The new "L-CSC" supercomputer at the GSI Helmholtz Centre for Heavy Ion Research is ranked as the world's most energy-efficient supercomputer
FRANKFURT/NEW ORLEANS. The new "L-CSC" supercomputer at the GSI Helmholtz Centre for Heavy Ion Research is ranked as the world's most energy-efficient supercomputer. The new supercomputer reached first place on the "Green500" list published in New Orleans on Thursday, comparing the energy efficiency of the fastest supercomputers around the world. With a computing power of 5.27 gigaflops per watt, the "L-CSC" has also set a new world record for energy efficiency among supercomputers. Second and third place on the new list are held by two Japanese supercomputers (Suiren, Tsukuba and Tsubame-KFC, Tokyo).
"L-CSC" was developed at the Frankfurt Institute for Advanced Studies (FIAS) and the Goethe University Frankfurt. The supercomputer was financed by the GSI Helmholtz Centre for Heavy Ion Research in Darmstadt, where it is used for simulations and calculations in basic physics research. It is also slated to prepare experiments at the large international accelerator centre FAIR (Facility for Antiproton and Ion Research), which is currently under development in Darmstadt. The super-fast and energy-saving supercomputer was developed by the Frankfurt computer sciences professor Volker Lindenstruth and his team. It primarily uses efficient cooling and conventional graphics cards, in order to reduce the energy consumption and investment cost for the supercomputer.
Obtaining the world champion title for the "L-CSC" is already the third success for the FIAS scientists within four years on the worldwide who's-who list of green supercomputers: in 2010, the Frankfurt supercomputer "LOEWE-CSC" at Goethe University reached eighth place as Europe's most environmentally-friendly supercomputer. Two years later, the Saudi Arabian computer "SANAM", developed in Frankfurt and Darmstadt, reached second place on the "Green500" list. The world record crowns this series. The list is based on an assessment of how many floating point operations per second a supercomputer optimized for speed achieves with one watt of power.
"L-CSC" is still under construction. At the moment, 56 out of a total of 160 servers are installed. This already makes the computer in Darmstadt one of the world's fastest. On the worldwide "Top500" ranking – which is based purely on speed – it currently holds 168th place with 316.7 trillion floating point operations per second – about three thousand times faster than a normal office PC. And it will perform calculations about three times faster once it is completed in the coming weeks.
"L-CSC" was developed on the basis of the "LOEWE-CSC" and "SANAM" supercomputers, and relies even more heavily on graphics cards for its computing power. Its name is based on its predecessor. However, "L-CSC" performs computations considerably more quickly than its four-year-old predecessor "LOEWE-CSC" and achieves over seven times the computing power with the same amount of energy. This was achieved by using more optimized high speed graphics chips and improved software developed at the FIAS.
The investment costs for "L-CSC" are around two million Euros. When it comes to supercomputers, saving energy isn't just a question of protecting the environment, but is also important in saving on the electricity bill. Thus "L-CSC" runs with significantly lower operating costs than less energy-efficient supercomputers which are just as fast.
The person who developed the "L-CSC", Chairman of the Board at FIAS, IT Director at GSI and professor for high-performance computing architecture at the Goethe-Universität Frankfurt, Volker Lindenstruth, feels that the top ranking of his supercomputer confirms the long-standing energy efficiency efforts: "We are also making a contribution which will allow supercomputers to be used increasingly in industry, because society also requires more and more computing power, whether for technical developments, big data applications, cloud computing or other things."
From a technical point of view, "L-CSC" is a computing cluster, a network of connected computers. Upon completion, the computer is slated to consist of a total of 160 servers (ASUS ESC4000 G2S/FDR), with 1,600 processor cores, each of which contains two Intel-Ivy-Bridge processors and four AMD FirePro graphics cards. Every server has 256 Gigabytes of working memory. The servers are connected through an FDR Infiniband network. In theory, "L-CSC" is capable of providing a peak computing power of 1.7 petaflops with double precision, so 1.7 quadrillion
floating point operations per second in this configuration. This makes it the fourth-fastest supercomputer in Germany.
Information: FIAS Public Relations Office, Reiner Korbmann, c/o Science&Media, firstname.lastname@example.org; Phone ++49(0)89-642 17 50; Frankfurt Institute for Advanced Studies (FIAS), Ruth-Moufang-Str. 1, 60438 Frankfurt am Main, Phone ++49(0)69-798 44100; email@example.com.
Hypoxia protein also regulates growth factors
FRANKFURT/GIESSEN. Healthy cells reduce their growth when there is a lack of oxygen (hypoxia). This makes it even more surprising that hypoxia is a characteristic feature of malignant tumours. In two publications in the current edition of the "Nature Communications" journal, researchers from Goethe University and the Justus-Liebig-University of Giessen report on how cancer cells succeed at circumventing the genetic program of growth inhibition.
It has long been known that PHD proteins (prolyl-hydroxylase domain proteins) play a key role among the regulators of hypoxia. They control the stability of the hypoxia-induced transcription factors (HIFs) which govern the adaptation of cells to a lack of oxygen. The two teams led by Professor Amparo Acker-Palmer, Goethe University, and Professor Till Acker, Justus-Liebig-University, have now discovered that a special PHD protein, PHD3, also controls the epidermal growth factor receptor (EGFR).
In healthy cells, PHD3 responds to stressors such as a lack of oxygen by stimulating the uptake of EGF receptors into the cell interior. Growth signals are down-regulated by this internalisation. "We have discovered that PHD3 serves as a scaffolding protein, binding to central adapter proteins such as Eps15 and Epsin1 in order to promote the uptake of EGFR into the cells," says Acker-Palmer. This process is disrupted in tumour cells due to the loss of PHD3. As a result, the internalisation of EGFR is suppressed, which leads to overactivity of EGFR signals, and thus to uncontrolled cell growth.
The research team was able to show that the loss of PHD3 is a crucial step in the growth of human malignant brain tumours (glioblastomas). The tumour cells thus become refractory to the growth-inhibiting signals under hypoxia. "Clinically, this discovery is highly relevant, because it shows an alternative mechanism for the hyperactivation of the EGF receptor that is independent of its genetic amplification. It can be therapeutically suppressed by EGFR inhibitors," explains Till Acker, a neuropathologist at the University of Giessen.
"Our work shows an unexpected and new function of PHD3 on the interface of two currently red-hot research areas: Oxygen measurement and EGFR signalling," Acker-Palmer explains. "This once again proves how significant growth receptor internalisation is to the development of cancer." This connection was already shown by the research team in 2010 for tumour angiogenesis (Sawamiphak et al, Nature 2010).
Henze et al: Loss of PHD3 allows tumours to overcome hypoxic growth inhibition and sustain proliferation through EGFR; Nature communications 25.11.2014; DOI 10.1038/ncomm6582
Garvalov et al.: PHD3 regulates EGFR internalization and signalling in tumours, Nature communications 25.11.2014, DOI: 10.1038/ncomms6577
Information: Prof. Amparo Acker-Palmer, Institute for Cell Biology and Neuroscience and the Buchmann Institute for Molecular Life Sciences, Campus Riedberg,Phone ++49(0)69 798- 42563, Acker-Palmer@bio.uni-frankfurt.de.Prof. Till Acker, Institute of Neuropathology, University Clinic Giessen and Marburg GmbH, Arndtstraße 16, 35392 Gießen, Phone ++49(0)641 99-41181, firstname.lastname@example.org
Structure of the ABC transporter, elucidated thanks to pioneering structure analysis/Publication in Nature
FRANKFURT. ABC-Transporters are proteins that are embedded in the cell membrane and facilitate the transport across cellular barriers not only of an almost unlimited variety of toxic substances, but also of substances that are essential for life. They also play a role in the development of antibiotic resistance. A research group at the Goethe University in Frankfurt am Main, in co-operation with American colleagues, has now succeeded in elucidating the detailed structure of this transporter.
"On the one hand, ABC transporters cause diseases such as cystic fibrosis, while on the other hand they are responsible for the immune system recognising infected cells or cancer cells," explains Professor Robert Tampé from the Institute for Biochemistry at the Goethe University. The considerable medical, industrial and economic significance of ABC transporters is also based on the fact that they cause bacteria and other pathogens to become resistant to antibiotics. Likewise, they can help cancer cells to defend themselves against cytostatic agents and thus determine whether chemotherapy will succeed.
For the first time, the group led by Robert Tampé, in collaboration with colleagues at the University of California in San Francisco, succeeded in determining the structure of an asymmetrical ABC transporter complex with the aid of a high-resolution cryo-electron microscope. "Over a period of five years, we have successfully implemented a number of innovative, methodological developments. These have enabled us to gain insights that previously were unimaginable," says Tampé.
The researchers report in the current issue of the renowned scientific journal, Nature that they have succeeded in investigating a single frozen ABC transport complex at a subnanometer resolution that has never before been achieved. For this purpose, they used a newly developed single electron camera, new imaging processes and specific antibody fragments in order to determine the structure and conformation of the dynamic transport machine.
"The combination of physical, biotechnological, biochemical and structural biological methods has led to a quantum leap in the elucidation of the structure of macromolecular complexes," says Tampé. The method facilitates the targeted development of a trend-setting therapeutic approach.
JungMin Kim et al.: Subnanometre-resolution electron cryomicroscopy structure of a heterodimeric ABC exporter, nature 2.11.2014, doi:10.1038/nature13872
Biomarkers and target proteins identified in vulnerable neurons
FRANKFURT Parkinson's Disease is the second most common neurodegenerative disorder. In Germany alone, almost half a million people are affected. The focus of the disease is the progressive degeneration of dopamine-producing nerve cells in a certain region of the midbrain, the substantia nigra. Misfolded proteins are the cause. Until recently, it was unclear why damage is confined to specific nerve cells. A team or researchers led by Frankfurt neurophysiologists has now defined how this selective disease process begins using a genetic mouse model of Parkinson´s disease.
The progressive death of a certain type of nerve cells – dopaminergic neurons - in the substantia nigra causes dopamine deficiency, which is the major cause for the motor deficits in Parkinson patients. Although it is possible to therapeutically compensate the dopamine deficiency for a certain period of time, by e.g. administration of L-dopa or dopamine agonists, these therapies do not stop the progressive death of neurons.
In the last two decades, researchers have identified gene mutations and toxic protein aggregates to cause neurodegeneration, with the protein a-synuclein having an essential role. Until recently, it was unclear why only specific types of nerve cells, such as dopaninergic neurons in the substantia nigra, are affected by this process, while others, also expressing the mutant a-syncuclein such as dopaminergic neurons in the immediate vicinity, survive the disease process with little damage.
The research group led by Dr. Mahalakshmi Subramaniam and Prof. Jochen Roeper at the Institute for Neurophysiology at the Goethe University, in collaboration with researchers from Frankfurt's Experimental Neurology Group and from Freiburg University, demonstrated for the first time how sensitive dopaminergic substantia nigra neurons functionally respond to toxic proteins in a genetic mouse model. A mutated a-synculein gene (A53T), which causes Parkinson's Disease in humans, is expressed in the mouse model.
In the current issue of the Journal of Neuroscience, the researchers report that the sensitive dopaminergic substantia nigra neurons respond to the accumulation of toxic protein by significantly increasing the electric activity in the affected midbrain regions. In contrast, the less sensitive, neighboring dopaminergic neurons were not affected in their activity. "This process begins as early as one year before the first deficits appear in the dopamine system, and as such it presents an early functional biomarker that may have future potential for preclinical detection of impending Parkinson's Disease in humans," explains Prof. Jochen Roeper. "The potential for early preclinical detection of subjects at risk is essential for the development of neuroprotective therapies."
The Frankfurt group, also identified a regulatory protein, an ion channel, which is causes the increase in electric activity and the associated stress in nerve cells in response to oxidative damage. This channel provides a direct new target protein for the neuroprotection of dopaminergic neurons. In brain slices, the dysfunction of this ion channel acting as an "electric brake" for dopamine neurons was reversible just by adding redox buffers. If therapeutic drugs could reduce the channel´s redox sensitivity in future mouse models, the death of dopaminergic neurons in the substantia nigra might be prevented. Currently, the researchers are studying whether similar processes occur with other Parkinson genes and in aging itself. "The long-term objective is to investigate the extent to which these results from mice might be transferred to humans," says Roeper.
Publikation: Mahalakshmi Subramaniam et al.: Mutant a-Synuclein Enhances Firing Frequencies in Dopamine Substantia Nigra Neurons by Oxidative Impairment of A-Type Potassium Channels, The Journal of Neuroscience, October 8, 2014 • 34(41):13586 –13599. doi:10.1523/JNEUROSCI.5069-13.2014.
Information: Prof. Dr. med. Jochen Roeper, Institute of Neurophysiology Goethe University Frankfurt, Phone +49(0)69 6301–84091, email@example.com.
A research group lead by scientists at the Goethe University Frankfurt discover details on how clouds form
FRANKFURT. New insights into cloud formation were obtained by scientists from the Goethe University of Frankfurt in an international collaboration. They found out that amines could play an important role in aerosol formation. They act as a kind of “superglue”. Aerosol particles influence the climate through their role in cloud formation because clouds can only form if so-called cloud condensation nuclei (CCN) are available.
It has been known for several years that sulfuric acid contributes to the formation of tiny aerosol particles, which play an important role in the formation of clouds. The new study by Kürten et al. shows that dimethylamine can tremendously enhance new particle formation. The formation of neutral (i.e. uncharged) nucleating clusters of sulfuric acid and dimethylamine was observed for the first time.
Previously, it was only possible to detect neutral clusters containing up to two sulfuric acid molecules. However, in the present study molecular clusters containing up to 14 sulfuric acid and 16 dimethylamine molecules were detected and their growth by attachment of individual molecules was observed in real-time starting from just one molecule. Moreover, these measurements were made at concentrations of sulfuric acid and dimethylamine corresponding to atmospheric levels (less than 1 molecule of sulfuric acid per 1 x 1013 molecules of air).
The capability of sulfuric acid molecules together with water and ammonia to form clusters and particles has been recognized for several years. However, clusters which form in this manner can vaporize under the conditions which exist in the atmosphere. In contrast, the system of sulfuric acid and dimethylamine forms particles much more efficiently because even the smallest clusters are essentially stable against evaporation. In this respect dimethylamine can act as “superglue” because when interacting with sulfuric acid every collision between a cluster and a sulfuric acid molecule bonds them together irreversibly. Sulphuric acid as well as amines in the present day atmosphere have mainly anthropogenic sources. Sulphuric acid is derived mainly from the oxidation of sulphur dioxide while amines stem, for example, from animal husbandry. The method used to measure the neutral clusters utilizes a combination of a mass spectrometer and a chemical ionization source, which was developed by the University of Frankfurt and the University of Helsinki. The measurements were made by an international collaboration at the CLOUD (Cosmics Leaving OUtdoor Droplets) chamber at CERN (European Organization for Nuclear Research).
The results allow for very detailed insight into a chemical system which could be relevant for atmospheric particle formation. Aerosol particles influence the Earth’s climate through cloud formation: Clouds can only form if so-called cloud condensation nuclei (CCN) are present, which act as seeds for condensing water molecules. Globally about half the CCN originate from a secondary process which involves the formation of small clusters and particles in the very first step followed by growth to sizes of at least 50 nanometers. The observed process of particle formation from sulfuric acid and dimethylamine could also be relevant for the formation of CCN. A high concentration of CCN generally leads to the formation of clouds with a high concentration of small droplets; whereas fewer CCN lead to clouds with few large droplets. Earth’s radiation budget, climate as well as precipitation patterns can be influenced in this manner. The deployed method will also open a new window for future measurements of particle formation in other chemical systems.
Kürten, A., Jokinen, T., Simon, M., Sipilä, M., Sarnela, N., Junninen, H., Adamov, A., Almeida, J., Amorim, A., Bianchi, F., Breitenlechner, M., Dommen, J., Donahue, N. M., Duplissy, J., Ehrhart, S., Flagan, R. C., Franchin, A., Hakala, J., Hansel, A., Heinritzi, M., Hutterli, M., Kangasluoma, J., Kirkby, J., Laaksonen, A., Lehtipalo, K., Leiminger, M., Makhmutov, V., Mathot, S., Onnela, A., Petäjä, T., Praplan, A. P., Riccobono, F., Rissanen, M. P., Rondo, L., Schobesberger, S., Seinfeld, J. H., Steiner, G., Tomé, A., Tröstl, J., Winkler, P. M., Williamson, C., Wimmer, D., Ye, P., Baltensperger, U., Carslaw, K. S., Kulmala, M., Worsnop, D. R., and Curtius, J.: Neutral molecular cluster formation of sulfuric acid-dimethylamine observed in real-time under atmospheric conditions, Proc. Natl. Acad. Sci. USA, doi/10.1073/pnas.1404853111, 2014.
Contact: Dr. Andreas Kürten, Institute for Atmospheric and Environmental Sciences, Goethe University Frankfurt am Main, Telefon 0049 (69) 798-40256, E-Mail: firstname.lastname@example.org