovation opportunities for the cloud ecosystem and the European software industry. OpenNaaS is currently being proposed as service management tool to provide with a unified way to configure networking resources and ease the administrative networking load across the different network segments end to end. © 2014 IEEE.

Francioli L.C.,University Utrecht | Menelaou A.,University Utrecht | Pulit S.L.,University Utrecht | Van Dijk F.,University of Groningen | And 93 more authors.
Nature Genetics | Year: 2014

Whole-genome sequencing enables complete characterization of genetic variation, but geographic clustering of rare alleles demands many diverse populations be studied. Here we describe the Genome of the Netherlands (GoNL) Project, in which we sequenced the whole genomes of 250 Dutch parent-offspring families and constructed a haplotype map of 20.4 million single-nucleotide variants and 1.2 million insertions and deletions. The intermediate coverage (∼13×) and trio design enabled extensive characterization of structural variation, including midsize events (30-500 bp) previously poorly catalogued and de novo mutations. We demonstrate that the quality of the haplotypes boosts imputation accuracy in independent samples, especially for lower frequency alleles. Population genetic analyses demonstrate fine-scale structure across the country and support multiple ancient migrations, consistent with historical changes in sea level and flooding. The GoNL Project illustrates how single-population whole-genome sequencing can provide detailed characterization of genetic variation and may guide the design of future population studies. © 2014 Nature America, Inc.

Moghaddam F.A.,VU University Amsterdam | Geenen T.,SURFsara | Lago P.,VU University Amsterdam | Grosso P.,VU University Amsterdam
2015 Sustainable Internet and ICT for Sustainability, SustainIT 2015 | Year: 2015

The growth of power consumption in ICT infrastructures emphasizes the importance of monitoring their usage and finding available room for improvement. Users can choose among several existing tools to determine the energy profile of a running application in order to provide more sustainable software. We conducted a field study in the SURFsara data center and we experimented with the tools available, assessing them in light of their informative power. We derived some recommendations for ICT users and infrastructure operators that highlight the relation between the intended use of the profile and the easiness of running a specific tool. We categorize users in two types: the generic user, who is interested in summary statistical results on power measurements and the software developer that intends to delve in the code details in order to reprogram the application more efficiently. We concluded that SLURM and Score-P are suitable for both types of users when their requirements are thoroughly studied and taken into account. © 2015 IFIP.

van der Poel E.P.,University of Twente | Ostilla-Monico R.,University of Twente | Donners J.,SURFsara | Verzicco R.,University of Twente | Verzicco R.,University of Rome Tor Vergata
Computers and Fluids | Year: 2015

We present a numerical scheme geared for high performance computation of wall-bounded turbulent flows. The number of all-to-all communications is decreased to only six instances by using a two-dimensional (pencil) domain decomposition and utilizing the favourable scaling of the CFL time-step constraint as compared to the diffusive time-step constraint. As the CFL condition is more restrictive at high driving, implicit time integration of the viscous terms in the wall-parallel directions is no longer required. This avoids the communication of non-local information to a process for the computation of implicit derivatives in these directions. We explain in detail the numerical scheme used for the integration of the equations, and the underlying parallelization. The code is shown to have very good strong and weak scaling to at least 64. K cores. © 2015 The Authors.

Genseberger M.,Deltares | Donners J.,SURFsara
Procedia Computer Science | Year: 2015

In the Netherlands, for coastal and inland water applications, wave modelling with SWAN has become a main ingredient. However, computational times are relatively high. Therefore we investigated the parallel efficiency of the current MPI and OpenMP versions of SWAN. The MPI version is not that efficient as the OpenMP version within a single node. Therefore, in this paper we propose a hybrid version of SWAN. It combines the efficiency of the current OpenMP version on shared memory with the capability of the current MPI version to distribute memory over nodes. We describe the numerical algorithm. With initial numerical experiments we show the potential of this hybrid version. Parallel I/O, further optimization, and behavior for larger number of nodes will be subject of future research. © The Authors. Published by Elsevier B.V.

Makkes M.X.,University of Amsterdam | Makkes M.X.,TNO | Taal A.,University of Amsterdam | Osseyran A.,SURFSara | Grosso P.,University of Amsterdam
Journal of Cloud Computing | Year: 2013

Cloud computing gives users much freedom on where they host their computation and storage. However the CO2 emission of a job depends on the location and the energy efficiency of the data centers where it is run. We developed a decision framework that determines to move computation with accompanying data from a local to a greener remote data center for a lower CO2 emissions. The model underlying the framework accounts for the energy consumption at the local and remote sites, as well as of networks among them. We showed that the type of network connecting the two sites has a significant impact on the total CO2 emission. Furthermore, the task's complexity is a factor in deciding when and where to move computation. © 2013 Makkes et al.

PubMed | University Utrecht, Leiden University, University of Groningen, VU University Amsterdam and 4 more.
Type: Journal Article | Journal: Nature genetics | Year: 2016

Genetic risk factors often localize to noncoding regions of the genome with unknown effects on disease etiology. Expression quantitative trait loci (eQTLs) help to explain the regulatory mechanisms underlying these genetic associations. Knowledge of the context that determines the nature and strength of eQTLs may help identify cell types relevant to pathophysiology and the regulatory networks underlying disease. Here we generated peripheral blood RNA-seq data from 2,116 unrelated individuals and systematically identified context-dependent eQTLs using a hypothesis-free strategy that does not require previous knowledge of the identity of the modifiers. Of the 23,060 significant cis-regulated genes (false discovery rate (FDR) 0.05), 2,743 (12%) showed context-dependent eQTL effects. The majority of these effects were influenced by cell type composition. A set of 145 cis-eQTLs depended on type I interferon signaling. Others were modulated by specific transcription factors binding to the eQTL SNPs.

PubMed | University Utrecht, Ontario Cancer Institute, Leiden University, University of Groningen and 4 more.
Type: Journal Article | Journal: Nature genetics | Year: 2016

Most disease-associated genetic variants are noncoding, making it challenging to design experiments to understand their functional consequences. Identification of expression quantitative trait loci (eQTLs) has been a powerful approach to infer the downstream effects of disease-associated variants, but most of these variants remain unexplained. The analysis of DNA methylation, a key component of the epigenome, offers highly complementary data on the regulatory potential of genomic regions. Here we show that disease-associated variants have widespread effects on DNA methylation in trans that likely reflect differential occupancy of trans binding sites by cis-regulated transcription factors. Using multiple omics data sets from 3,841 Dutch individuals, we identified 1,907 established trait-associated SNPs that affect the methylation levels of 10,141 different CpG sites in trans (false discovery rate (FDR) < 0.05). These included SNPs that affect both the expression of a nearby transcription factor (such as NFKB1, CTCF and NKX2-3) and methylation of its respective binding site across the genome. Trans methylation QTLs effectively expose the downstream effects of disease-associated variants.

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