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  • richardmitnick 7:04 pm on February 22, 2019 Permalink | Reply
    Tags: "Supercomputing Neutron Star Structures and Mergers", , Bridges at Pittsburgh Supercomputer Center, , , SDSC Dell Comet supercomputer, Stampede2 at the Texas Advanced Computing Center (TACC), , ,   

    From insideHPC: “Supercomputing Neutron Star Structures and Mergers” 

    From insideHPC

    This image of an eccentric binary neutron star system’s close encounter is an example of the large surface gravity wave excitations, which are similar to ocean waves found in very deep water. Credit: William East, Perimeter Institute for Theoretical Physics

    Perimeter Institute in Waterloo, Canada

    Over at XSEDE, Kimberly Mann Bruch & Jan Zverina from the San Diego Supercomputer Center write that researchers are using supercomputers to create detailed simulations of neutron star structures and mergers to better understand gravitational waves, which were detected for the first time in 2015.

    SDSC Dell Comet* supercomputer

    During a supernova, a single massive star explodes – some die and form black holes while others survive, depending on the star’s mass. Some of these supernova survivors are stars whose centers collapse and their protons and electrons form into a neutron star, which has an average gravitational pull that is two billion times the gravity on Earth.

    Researchers from the U.S., Canada, and Brazil have been focusing on the construction of a gravitational wave model for the detection of eccentric binary neutron stars. Using Comet* at the San Diego Supercomputer Center (SDSC) and Stampede2 at the Texas Advanced Computing Center (TACC), the scientists performed simulations of oscillating binary neutron stars to develop a novel model to predict the timing of various pericenter passages, which are the points of closest approach for revolving space objects.

    Texas Advanced Computer Center

    TACC DELL EMC Stampede2 supercomputer

    Their study, Evolution of Highly Eccentric Binary Neutron Stars Including Tidal Effects was published in Physical Review D. Frans Pretorius, a physics professor at Princeton University, is the Principal Investigator on the allocated project.

    “Our study’s findings provide insight into binary neutron stars and their role in detecting gravitational waves,” according to co-author Huan Yang, with the Perimeter Institute for Theoretical Physics in Waterloo, Ontario, Canada. “We can see that the oscillation of the stars significantly alters the trajectory and it is important to mention the evolution of the modes. For this case, during some of the later close encounters, the frequency of the orbit is larger when this evolution is tracked – compared to when it is not – as energy and angular momentum are taken out of the neutron star oscillations and put back into orbit.”

    In other words, probing gravitational waves from eccentric binary neutron stars provides a unique opportunity to observe neutron star oscillations. Through these measurements, researchers can infer the internal structure of neutron stars.

    “This is analogous to the example of ‘hearing the shape on a drum,’ where the shape of a drumhead can be determined by measuring frequencies of its modes,” said Yang. “By ‘hearing’ the modes of neutron stars with gravitational waves, the star’s size and internal structure will be similarly determined, or at least constrained.”

    “In particular, our dynamical space-time simulations solve the equations of Einstein’s theory of general relativity coupled to perfect fluids,” said co-author Vasileios Paschalidis, with the University of Arizona’s Theoretical Astrophysics Program. “Neutron star matter can be described as a perfect fluid, therefore the simulations contain the necessary physics to understand how neutron stars oscillate due to tidal interactions after every pericenter passage, and how the orbit changes due to the excited neutron star oscillations. Such simulations are computationally very expensive and can be performed only in high-performance computing centers.”

    “XSEDE resources significantly accelerated our scientific output,” noted Paschalidis, whose group has been using XSEDE for well over a decade, when they were students or post-doctoral researchers. “If I were to put a number on it, I would say that using XSEDE accelerated our research by a factor of three or more, compared to using local resources alone.”

    Neutron Star Mergers Form the Cauldron that Brews Gravitational Waves

    Merging neutron stars. Image Credit: Mark Garlick, University of Warwick.

    The merger of two neutron stars produces a hot (up to one trillion degrees Kelvin), rapidly rotating massive neutron star. This remnant is expected to collapse to form a black hole within a timescale that could be as short as one millisecond, or as long as many hours, depending on the sum of the masses of the two neutron stars.

    Featured in a recent issue of the Monthly Notices of the Royal Astronomical Society, Princeton University Computational and Theoretical Astrophysicist David Radice and his colleagues presented results from their simulations of the formation of neutron star merger remnants surviving for at least one tenth of a second. Radice turned to XSEDE for access to Comet, Stampede2, and Bridges, which is based at the Pittsburgh Supercomputing Center (PSC).

    Pittsburgh Supercomputer Center

    Bridges supercomputer at PSC

    It has been long thought that this type of merger product would be driven toward solid-body rotation by turbulent angular momentum transport, which acts as an effective viscosity. However, Radice and his collaborators discovered that the evolution of these objects is actually more complex.

    The massive neutron star shown in this three-dimensional rendition of a Comet-enabled simulation shows the emergence of a wind driven by neutrino radiation. The star is surrounded by debris expelled during and shortly after the merger. Credit: David Radice, Princeton University

    “We found that long-lived neutron star merger remnants are born with so much angular momentum that they are unable to reach solid body rotation,” said Radice. “Instead, they are viscously unstable. We expect that this instability will result in the launching of massive neutron rich winds. These winds, in turn, will be extremely bright in the UV/optical/infrared bands. The observation of such transients, in combination with gravitational-wave events or short gamma-ray bursts, would be ‘smoking gun’ evidence for the formation of long-lived neutron star merger remnants.”

    If detected, the bright transients predicted in this study could allow astronomers to measure the threshold mass below which neutron star mergers do not result in rapid black hole formation. This insight would be key in the quest to understand the properties of matter at extreme densities found in the hearts of neutron stars.

    Radice’s research used 35 high-resolution, general-relativistic neutron star merger simulations, which calculated the geometry of space-time as predicted by Einstein’s equations and simulated the neutron star matter using sophisticated microphysical models. On average, one of these simulations required about 300,000 CPU-hours.

    “My research would not be possible without XSEDE,” said Radice, who has used XSEDE resources since 2013, and for this study collaborated with Lars Koesterke at TACC to run his code efficiently on Stampede2. Specifically, this work was conducted in the context of an XSEDE Extended Collaborative Support Services (ECSS) project, which will be of benefit to future research.”

    “The cost can be up to a factor of three times higher for the selected models that were run at even higher resolution and depending on the detail level in the microphysics,” added Radice. “Because of the unique requirements of this study, which included a large number of intermediate-size simulations and few larger calculations, a key enabler was the availability of a combination of capability and capacity supercomputers including Comet and Bridges.”

    See the full article here .


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    Founded on December 28, 2006, insideHPC is a blog that distills news and events in the world of HPC and presents them in bite-sized nuggets of helpfulness as a resource for supercomputing professionals. As one reader said, we’re sifting through all the news so you don’t have to!

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  • richardmitnick 10:32 am on December 20, 2017 Permalink | Reply
    Tags: , Computation combined with experimentation helped advance work in developing a model of osteoregeneration, Genes could be activated in human stem cells that initiate biomineralization a key step in bone formation, , SDSC Dell Comet supercomputer, Silk has been shown to be a suitable scaffold for tissue regeneration, Silky Secrets to Make Bones, Stampede1, , ,   

    From TACC: “Silky Secrets to Make Bones” 

    TACC bloc

    Texas Advanced Computing Center

    December 19, 2017
    Jorge Salazar

    Scientists used supercomputers and fused golden orb weaver spider web silk with silica to activate genes in human stem cells that initiated biomineralization, a key step in bone formation. (devra/flickr)

    Some secrets to repair our skeletons might be found in the silky webs of spiders, according to recent experiments guided by supercomputers. Scientists involved say their results will help understand the details of osteoregeneration, or how bones regenerate.
    A study found that genes could be activated in human stem cells that initiate biomineralization, a key step in bone formation. Scientists achieved these results with engineered silk derived from the dragline of golden orb weaver spider webs, which they combined with silica. The study appeared September 2017 in the journal Advanced Functional Materials and has been the result of the combined effort from three institutions: Tufts University, Massachusetts Institute of Technology and Nottingham Trent University.

    XSEDE supercomputers Stampede at TACC and Comet at SDSC helped study authors simulate the head piece domain of the cell membrane protein receptor integrin in solution, based on molecular dynamics modeling. (Davoud Ebrahimi)

    SDSC Dell Comet supercomputer

    Study authors used the supercomputers Stampede1 at the Texas Advanced Computing Center (TACC) and Comet at the San Diego Supercomputer Center (SDSC) at the University of California San Diego through an allocation from XSEDE, the eXtreme Science and Engineering Discovery Environment, funded by the National Science Foundation. The supercomputers helped scientists model how the cell membrane protein receptor called integrin folds and activates the intracellular pathways that lead to bone formation. The research will help larger efforts to cure bone growth diseases such as osteoporosis or calcific aortic valve disease.

    “This work demonstrates a direct link between silk-silica-based biomaterials and intracellular pathways leading to osteogenesis,” said study co-author Zaira Martín-Moldes, a post-doctoral scholar at the Kaplan Lab at Tufts University. She researches the development of new biomaterials based on silk. “The hybrid material promoted the differentiation of human mesenchymal stem cells, the progenitor cells from the bone marrow, to osteoblasts as an indicator of osteogenesis, or bone-like tissue formation,” Martín-Moldes said.

    “Silk has been shown to be a suitable scaffold for tissue regeneration, due to its outstanding mechanical properties,” Martín-Moldes explained. It’s biodegradable. It’s biocompatible. And it’s fine-tunable through bioengineering modifications. The experimental team at Tufts University modified the genetic sequence of silk from golden orb weaver spiders (Nephila clavipes) and fused the silica-promoting peptide R5 derived from a gene of the diatom Cylindrotheca fusiformis silaffin.

    The bone formation study targeted biomineralization, a critical process in materials biology. “We would love to generate a model that helps us predict and modulate these responses both in terms of preventing the mineralization and also to promote it,” Martín-Moldes said.

    “High performance supercomputing simulations are utilized along with experimental approaches to develop a model for the integrin activation, which is the first step in the bone formation process,” said study co-author Davoud Ebrahimi, a postdoctoral associate at the Laboratory for Atomistic and Molecular Mechanics of the Massachusetts Institute of Technology.

    Integrin embeds itself in the cell membrane and mediates signals between the inside and the outside of cells. In its dormant state, the head unit sticking out of the membrane is bent over like a nodding sleeper. This inactive state prevents cellular adhesion. In its activated state, the head unit straightens out and is available for chemical binding at its exposed ligand region.

    “Sampling different states of the conformation of integrins in contact with silicified or non-silicified surfaces could predict activation of the pathway,” Ebrahimi explained. Sampling the folding of proteins remains a classically computationally expensive problem, despite recent and large efforts in developing new algorithms.

    The derived silk–silica chimera they studied weighed in around a hefty 40 kilodaltons. “In this research, what we did in order to reduce the computational costs, we have only modeled the head piece of the protein, which is getting in contact with the surface that we’re modeling,” Ebrahimi said. “But again, it’s a big system to simulate and can’t be done on an ordinary system or ordinary computers.”

    The Computational team at MIT used the molecular dynamics package called Gromacs, a software for chemical simulation available on both the Stampede1 and Comet supercomputing systems. “We could perform those large simulations by having access to XSEDE computational clusters,” he said.

    “I have a very long-standing positive experience using XSEDE resources,” said Ebrahimi. “I’ve been using them for almost 10 years now for my projects during my graduate and post-doctoral experiences. And the staff at XSEDE are really helpful if you encounter any problems. If you need software that should be installed and it’s not available, they help and guide you through the process of doing your research. I remember exchanging a lot of emails the first time I was trying to use the clusters, and I was not so familiar. I got a lot of help from XSEDE resources and people at XSEDE. I really appreciate the time and effort that they put in order to solve computational problems that we usually encounter during our simulation,” Ebrahimi reflected.

    Computation combined with experimentation helped advance work in developing a model of osteoregeneration. “We propose a mechanism in our work,” explained Martín-Moldes, “that starts with the silica-silk surface activating a specific cell membrane protein receptor, in this case integrin αVβ3.” She said this activation triggers a cascade in the cell through three mitogen-activated protein kinsase (MAPK) pathways, the main one being the c-Jun N-terminal kinase (JNK) cascade.

    Proposed mechanism for hMSC osteogenesis induction on silica surfaces. The binding of integrin αVβ3 to the silica surface promotes its activation, that triggers an activation cascade that involves the three MAPK pathways, ERK, p38, but mainly JNK (reflected as wider arrow), which promotes AP-1 activation and translocation to the nucleus to activate Runx2 transcription factor. Runx2 is the finally responsible for the induction of bone extracellular matrix proteins and other osteoblast differentiation genes. B) In the presence of a neutralizing antibody against αVβ3, there is no activation and induction of MAPK cascades, thus no induction of bone extracellular matrix genes and hence, no differentiation. (Davoud Ebrahimi)

    She added that other factors are also involved in this process such as Runx2, the main transcription factor related to osteogenesis. According to the study, the control system did not show any response, and neither did the blockage of integrin using an antibody, confirming its involvement in this process. “Another important outcome was the correlation between the amount of silica deposited in the film and the level of induction of the genes that we analyzed,” Martín-Moldes said. “These factors also provide an important feature to control in future material design for bone-forming biomaterials.”

    “We are doing a basic research here with our silk-silica systems,” Martín-Moldes explained. “But we are helping in building the pathway to generate biomaterials that could be used in the future. The mineralization is a critical process. The final goal is to develop these models that help design the biomaterials to optimize the bone regeneration process, when the bone is required to regenerate or to minimize it when we need to reduce the bone formation.”

    These results help advance the research and are useful in larger efforts to help cure and treat bone diseases. “We could help in curing disease related to bone formation, such as calcific aortic valve disease or osteoporosis, which we need to know the pathway to control the amount of bone formed, to either reduce or increase it, Ebrahimi said.

    “Intracellular Pathways Involved in Bone Regeneration Triggered by Recombinant Silk–Silica Chimeras,” DOI: 10.1002/adfm.201702570, appeared September 2017 in the journal Advanced Functional Materials. The National Institutes of Health funded the study, and the National Science Foundation through XSEDE provided computational resources. The study authors are Zaira Martín-Moldes, Nina Dinjaski, David L. Kaplan of Tufts University; Davoud Ebrahimi and Markus J. Buehler of the Massachusetts Institute of Technology; Robyn Plowright and Carole C. Perry of Nottingham Trent University.

    See the full article here .

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    The Texas Advanced Computing Center (TACC) designs and operates some of the world’s most powerful computing resources. The center’s mission is to enable discoveries that advance science and society through the application of advanced computing technologies.

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