PHYSICS OF EARLY UNIVERSE WITH ATLAS AT CERN'S LHC
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Number 1 : 2014
A magazine published by the Notur II project
PHYSICS OF EARLY
UNIVERSE WITH
ATLAS AT CERN'S LHC
Microbial Communities
in permafrost-affected
peatlands; Supercomputing- Engineering
important players enabled study Nanoparticles
in Earth’s carbon of subcellular for Oil Field
cycle calcium dynamics Applications
The Norwegian metacenter for computational science
E D I TO R I A L
Documenting the utility value of the national e-infrastructure is important
to secure funding for future development. The articles in this edition of
F E ATURE S
META show that there is a wide diversity in the scientific disciplines
CON TEN TS utilizing the e-infrastructure. This underlines the importance of e-infra-
structure as tool for science.
The article on subcellular calcium dynamics on Tianhe-2 is particularly
Physics of Early Universe with ATLAS at CERN's LHC p: 4 interesting in terms of the exploitation of a HPC compute hierarchy – from
the national level to a top international system. In a future computational
Microbial Communities in permafrost-affected peatlands; infrastructure, a careful and cooperative provision of integrated services
p : 10
important players in Earth’s carbon cycle at the national and international level will be of growing importance, both
Supercomputing-enabled study of subcellular calcium dynamics p : 14
in terms of hardware and software. Are there more Higgs particles
than the one already observed?
We also present a short overview of the Notur and NorStore statistics
which indicates that the demand for resources continues to increase.
Engineering Nanoparticles for Oil Field Applications p : 18 Also worth mentioning is that statistics from CRIStin (Current Research Supersymmertry
Information System in Norway) shows that a considerable number of predicts five Higgs bosons.
NorStore launches pilot research data archive p : 22
:4
publications are referring to the use of Notur and NorStore as a neces-
sary tool for their work.
From PRACE-3IP: Exploiting HPC Tools and Techniques p : 24 On this background it is very important and good news that a decision has
been made to introduce a new model for investment in and operation of
national high-performance computing and storage solutions for scientific
Usage Statistics of the national e-infrastructure p : 28
data. As the current contract between UNINETT Sigma and The Research
Council is finishing at the end of this year, a new company will be
established. Still being a subsidiary of UNINETT this company will,
The sequence comparison is
compared to UNINETT Sigma, have a broader strategic responsibility and computationally very demanding, but using a
stronger operative control in addition to more long-term funding. The
overall aim is to make a foundation for better services to the scientific high performance cluster
disciplines. An interim board has been formed and work has been started
to establish the new company which will be going live on 1. January 2015. such as Stallo, millions of sequences
Based on a broad community-driven request we announced in March
can be compared within days.
Cover picture: © CERN
a new service for archiving and sharing large-scale research data. The
Archive provides functions to deposit, describe and manage datasets from
the user community. You can read more about this new service both in
:10
this edition of META and by visiting our web sites.
Number 1 : 2014 Number 1 : 2014
A magazine published by the Notur II project – The Norwegian metacenter for computational science
A magazine published by the Notur II project
Editorial Director: Arild Halsetrønning
Instead of passively waiting for the arrival
PHYSICS OF EARLY Contributing Editor: Vigdis Guldseth of exascale supercomputers,
UNIVERSE WITH
ATLAS AT CERN'S LHC
Subscription: An electronic version is available on www.notur.no. Here you can download a
PDF-file of the magazine and subscribe or unsubscribe to the magazine. Arild Halsetrønning we believe that progresses can be made in the
ISSN: 1890-1956 Managing Director
UNINETT Sigma AS current numerical scheme to
facilitate faster simulations.
Microbial Communities
in permafrost-affected
peatlands; Supercomputing- Engineering
Reproduction in whole or in part without written permission is strictly prohibited.
e-mail address: sigma@uninett.no. Phone: +47 73 55 79 00. Fax: +47 73 55 79 01.
important players enabled study Nanoparticles
in Earth’s carbon of subcellular for Oil Field
:14
cycle calcium dynamics Applications
The Norwegian metacenter for computational science
Print: Skipnes kommunikasjon AS
Disclaimer: UNINETT Sigma is not responsible for errors, opinions or views expressed by the authors or the contents of external information referred to in this magazine.
2 3
PHYSICS OF EARLY
UNIVERSE WITH
Figure 1. Standard Model particles. Fermions (quarks
Copyright 2013 CERN. Photo: Dominiguez, Daniel.
and leptons) as well as the W and Z weak bosons ac-
quire their masses by interacting with the Higgs field.
The photon and gluon do not interact directly with the
THE ATLAS AT THE
Higgs field, and thus stay massless. The Higgs particle
observed by ATLAS and CMS at LHC is the manifesta-
tion of this Higgs field.
CERN’S LARGE experiment at the South Pole. This discovery
is a further brilliant confirmation of the theory
of general relativity of Einstein and may be
decayed to lighter particles as the Universe
cooled down. Today they are produced in high-
energy particle collisions and some are found
theory, which happens by introducing particle
masses per hand, a scalar field is predicted to
populate the vacuum. The whole Universe
HADRON COLLIDER interpreted as a first hint towards the existence
of the graviton, the hypothetical mediator of
gravity at the elementary particles scale. At the
in cosmic rays.
A POWERFUL THEORY MISCALLED
swims in an invisible, cosmic field, Higgs-field,
which acts on particles and provide them with
what is called mass. As all fields have associ-
level of quarks and electron, gravity is some “STANDARD MODEL” ated bosons (the photon is associated to the
AUTHOR High Energy Particle Physics has recently extended the frontiers of physics forty orders of magnitude weaker than electro- The Standard Model (SM) is the theoretical electromagnetic filed), the Higgs-field has its
Farid Ould-Saada magnetism, itself a factor of ten weaker than framework that elegantly describes nearly all Higgs-boson. It is that particle that the ATLAS
Physics Professor knowledge using the advanced technology of the world's largest and
the strong force. Electrons and quarks feel a existing particle physics data with astonishingly and CMS experiments at the LHC observed in
University of Oslo,
highest energy particle accelerator, the Large Hadron Collider (LHC) at fourth fundamental force of Nature: the weak good precision. The resulting quantum field 2012.
Leader, Norwegian CERN-
interaction, mediated by three force particles theory relies on quantum mechanics and
related HEPP project the CERN laboratory in Geneva, and the world's largest and most
W+, W- and Z0, responsible for phenomena such special relativity unifying space and time into Englert and Higgs, two of the people behind the
sophisticated particle detectors, one of them being the ATLAS experiment, as nuclear radioactivity and burning of stars. a four-dimensional space-time. To each so-called BEH-mechanism of spontaneous
by discovering the last missing building block of the Standard Model (SM) To this force is associated the neutrino, an particle is associated a field describing its breaking the electroweak symmetry, thus
essential ingredient of nuclear ß-decay, where probability of presence at some space-time generating masses of the W, Z and fermions,
of elementary particles, the Higgs boson. The coming LHC running at a neutron (d-quark) decays into a proton point. Forces in nature originate from some were awarded the 2014 Nobel price.
higher energy and higher collision rates is crucial to settle the properties (u-quark), an electron and an anti-neutrino, symmetry required to hold at each space-time How important is this? It is well known that
and of other phenomena involving transfor- point. These symmetries are related to definite more than 99% of the mass the atom, i.e. of
of the Higgs particle and to continue the exciting “travel” towards “new mation of matter from one state to another. The conservation laws, such as the conservation of protons and neutrons, comes from the kinetic
physics” that may be expected in a previously unexplored energy regime. neutrino and electron belong to the family of electric charge. energy of quarks and gluons. However, without
leptons. Matter particles, quarks and leptons, the relatively tiny mass of the electron (~2000
as well as the anti-matter counter parts, The Standard Model describes interactions times lighter than the proton) the atom would
THE PARTICLE CONTENT OF THE the photon, syntesizes nuclei and electrons into positrons and anti-quarks, are named between elementary particles grouped in not form as the electron would be traveling
UNIVERSE atoms, atoms into molecules, and molecules fermions, whereas force particles are called 3 families of quarks and leptons (Figure 1). undisturbed at the speed of light, and life would
A few elementary particles play a role in the into matter stars and we are made of. Gravity bosons. Fermions interact by exchanging At high energies, it unifies electromagnetism, not be. Idem, if the weak boson were massless,
world we leave in. Two quarks dubbed up (u) acts on matter at larger scales of macroscopic bosons. a long-range, macroscopic force, carried by the weak force would be as strong as electro-
and down (d) combine to make the proton (uud) objects, planets, stars, galaxies and black the massless photon, and the weak force, magnetism and radioactivity would be rather
and the neutron (udd) under the influence holes. The weak force is responsible for the fact that a short-range, microscopic force carried the rule then the exception. Finally the
of the strong force or interaction, which is the content of the Universe evolves with energy, by heavy W and Z bosons. The resulting existence of scalar particles could be the
mediated by a force carrier named gluon. The The observation of gravitational waves that set temperature and distance scale. We know that electroweak symmetry must be broken at low source of inflation, the incredible acceleration
same force is responsible for the nuclear force on the space-time infl ation of the Universe two additional families of heavier fermions energies in order to give the weak bosons of the expansion of the Universe just after the
holding protons and neutrons together to form some 13.8 billion years ago was recently existed just after the big bang, although they (W, Z), as well as all matter particles, masses. big bang, in connection with the gravitational
nuclei. The electromagnetic force, carried by announced by the radio telescope Bicep2 do not form the matter surrounding us. They In order not to spoil the predictability of the waves mentioned above.
4 5
TO SEE WITH THE LHC
The Large Hadron Collider (LHC) at the CERN
laboratory in Geneva is the first particle
accelerator to directly explore the Tera-
electron-Volt (TeV)1 scale, a new energy
frontier. By colliding beams of protons or lead
nuclei, the LHC probes deeper into matter than
ever before, reproducing conditions in the first
picoseconds in the life of the Universe.
Copyright 2013 CERN. Photo: Dominiguez, Daniel.
Several experiments at accelerators and
colliders were built with the goal to, among
others, discover the Higgs particle. LHC and
the accompanying multipurpose experiments
were planned such as not to miss the Higgs, if
it exists.
The higher the beam energy and collision rates
are, the greater the discovery potential. How
come? To produce particles of large mass re-
quires a lot of energy, according to the known
Einstein relation E = Mc2, stating the equiva- Figure 2. ATLAS event display showing a candidate Higgs boson of mass 125 GeV decaying into two Z bosons each
of which subsequently decays into two muons (red lines). The inset on the right-hand side shows a zoom into the
lence of mass M and energy E, related to each
tracking detector. The inset on top left shows a zoom into the vertex region, indicating that the 4 muons originate
other by the speed of light c. A mass of a proton from the same primary vertex. This picture of a particle collision, demonstrates that the ATLAS detector performs Figure 3. Invariant mass of 4 leptons
corresponds to ca. 1 GeV. Two protons at rest very well. The Norwegian scientists made a strong contribution to the semi-conductor tracker, one of the central featuring the Higgs signal (in red)
detectors with the aim of identifying charged particles, such as electrons and muons. The tracker has been consistent with the prediction of the
have energy equivalent to ca. 2 GeV. The total instrumental in dealing with the harsh conditions of extremely high collision rates with up to 40 proton-proton col- Standard Model. The rest of the spec-
LHC energy of 8 TeV, equivalent to 8000 proton lisions reconstructed per event. Other detector types – calorimeters – measure the energy of electrons, photons trum (blue) is due to well-understood
masses, is due to the kinetic energy of the and hadrons (protons, neutrons, pions). All other particles have a too short lifetime to be observed in detectors. electroweak processes.
Those are inferred from their decay products with the help of conservation laws, such as energy and momentum.
accelerated protons. It is this kinetic energy This is the case of the Higgs and Z bosons, leading to muons in the picture above. Figure 4. IInvariant mass of 2 photons
that allows the creation of heavy particles such featuring the Higgs signal, A Gaussian
as the known top quark and Higgs boson. The peak, on top of well-understood back-
ground processes due to the strong
higher the particle mass, the harder it is to interaction. The signal, shown in the
produce it. This is where luminosity enters. lower plot after background subtrac-
tion, is consistent with the prediction
Luminosity gives a measure of how many SHAKING THE VACUUM Approximately 500 Higgs events were observed
of the Standard Model.
collisions are happening in a particle collider: Billions of events were recorded in 2011 and through fi ve decay channels. Figure 3 and
the higher the luminosity, the more particles 2012 that lead to the “re-discovery” and study Figure 4 show the Higgs signal through its
are likely to collide. When looking for rare of all known elementary particles, such as decay into two Z particles leading to 4 leptons
processes, this is important. The Higgs the mediators of weak interactions (W and Z and two photons, respectively, both featuring The discovery of the Higgs particle has been a the world on the worldwide LHC Computing Other computing facilities in universities and
particle would be produced very rarely, so particles) and the top quark, the heaviest of a particle at a mass of ~125 GeV. Decays to pairs “global effort leading to a global success”, to Grid (WLCG). The mission of the WLCG (Figure laboratories take part in LHC data analysis as
for a conclusive discovery or disproof of its all. LHC is a top quark and weak boson of W bosons and tau leptons were also repeat the words used by the CERN DG, Rolf 5) is to build and maintain data storage and Tier-3 facilities, allowing scientists to access
existence, a large amount of data was factory. Millions of events have been re- observed. It has been proven that the observed Heuer. “Results today only possible due to analysis infrastructure for the entire High Tier-1 and Tier-2 facilities. With the rapid
required. Peak luminosity close to the LHC constructed and studied through their decays particle is a boson of spin 0, a scalar compat- extraordinary performance of accelerators, Energy Physics (HEP) community around increase of data produced by LHC, Norway
design luminosity was reached in 2012. The into leptons: 108 W, 107 Z, and 5x105 top events. ible with the missing ingredient of the Standard experiments and Grid computing”. So, it would the LHC. Raw data emerging from the unfortunately missed the opportunity to host
total number of proton collisions amounted The ATLAS and CMS collaborations, in a Model, coupling to both bosons and fermions. have been impossible to release so many experiments are recorded and initially the extension of the Tier-0 outside CERN. The
to 1.80 X 1015. heroic “dugnad” of thousands of physicists, The decays to pairs of bottom quarks and other results and discover the Higgs particle so processed, reconstructed and stored at the Wigner centre in Budapest is related to CERN
An LHC collision leads to hundreds of particles students and engineers, made the first major rare decays still need confirmation. A future quickly without the outstanding performance Tier-0 centre at CERN, before a copy is by a 100 Gbit/s connection.
measured by detectors, such as ATLAS, which discovery of a new boson at the LHC in 2012, goal is to study the coupling of the Higgs of the Grid. distributed across 11 Tier-1s, which are large
can be thought of as a sort of digital cameras announced on July 4. particle to its self, and confirm that the Higgs computer centres with sufficient storage
with millions of readout channels instead of boson acquires its mass through the BEH A WORLDWIDE DISTRIBUTED capacity and with 24/7 operation. The role of
pixels. Figure 2 shows an example of a Higgs mechanism. COMPUTING SYSTEM Tier-2s is mainly to provide computational
candidate event observed in ATLAS. The real data collected by the LHC experi- capacity and appropriate storage services for
ments have been distributed smoothly around event simulation and for end-user analysis.
1
Tera-electron-Volt. 1 TeV = 1000 GeV is equivalent to the energy of ca. 1000 proton masses.
6 7
WLCG BEYOND MOORE’S LAW
The WLCG has handled hundreds of peta-
bytes of data at rates far beyond the design
goals. The size of the data is close to the
content uploaded to the social media. With Figure 7. At any given time,
there are more than 160,000
the advent of higher LHC luminosities, concurrent ATLAS jobs running
larger data sets and more complicated on the Grid.
events to be recorded and analysed, an
upgrade of the ATLAS computing system,
and of WLCG in general, is foreseen. Until
2017 the LHC numbers in terms of CPU and
disk are probably sustainable with close to
flat computing budgets. The progress predicts five Higgs bosons. Super- col le c te d b y th e dete c to r s . Tw o
achieved due to Moore’s law increase in symmetry proposes a good candidate for hundred institutes from 41 countries
computing power is being halted by Dark Matter observed in the Universe. par ticipated in the 2014 program.
limitations on power and cooling. Multi and Why is gravity much weaker than other Exciting measurements are proposed to Further reading
many-core processors and the use of Nature’s fundamental forces? Are there the students to extract properties of
co - p r o ce s s o r s such a s G r ap hic al more space dimensions than the usual known particles, such as the W and Z 1. CERN, Accelerating Science,
Processor Units (GPUs) are possible ways known 3, which would allow gravity- bosons, mediators of the weak force, and home.web.cern.ch
forward. Any efficient use of the new hard- related phenomena, such as microscopic various hadrons, particles made of
ware architectures must be followed by the black holes and gravitons, be produced, quarks, as well as searching for new force 2. ATLAS Experiment,
challenging modification or rewriting of the to occur at the LHC energy era? particles linked to new interactions. atlas.ch
current application code. The adaptation of If accessible, LHC can produce such new T he educ ational mater ial , p ar tly
the code has started in order to make use par ticles and phenomena could be developed by the University of Oslo, is 3. A Particle Consistent with the Higgs Boson Observed
of opportunistic resources: volunteer produced at the LHC and observed and tuned and expanded to follow LHC with the ATLAS Detector at the Large Hadron
computing (Boinc) and supercomputers studied by ATLAS. “heartbeats”. Collider, Science 338 (6114), 2012, 1576-1582.
(High Performance Computing) for special, Despite enormous gains in mass reach [DOI:10.1126/science.1232005]
CPU intensive, short jobs. NorduGrid/ARC since the previous experiments, there is LHC SOON BACK TO EXPLORE A NEW
is critical part of both these activities. as yet no direct evidence for new physics. TERRITORY 4. "The Nobel Prize in Physics 1979",
However, we have collected only a few % LHC´s physics research programme has nobelprize.org/nobel_prizes/physics/laureates/1979/
THE ROAD TO “NEW PHYSICS” of the data planned for the full LHC definitively started. The first running
Despite the success of the Standard Model program and already in 2015 the doubling period ended on a high tone. ATLAS, to 5. "The Nobel Prize in Physics 2013",
Figure 5. The success of the Worldwide LHC Computing Grid relies on a high-volume performance of the world it is not the ultimate theory of Nature. of the collision energy could yield some name only one experiment, made three nobelprize.org/nobel_prizes/physics/laureates/2013/
network, allowing high and efficient data transfers between data centres: Tier-0 (data processing), 11 Tier 1s (simu-
It does not account for dark matter or dark surprises. discoveries: “jet quenching”, probably a
lation, reprocessing), 140 Tier 2s (simulation, user analysis) and many Tier 3s (user analysis). In total there are, as of
April 2014, 270 PB disk and 201 PB tape storage space, and 500,000 processors available on WLCG. The NDGF Tier 1 energy, and does not incorporate gravity. sign of the primordial quark-gluon 6. “LHC research started … WLCG busy”,
(Norwegian UNINETT Sigma Tier 2) has 6.4 PB (320 TB) storage and 42,000 (1,480) processors available. Various extensions have been proposed SHARING ATLAS DATA AND DISCOVERIES plasma, in 2010 (META 2/2011), a new notur.no/sites/notur.no/files/publications/pdf/
incorporating new symmetries, additional WITH HIGH-SCHOOL STUDENTS B-meson state in 2011 and a scalar particle meta_2011_2.pdf
space dimensions, substructure of the The ambition to bring to the “classrooms” compatible with the long-sought Standard
fermions and bosons, to name only those. any important LHC discovery is fulfilled Model Higgs boson in 2012. The LHC 7. The Worldwide LHC Computing Grid,
NORDIC E-INFRASTRUCTURE ATLAS distributed computing infrastructure. ATLAS looked for a large spectrum of new with the recent discovery of the Higgs bo- machine and its detectors are in the wlcg.web.cern.ch
The Nordic countries participate in the The operation of the Nordic Tier-1 and phenomena, leading to new heavy particles son. Approximately 10% the 8-TeV ATLAS middle of a two-year shutdown period.
Nordic Tier-1 component of the WLCG Norwegian Tier-2 is done in collaboration or new interactions from the unification of discovery data are made available for Starting from spring 2015 the LHC will 8. The Nordic e-infrastructure Collaboration,
collaboration, through the Nordic Data Grid with USIT (University of Oslo IT department) the electroweak and strong forces, or even students to search for the Higgs boson, deliver 13-14 TeV energies and ATLAS is neic.nordforsk.org
Facility (NDGF), now part of the Nordic and UNINETT Sigma, within NDGF. ATLAS including gravity. Down to 10 -20 meter the the particle responsible for spontaneous being consolidated and tuned to cope with
e-infrastructure Collaboration (NeIC). NGDF data - more than 150 petabytes (Figure 6) - fundamental constituents of matter seem breaking of the electroweak symmetry, the much higher luminosities and data 9. NorduGrid Advanced Ressuorce Connector,
is the only distributed Tier-1, with 2 of its are distributed, processed and analysed at without structure. Following the discovery through which all elementary particles of rates expected. The WLCG has as a nordugrid.org
7 centres located at universities of Oslo more than 130 sites across the world, of the Higgs boson, further data will allow the Universe acquire mass. In the future challenge to incorporate new ideas and
and Bergen. A key contribution is made in including Oslo. At any given time, there are in-depth investigation of the boson's the hope is to bring new discoveries to sustain a computing infrastructure for
developing and deploying Grid middleware more than 160,000 concurrent jobs running properties and thereby of the origin of high school and university students. another period of 20 years, allowing
– NorduGrid Advanced Resource Connector (Figure 7) and more than a million jobs are mass. Do more Higgs particles exist than The international masterclasses in the physicists all over the world to explore a
(ARC) – and software and setting up a the submitted on a daily basis. the one already observed? Supersymmetry LHC era feature the use of real fresh ex- new territory full of promises. Stay tuned!
perimental data as they are produced and
8 9
MICROBIAL COMMUNITIES IN PERMAFROST-AFFECTED PEATLANDS;
IMPORTANT PLAYERS IN
EARTH’S CARBON CYCLE
Photo: Mette M. Svenning
Photo: Christiane Graef
Figure 1. Peter Frenzel is sampling methane gas and soil from the Arctic peat, Ny-Ålesund, Svalbard.
ARCTIC SOILS, MAJOR SOURCES are still poorly understood. Advanced T, G, and C in DNA and A, U, G, and C in RNA)
FOR GREENHOUSE GASES molecular methods combined with high in millions of gene and transcript frag-
Recent estimates point out that 277 Pg throughput computer analyses are ments. Sequences from cultivated model
(1 petagram (Pg) = 1000 Terragrams (Tg) = necessary tools to address the underlying microbes are available from public data-
1 billion metric tons) of SOC are stored in complex microbial processes in these high bases. With the computational resources
Arctic peatlands (1), which is approximately organic soils. We have applied metage- available at Stallo (Notur), we have
1/3 of the current greenhouse gas content nomics and metatranscriptomics to identify compared the metagenomes and meta-
in the atmosphere. These peatlands have the microbial genetic diversity and activity transriptomes with the sequence entries in
acted as a carbon sink since the Holocene in high-Arctic peatlands from Svalbard. One the public databases. If the similarity of two
(2, 3). In contrast, they are substantial of four field sites in Ny-Ålesund, Svalbard, sequences is below a threshold, we can
sources of methane (CH4), releasing ap- is shown in Figure 1. The taxonomic and assume that the two sequences stem from
proximately 35Tg per year, which corre- metabolic diversity of microorganisms in phylogenetically related organisms, and
sponds to 6% of the global CH4 emissions soil ecosystems is immense. A challenge share the same or a very similar function.
(4). CH4 is a much more potent greenhouse in the study of microbial ecology is there- The sequence comparison is computation-
gas than carbon dioxide (CO 2 ), being fore to identify the function of the different ally very demanding, but using a high per-
26 times more efficient (on a mol to mol microorganisms in the soil, and how formance cluster such as Stallo, millions
basis) in absorbing the infrared radiation changes in the microbial community of sequences can be compared within days.
from Earth (5). Arctic and especially high- structure and activities affect the rates of
A substantial part of the Earths' soil organic carbon (SOC) is stored in arctic peatlands, ecosystems Arctic regions are already exposed to, and biogeochemical transformations. FROM GENE TO ECOSYSTEM
that are sensitive to global warming. These peatlands represent large sources for emissions of the predicted to experience an even stronger Metagenomics, the study of all DNA Plant litter is the major component of SOC
temperature increase until the end of the fragments in an environmental sample is a in Arctic peatlands. The major players in
greenhouse gases methane (CH4) and carbon dioxide (CO2), end products of microbial soil organic century (1-5°C for summer and 2.5-11°C powerful genomic technique, yielding the SOC degradation are microorganisms
carbon degradation. Global warming might promote microbial processes, increasing CH 4 and CO2 for winter, surface temperatures) (6), which know-ledge about the genetic potential of of all three domains of life including
is expected to lead to expanded frost free the entire microbial community directly in Bacteria, Archaea and Eukarya. They
emissions from the Arctic. To predict future CH4 and CO2 emissions, an in depth understanding of vegetation periods and increased active lay- their natural environment. Using this participate in a cascade of degradation
er depths in permafrost affected soils (1). method one can also identify functional steps, eventually resulting in the emission
microorganisms and microbial metabolic networks in Arctic soils is required.
Microorganisms play a key role for degra- aspects of the microorganisms. However, of CH4 and CO2. The initial step of degrada-
dation of the stored carbon and are respon- DNA based studies do not provide informa- tion is the hydrolysis of large polymeric
sible for climate gas production. To under- tion about the activities of microorganisms. plant compounds such as cellulose and
stand their role and how their activity is For this purpose, metatranscriptomics, the hemicellulose, catalysed by extracellular
affected by climate changes is therefore study of expressed genes (transcripts) of a enzymes from microorganisms. Further
important as a basis both for modelling of community, can complement metage- steps in the degradation are carried out
AUTHOR AUTHOR permafrost ecosystems and predictions nomics and provide information on the through anaerobic respiration and fermen-
Mette Marianne Svenning Tim Urich about future CH4 and CO2 emissions. presumably active community members (7). tative and methanogenic metabolic path-
Department of Arctic and Marine Biology Department of Ecogenomics and System Biology We have applied these direct high-through- ways leading to production of CH4. Before
UiT The Arctic University of Norway University of Vienna, Austria METAGENOMICS AND put methods on the active soil layer of reaching the atmosphere, CH4 can be con-
Photo: Mette M. Svenning
METATRANSCRIPTOMICS Arctic permafrost ecosystems. sumed by CH4 oxidizing bacteria that re-
The microorganisms responsible for the Using high-throughput 454 pyrosequencing quire oxygen. They are the biological filters
AUTHOR AUTHOR breakdown and mineralization of soil or Illumina sequencing, we identify the base for CH4 in the environment. Their activity
Alexander Tøsdal Tveit Peter Frenzel organic carbon (SOC) in permafrost soils composition (combination of the bases A, will depend on the water level in the soil.
Department of Arctic and Marine Biology Max Planck Institute for Terrestrial Microbiology
UiT The Arctic University of Norway Marburg, Germany
10 11
one single species of Bacteria, Methylobacter tundri- Acknowledgements
paludum. Therefore, this special bacterium represents NOTUR High Performance Computing, is acknowledged for very
a key organism as CH4 filter in the Arctic soil (11). The professional service and access to the resources on Stallo. The
emission of CH4 from this ecosystem might thus be sequencing service was provided by the Norwegian Sequencing
particularly vulnerable to climatic changes, depend- Centre (www.sequencing.uio.no). Our research in Arctic microbial
ing on the response of these key microorganisms. ecology has been funded through The Research Council of Norway
Grant 191696/V49.
COMPUTATIONAL RESOURCES: STALLO 1. Tarnocai C, Canadell JG, Schuur EAG, et al. 2009. Soil organic
Our research depends on the high performance carbon pools in the northern circumpolar permafrost region. Glob.
cluster facilities at UiT, The Arctic University of Biogeochem. Cycle 23.
Norway (Stallo). Our main task is the screening of 2. Post WM, Emanuel WR, Zinke PJ, et al. 1982. Soil Carbon Pools
large datasets containing genetic information using and World Life Zones. Nature 298:156-159.
the BLAST (12) and HMMER (13) algorithms. In future
3. Harden JW, Mark RK, Sundquist ET, et al. 1992. Dynamics of
work, it is expected that this will be broadened to
Soil Carbon During Deglaciation of the Laurentide Ice Sheet.
include the modelling of climate change effects on
Science 258:1921-1924.
Arctic microbial networks.
4. Cao M, Marshall S, Gregson K. 1996. Global carbon exchange
Figure 2. The microbial community in the Arctic and methane emissions from natural wetlands: Application of a
peatlands of Svalbard based on the relative abundance process-based model. J. Geophys. Res., 101:399-414.
of small subunit rRNA molecules (8). The size of the
squares corresponds to the biomass of the different 5. Lelieveld J, Crutzen PJ, Bruhl C. 1993. Climate effects of
groups. Bacteria are divided into the major sub-
atmospheric methane. Chemosphere 26:739-768.
groups called phyla. Metazoa, Protists and Fungi, all
eukaryotic microorganisms with larger cell struc- 6. van Oldenborgh GJ, Collins M, Arblaster J, et al. 2013. IPCC:
tures, are also divided into their respective phyla.
Annex I: Atlas of Global and Regional Climate Projections.
Photo: Peter Frenzel
Figure 3. A model showing the major processes carried out by microorganisms in Arctic peatlands (8). The stored 7. Carvalhais LC, Dennis PG, Tyson GW, et al. 2012. Application
If the soil is water saturated and thus oxygen SOC are in the form of plant compounds such as cellulose, hemicellulose, pectin, lignin and polyphenols. of metatranscriptomics to soil environments. J Microbiol Methods
These compounds are degraded to the finale products CH4 and CO2 emitted to the atmosphere. Amount of CH4 91:246-251.
is absent, CH4 will be released directly to the emitted is dependent on the activity of Methylobacter tundripaludum. Each step of the degradation is performed
atmosphere. by specific groups of microorganisms, shown in yellow. These names correspond to those shown in figure 2. The 8. Tveit A, Schwacke R, Svenning MM, et al. 2013. Organic carbon
degradation is mainly anaerobic (without oxygen).
Our combined study of the genes (meta- transformations in high-Arctic peat soils: key functions and
genomics) and the transcripts (meta- CONCLUSIONS AND OUTLOOK microorganisms. Isme J 7:299-311.
transcriptomics) in the Arctic soil has given the microbial community, but may still have such as increased temperatures will affect the Our studies have revealed the complex structure of 9. Bradford MA. 2013. Thermal adaptation of decomposer
us a detailed insight into this “invisible”, very important roles in this ecosystem. composition of microorganisms (9). microbial communities in Arctic peatland ecosystems, communities in warming soils. Front Microbiol. 2013 Nov 12;4:333.
but very important microbial world. Differ- It can also be expected that such changes may comprising individual taxa or populations having a eCollection 2013.
ences in the genetic code were used to The genes and transcripts encode enzymes affect the metabolism of microbial communi- distinct role in the degradation of organic matter.
10. Hall EK, Neuhauser C, Cotner JB. 2008. Toward a mechanistic
distinguish the different groups of micro- that catalyse different reactions in the micro- ties (10). Thus, identifying the presence and These microbes are sensitive to changes, and there-
understanding of how natural bacterial communities respond to
organisms. From the number of genes or organisms. From the similarity to genes and activity of the key microorganisms related to fore will affect the emissions of CH4 and CO2 from the changes in temperature in aquatic ecosystems. Isme J 2:471-481.
transcripts corresponding to the different transcripts in the databases, we identified the climate change is of outmost importance. Our soil to the atmosphere. Further studies will
microorganisms we have constructed a microorganisms responsible for the results show that some microbial groups have address I; how this community act when the temper- 11. Svenning MM, Hestnes AG, Wartiainen I, et al. 2011. Genome
schematic overview of the microbial com- different biochemical reactions needed to pro- very specific roles, while other groups have ature increases and II; if changes in activity and Sequence of the Arctic Methanotroph Methylobacter tundripaludum
SV96. J. Bacteriol. 193:6418-6419.
munity of the Svalbard peatlands (Figure d u ce a n d ox i d i z e C H 4 . We f u r t h e r many different functions in the Arctic interactions influence the amount of climate gas
2). In these ecosystems, the microbial com- constructed a complete model of SOC degra- peatlands. Actinobacteria has a very broad emissions. These cold Arctic environments may also 12. Altschul SF, Madden TL, Schaffer AA, et al. 1997. Gapped
munity is dominated by small single celled dation in Arctic peat, including the complex metabolic range, while Firmicutes and Proteo- select for microbial adaptation to low temperatures BLAST and PSI-BLAST: a new generation of protein database
microorganisms within the domain Bacte- network of anaerobic respiratory and bacteria are restricted to specific metabolisms. and thereby causing population shifts related to search programs. Nucleic Acids Res. 25:3389-3402.
ria. Most of the larger eukaryotic microbes, fermentative pathways, CH4 production and The last steps of decomposition leading to CH4 increased temperature. How this will affect the 13. Eddy SR. 2011. Accelerated Profile HMM Searches. PLoS
many of which feed on the smaller Bacteria CH4 oxidation. This metabolic network together and CO2 production are carried out by only microbial communities and their metabolic proper- Comput Biol 7:e1002195.
and Archaea, are found within two major with the active soil microorganisms are illus- three groups of Archaea,Methanomicrobiales, ties need to be further investigated.
groups called Protists and Metazoa. Fungi trated in Figure 3. Methano-bacteriales and Methanosarcinales.
and Archaea make up smaller fractions of It is recognized that environmental changes The oxidation of CH4 to CO2 is carried out by
12 13
Figure 1: A schematic overview of a sarcomere (left) and a calcium release unit (right)
Photo: Shutterstock/www.phys.org
making nanometer-resolution simulations of co-processor, which adopts the new many- total. This means that employing a sizable
SUPERCOMPUTING-ENABLED STUDY sub-cellular calcium dynamics
extremely time consuming.
integrated-core (MIC) architecture. Each
Xeon Phi contains between 57 and 61 cores,
portion of Tianhe-2 requires performance
scalability on thousands of nodes. Although
OF SUBCELLULAR CALCIUM DYNAMICS
where each core can spawn four hardware this is a classical problem with using large-
The arrival of petascale supercomputers threads and has a private 32KB L1 data scale clusters, an extra difficulty associated
has ignited new thinking about the feas- cache, together with a 512KB L2 cache that with Tianhe-2 is due to its three-coproces-
ibility of detailed subcellular simulations. is kept fully coherent with L2 caches on the sor configuration per node, meaning that
Although these parallel systems are still other cores. The vector processing unit on hiding the overhead of data movement
not powerful enough for 3D simulations Xeon Phi uses a 512-bit SIMD instruction needs to consider more levels.
with 1-nm resolution, experiences thus set, theoretically capable of simultaneously
Calcium dynamics is of paramount importance for the heart. Every obtained will guide the preparation of producing 8 double-precision values per HANDLING THE CHALLENGES
AUTHORS extreme simulations that target future clock cycle. In comparison with Intel's multi- We have adopted a straightforward numeri-
Xing Cai heartbeat is triggered by an increase in the intracellular calcium exascale systems. core architecture, it is considerably more cal scheme, based on explicit time integra-
Simula Research Laboratory.
difficult to achieve a decent fraction of tion and 3D finite differences. The target
Department of Informatics, concentration, for which calcium channels open in the cell membrane and
TIANHE-2 Xeon Phi's more than 1 Tflop/s peak mathematical model consists of five
University of Oslo
allow calcium ions to flow inward. This calcium inflow triggers a further Thanks to an ongoing collaboration performance. coupled 3D reaction-diffusion equations
between Simula Research Laboratory and and two ordinary differential equations in
release from the internal calcium storage, which is called the sarcoplasmic National University of Defense Technology The second challenge arises from the each grid node. Moreover, at every time
reticulum. Each heart cell has about 20,000 calcium release units (CRUs). in China, we were given the opportunity to unique hardware configuration of step, each ryanodine receptor, which is the
test simulations of subcellular calcium Tianhe-2's compute nodes, each having calcium release channel, is subject to a sto-
Contrary to being stable and synchronous in healthy heart cells, calcium dynamics on Tianhe-2: the world's current namely three Xeon Phi coprocessors that chastic Markov-chain computation deciding
Johan Hake release during heart failure is less reliable, slower and dyssynchronous. No.1 supercomputer. Challenges on three are connected to a CPU host through dis- whether calcium release happens or not.
Simula Research Laboratory levels, however, had to be overcome in tinct PCIe buses. In comparison with the
The resulting random Ca releases can trigger whole-cell calcium waves, order to effectively use Tianhe-2 to run the common design of one Xeon Phi per node, The key to achieving high performance on
which are arrhythmogenic and potentially lethal under unfortunate simulations with an unprecedented Tianhe-2's node configuration requires the Tianhe-2 lies in an efficient execution of
resolution. additional MIC-MIC collaboration, while all the involved triply nested for-loops. First
circumstances. Intricate details that happen at the subcellular level are putting more pressure on the CPU host. of all, the entire 3D uniform mesh of
Glenn Terje Lines
thus vital for understanding the changes in calcium handling during First of all, the basic hardware building The host has to offload three pieces of computational voxels is evenly partitioned
Simula Research Laboratory.
block of Tianhe-2 is Intel's Xeon Phi computation to the three coprocessors, in into a set of subdomains, matching the
Department of Informatics,
University of Oslo
different pathologies addition to orchestrating MIC-MIC and number of Tianhe-2 nodes used. The
MIC-host data movements and carrying out computations per subdomain are further
One of the main obstacles to accurately s a rc o m e re , w h i c h o c c u p i e s a 3 D inter-node MPI communication. The actual divided between the CPU host and the three
simulating calcium releases, for both volume of 10x10x2 µm3, it would require in programming thus becomes rather coprocessors, such that each coprocessor
healthy and pathological situations, is the total 2x1011 computational voxels, each of one complex. is responsible for a 3D subpartition of the
www-top500.org
enormous computational requirement. cubic nanometer in volume. For example, a subdomain. During each time step, the CPU
Ideally, 1-nm resolution is needed to simu- straightforward numerical algorithm is esti- The last challenge for effective usage of host invokes the three coprocessors to each
late the details of the CRUs. If such an ex- mated to require 1019 floating point operations Tianhe-2 is associated with its large compute within its respective subpartition.
treme resolution is used throughout a single for simulating one sarcomere over 1ms, thus number of nodes, amounting to 16,000 in In addition to computing the remaining 3D
Tianhe-2
14 15
1.0 1.0 1.0
c at t=1 ms c at t=8 ms c at t=24 ms
3.0 0.9 3.0 0.9 3.0 0.9
0.8 0.8 0.8
2.5 2.5 2.5
0.7 0.7 0.7 For the single-node performance on performance obtained on a single Xeon Phi or GPUs of a supercomputer. Challenges will
2.0 2.0 2.0
Tianhe-2, we have focused on carefully coprocessor came, though, at the cost of lie in mesh generation, load balancing and the
0.6 0.6 0.6
orchestrating the different tasks that need meticulous code optimizations. Luckily, these numerical treatment of interfaces that are
[µm]
[µm]
[µm]
1.5 1.5 1.5
0.5 0.5 0.5 to be handled by the CPU host, with help of optimizations are not restricted to simulations between two mesh patches of different
1.0
0.4
1.0
0.4
1.0
0.4
OpenMP threads. In particular, care was of subcellular calcium dynamics, but generi- resolutions.
taken to make data movements happen at cally reusable for many other similar com-
0.5 0.5 0.5
0.3 0.3 0.3
the same time while computations were putations. Scalable performance was With respect to programming, progress can
0.0 0.2 0.0 0.2 0.0 0.2 being carried out on the coprocessors achieved on more than 12,000 Xeon Phi co- be made to generalize the various code
0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0 0.0 0.5 1.0 1.5 2.0 2.5 3.0
[µm] [µm] [µm] and the CPU host. The overhead associated processors, by carefully applying pipelining optimizations as reusable software libraries,
0.1 0.1 0.1
Limits c: [0.14, 14.1] µM; mean 0.21 µM Limits c: [0.14, 14.7] µM; mean 0.62 µM Limits c: [0.14, 8.6] µM; mean 0.75 µM with various data movements was thus strategies to hide data movements on the or even automated source code generators.
effectively hidden, resulting in a very good various hardware levels. Such programming innovations will not only
1.4 1.4 1.4 performance scaling from using one co- simplify the coding effort of similar compu-
csr at t=1 ms csr at t=8 ms csr at t=24 ms processor to three coprocessors per node. WHAT NEXT? tations, but also ease the transition to new
1.3 1.3 1.3
3.0 3.0 3.0 Our experiences mean that petascale super- hardware architectures in future.
2.5
1.2
2.5
1.2
2.5
1.2 For using a large number of Tianhe-2 computers can easily simulate a single Progress should also be made to improve
1.1 1.1 1.1
nodes, similar care was also taken to hide sarcomere over 100ms with 3-nanometer the current mathematical model, based on
2.0 2.0 2.0 the overhead associated with data move- spatial resolution. Allocating the entire observations from the high-resolution
1.0 1.0 1.0
ments, both intra-node and inter-node. By Tianhe-2 system for several days, if ever simulations. Effort should be made to
[µm]
[µm]
[µm]
1.5 1.5 1.5
0.9 0.9 0.9 pipelining the various tasks on both the CPU possible, should enable a simulation of the couple calcium dynamics on different
1.0 1.0 1.0 hosts and the coprocessors, we managed single sarcomere with the ultimate 1-nm levels: subcellular, cellular and tissue. The
0.8 0.8 0.8
to obtain satisfactory scalability on a large spatial resolution. However, simulations of latter progress is important for discovering
0.5 0.7 0.5 0.7 0.5 0.7 number of nodes. In one particular perfor- one cell, which has 50 sarcomeres connected the medical implications of abnormal
0.0 0.6 0.0 0.6 0.0 0.6
mance test, we achieved an aggregate per- together, are still beyond the capability of the calcium dynamics.
0.0 0.5 1.0 1.5
[µm]
2.0 2.5 3.0 0.0 0.5 1.0 1.5
[µm]
2.0 2.5 3.0 0.0 0.5 1.0 1.5
[µm]
2.0 2.5 3.0
formance of 1.27 Pflop/s by utilizing 4096 world's No.1 supercomputer.
Limits csr : [0.01, 1.3] mM; mean 1.29 mM
0.5
Limits csr : [0.01, 1.3] mM; mean 1.22 mM
0.5
Limits csr : [0.01, 1.3] mM; mean 0.88 mM
0.5 nodes on Tianhe-2. NOTUR
Instead of passively waiting for the arrival Last but not least, a remark about the
20 20 20 FINDINGS of exascale supercomputers, we believe NOTUR facilities is in order here. The Abel
cCSQN at t=1 ms cCSQN at t=8 ms cCSQN at t=24 ms We used Tianhe-2 to carry out several sim- that progresses can be made in the current system, in particular, has played a central
19 19 19
3.0 3.0 3.0 ulations of calcium dynamics within one numerical scheme to facilitate faster simu- role in developing our software code. Most
18 18 18 sarcomere, with 3-nm resolution. Among lations. While the current scheme uses a of the initial programming work was done
2.5 2.5 2.5
17 17 17 other things, we simulated the evolution of unified small time step that is dictated by and tested on Abel, before further porting
2.0 16 2.0 16 2.0 16
a calcium wave that started with an initial the strongest diffusion term, an obvious to Tianhe-2. The same was true for numer-
increase in the calcium concentration due improvement lies in allowing individually ous coarse-resolution simulations that
[µm]
[µm]
[µm]
15 15 15
1.5 1.5 1.5 to a spontaneous activity at two CRUs. The determined time steps for the different were used to determine the many para-
1.0
14
1.0
14
1.0
14 simulation then confirmed a subsequent diffusion and reaction terms. The conse- meter values. As long as access to top-
13 13 13 spread of the activity. With an increased quence is that the computing time used on range supercomputers remains indirect
0.5 0.5 0.5 calcium concentration, the simulation also the reaction terms will become negligible and/or restricted, it is vital to have easy
12 12 12
revealed an increased probability in in comparison with the diffusion terms. An- access to middle-range computing facili-
0.0 0.0 0.0
0.0 0.5 1.0 1.5 2.0 2.5 3.0 11 0.0 0.5 1.0 1.5 2.0 2.5 3.0 11 0.0 0.5 1.0 1.5 2.0 2.5 3.0 11
triggering neighboring CRUs, which is the other more advanced improvement is to ties, such as provided by NOTUR.
[µm] [µm] [µm]
10 10 10 mechanism behind calcium wave propaga- avoid using a uniform global mesh over the
Limits cCSQN : [6.07, 20.1] mM; mean 20.04 mM Limits cCSQN : [6.80, 20.1] mM; mean 19.18 mM Limits cCSQN : [4.88, 18.8] mM; mean 16.37 mM
tion. Although such preliminary numerical entire 3D solution domain. Instead, nano-
Figure 2: Snapshots of a 2D slice from a 3D simulation of a calcium wave, first published in Chai et al. (2013) experiments were only a proof-of-concept, meter resolution should only be applied in Reference
nanometer-resolution simulations have certain small regions, such as within and
volume exterior to the three subpartitions, A total number of 4x56=224 threads are single-coprocessor implementation demonstrated the potential of becoming an around the CRUs. In the remaining vast J. Chai, J. Hake, N. Wu, M. Wen, X. Cai, G. T. Lines,
the CPU host is also responsible for con- spawned per Xeon Phi 31S1P coprocessor achieved 138 GB/s, which amounted to indispensable research tool. areas a much coarser mesh resolution J. Yang, H. Su, C. Zhang & X. Liao (2013). Towards
trolling all the necessary intra-node and on Tianhe-2. To achieve good data reuse in more than 90% of Xeon Phi's realistically should suffice. On the other hand, this simulation of subcellular calcium dynamics at
inter-node data movements. the caches, we have adopted loop fusion achievable memory bandwidth. In terms of With respect to high-performance comput- approach should not adopt completely nanometre resolution. The international Journal
and hierarchical blocking. Moreover, we number of floating-point operations per ing, our experiences with Tianhe-2 show unstructured meshes, because these are of High Performance Computing Applications.
The computations offloaded to each co- have enforced explicit reuse of Xeon Phi's second, the achieved performance was 118 that it is possible to effectively use the cut- inherently slow when used on super- DOI: 10.1177/1094342013514465
processor are also triply nested for-loops. vector registers, in addition to using the Gflop/s, amounting to 11.8% of the theoreti- ting-edge MIC architecture for numerically computers. A good compromise is to use a
OpenMP threads have therefore been used 512-bit SIMD instructions. Measured in the cal peak double-precision capa-bility of the solving a coupled system of several reac- patch-wise uniform mesh, where the differ-
for parallelization within each coprocessor. actually obtained memory bandwidth, our coprocessor. tion-diffusion equations. The good ent patches are assigned to the coprocessors
16 17
INTRODUCTION exploration, drilling and completion, production nanoparticle multiphase system. Nano-
Photo: Shutterstock
Energy is the number one in the humanity’s top and especially enhanced oil recovery. This particles are placed in middle of both oil and
ten problems for the next 50 years. Currently, article presents some insights on the effect of water aqueous. After a simulation time of
the main source of energy comes from the nanoparticle on oil/water binary mixture 4 nanoseconds, nanoparticles move towards
easily accessible energy such as oil, gas, and transport through a nano-sized channel by MD and stick to the clay wall due to both van der
coal. And the oil and gas resource will still simulation [1]. In addition, we also discuss the Waals and coulombic force between nano-
dominate the energy mix in near future, study of nanoparticle-based smart cement for particles and clay. This implies that the pres-
although renewable energy such as solar, wind oil and gas production by using large scale ence of nanoparticles changes the interface
power, bio-mass/-fuel, and geothermal computational resource. properties between aqueous and clay due to a
energy, will experience fast growth. With the new surface formation by nanoparticle. The
passing of the era of easy oil and the in- NANOPARTICLES FOR same phenomenon is observed for the cases
creasing difficulty of finding new economic ENHANCED-OIL-RECOVERY of nanoparticle placed only in oil or in water.
resources, much attention of the traditional oil Up to now, oil recovery has experienced its
and gas industry has been directed to extract primary and secondary stages, some bottle- To reveal the effect of nanoparticles on the oil-
more resources from existing mature oilfields necks are met in the conventional methods. water flow through the nanochannel, three
and from the fields exposed to extremely harsh One of the most promising potentials is to cases of one, two and four nanoparticles placed
environments by exploring new technologies utilize the nanoparticles to increase the in water phase of left reservoir were investi-
and solutions. recovery efficiency of oil in the reservoirs. It gated, respectively. Figure 2 displays a typically
mainly reflects in theses aspects: changing the perspective snapshot of oil/water fluid with
Nanoparticles defined between 1 and 100 nano- properties of the fluid, wettability alternation four nanoparticles in a clay nanochannel. It is
meters in size hold unexpected properties that of rocks, advanced drag reduction, strength- observed that the flow pressure of oil-water
differ remarkably from those observed in bulk ening sand consolidation, reducing the inter- mixture with nanoparticle through the confined
ENGINEERING NANOPARTICLES materials primarily originating from the large
surface-area-to-volume ratio. Structurally, the
facial tension and increasing the mobility of
the capillary-trapped oil. MD simulation is a
nanochannel is found to be strongly channel
size dependent. The presence of nanoparticles
FOR OIL FIELD APPLICATIONS
decreasing of particle size can directly result powerful tool to understand the deformation not only alters the dynamical and structural
in changes in spacing between atoms. This and flow behavior of nanoparticles and its link properties of oil-water-clay systems, but also
effect is related to the compressive strains to the atomistic structures. A fundamental enhances the oil-water flow through the nano-
induced by the compression of surface atoms understanding of the role of nanoparticles on channel at a small nanoparticle concentration,
as a result of reduction of surface energy. the oil-water binary mixture in a confined which implies that nanoparticles can be poten-
Small nanoparticles therefore adopt a nanochannel was studied by using MD simula- tially utilized for enhanced oil recovery. While
different crystal structure than their bulky tions based on CLAY force-field. A set of the nanoparticle-free oil-water flow behaves
counterpart. Once the compressive strain computational experiments in which hydro- in a laminar flow manner, with the increase
becomes critical, phase transformation philic silica nanoparticles mixed with an concentration of nanoparticle the flow tends to
spontaneously occurs. From the chemical point oil-water system confined in kaolinite clay change from a laminar to turbulent type.
of view, size reduction changes the chemical nanochannels were performed by MD The nanoparticle first slides along the clay wall
Nanoparticles have already contributed to the technological advances in a variety of reaction ability due to the increase in surface simulations. in a local low velocity with the process of break-
area to volume ratio. For example, the ing and forming hydrogen bonds, whereas it
industries, such as medicine, electronics, biomaterials and renewable energy production, utilization of nanoscale particle catalysis can We first examine the effect of nanoparticle on rotates forwards in a local high velocity
significantly enhance the rate, selectivity and a clay-oil-water system without a driving pres- aqueous environment, and escapes from the
etc., over the last decade. Recently, a new interest springs up with the application of efficiency of chemical reactions, and simulta- sure. Figure 1 presents initial and equilibrium attractive clay wall ultimately to enter into the
neously result in reduction of waste and configuration snapshots of a clay-oil-water- nanochannel.
nanoparticle-based technology in the upstream petroleum industry. Large-scale molecular pollution. Moreover, a substance can dissolve
easily at nanoscale although may not be
dynamics simulations could provide fundamental understanding of the role of smart soluble in water at micro scale. Mechanically,
NTNU nanomechanical lab demonstrated by
nanoparticles on the upstream oil production, such as enhancing oil transport in micro/ both experiment and molecular dynamics (MD)
simulation that there exists a strong size effect
nano-sized channel and the prevention of pressure-induced crack of cement sheath behind in polymeric particles with diameters at
nanometer length scale. The source for the
the casing. increases in modulus is the increase in
relative surface energy for decreasing particle
sizes. Because of the unique properties of
nanoparticles, it is believed that engineered
nanoparticle can play a significant role in an
upstream oil and gas industry, including
Figure 1 Representative side-views of a clay-oil-water-nanoparticle multiphase system simulation box. (a) Initial configu-
AUTHORS Jianying He ration, one nanoparticle in oil and one in water. (b) Equilibrium configuration, two nanoparticles stick to the clay wall and
Jianyang Wu, PhD Associate Professor, stand in a water-surrounded environment. Green: water; red: oil; and blue: clay and silica nanoparticle
Nanomechanical Lab Nanomechanical Lab
18 NTNU NTNU
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