From [CERN][La Organización Europea para la Investigación Nuclear][ Organization européenne pour la recherche nucléaire] [Europäische Organization für Kernforschung](CH): “BioDynaMo modelling platform accelerates biological simulation and more” 

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From [CERN][La Organización Europea para la Investigación Nuclear][ Organization européenne pour la recherche nucléaire] [Europäische Organization für Kernforschung](CH)

12.7.22
Andrew Purcell

The BioDynaMo project launched by CERN openlab in 2015 has now reached maturity and is seeking new applications.

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A simulation created with the BioDynaMo platform (Image: CERN)

BioDynaMo (Biology Dynamics Modeller) is an open-source software platform for creating, running and visualizing all kinds of 3D agent-based simulations. Agent-based modelling focuses on the individual active components of a system. It is a powerful methodology for studying complex systems in biology, epidemiology, economics, social sciences, medicine and more.

The BioDynaMo project was launched in 2015 as part of CERN openlab’s work with Intel on code modernization, and received support from the CERN budget for knowledge transfer for medical applications. Its primary goal was to accelerate biological simulation.

The main advantage of BioDynaMo compared with similar tools is that it has been heavily optimized to take full advantage of modern (multi-core and GPU) hardware and can greatly reduce simulation time, thus allowing researchers to simulate several scenarios in a reasonable time frame. These features have convinced several laboratories to switch to BioDynaMo for running their simulations. For example, the platform has been used to simulate the spread of COVID-19 in enclosed spaces and to examine socio-economic inequities in the Netherlands.

The technical coordination of the BioDynaMo project has now been transferred from CERN to the University of Cyprus. This marks a significant milestone in the lifecycle of the project. The project team thanks Fons Rademakers and his colleagues for the excellent job they have done guiding BioDynaMo’s development and is now actively seeking new applications for this powerful platform. “We are proud to have incubated this successful project,” says Alberto Di Meglio, head of CERN openlab. “With BioDynaMo having reached a sufficient level of technical maturity, the time is right for the consortium to explore new applications in and partnerships with other research fields, ensuring maximum impact for society.”

BioDynaMo is one of the technologies selected for the CERN Technology Impact Fund, a new scheme that supports CERN technologies with a strong potential to address global societal issues.

See the full article here.

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THE FOUR MAJOR PROJECT COLLABORATIONS

LHC

The European Organization for Nuclear Research [La Organización Europea para la Investigación Nuclear][ Organization européenne pour la recherche nucléaire] [Europäische Organization für Kernforschung](CH)[CERN] map.

3D cut of the LHC dipole CERN LHC underground tunnel and tube.

CERN SixTrack LHC particles.

The European Organization for Nuclear Research (Organization européenne pour la recherche nucléaire)(EU), known as CERN, is a European research organization that operates the largest particle physics laboratory in the world. Established in 1954, the organization is based in a northwest suburb of Geneva on the Franco–Swiss border and has 23 member states. Israel is the only non-European country granted full membership. CERN is an official United Nations Observer.

The acronym CERN is also used to refer to the laboratory, which in 2019 had 2,660 scientific, technical, and administrative staff members, and hosted about 12,400 users from institutions in more than 70 countries. In 2016 CERN generated 49 petabytes of data.

CERN’s main function is to provide the particle accelerators and other infrastructure needed for high-energy physics research – as a result, numerous experiments have been constructed at CERN through international collaborations. The main site at Meyrin hosts a large computing facility, which is primarily used to store and analyse data from experiments, as well as simulate events. Researchers need remote access to these facilities, so the lab has historically been a major wide area network hub. CERN is also the birthplace of the World Wide Web.

The convention establishing CERN was ratified on 29 September 1954 by 12 countries in Western Europe. The acronym CERN originally represented the French words for Conseil Européen pour la Recherche Nucléaire (European Council for Nuclear Research), which was a provisional council for building the laboratory, established by 12 European governments in 1952. The acronym was retained for the new laboratory after the provisional council was dissolved, even though the name changed to the current Organization Européenne pour la Recherche Nucléaire (European Organization for Nuclear Research)(EU) in 1954. According to Lew Kowarski, a former director of CERN, when the name was changed, the abbreviation could have become the awkward OERN, and Werner Heisenberg said that this could “still be CERN even if the name is [not]”.

CERN’s first president was Sir Benjamin Lockspeiser. Edoardo Amaldi was the general secretary of CERN at its early stages when operations were still provisional, while the first Director-General (1954) was Felix Bloch.

The laboratory was originally devoted to the study of atomic nuclei, but was soon applied to higher-energy physics, concerned mainly with the study of interactions between subatomic particles. Therefore, the laboratory operated by CERN is commonly referred to as the European laboratory for particle physics (Laboratoire européen pour la physique des particules), which better describes the research being performed there.

Founding members

At the sixth session of the CERN Council, which took place in Paris from 29 June – 1 July 1953, the convention establishing the organization was signed, subject to ratification, by 12 states. The convention was gradually ratified by the 12 founding Member States: Belgium, Denmark, France, the Federal Republic of Germany, Greece, Italy, the Netherlands, Norway, Sweden, Switzerland, the United Kingdom, and “Yugoslavia”.

Scientific achievements

Several important achievements in particle physics have been made through experiments at CERN. They include:

1973: The discovery of neutral currents in the Gargamelle bubble chamber.
1983: The discovery of W and Z bosons in the UA1 and UA2 experiments.
1989: The determination of the number of light neutrino families at the Large Electron–Positron Collider (LEP) operating on the Z boson peak.
1995: The first creation of antihydrogen atoms in the PS210 experiment.
1999: The discovery of direct CP violation in the NA48 experiment.
2010: The isolation of 38 atoms of antihydrogen.
2011: Maintaining antihydrogen for over 15 minutes.
2012: A boson with mass around 125 GeV/c2 consistent with the long-sought Higgs boson.

In September 2011, CERN attracted media attention when the OPERA Collaboration reported the detection of possibly faster-than-light neutrinos. Further tests showed that the results were flawed due to an incorrectly connected GPS synchronization cable.

The 1984 Nobel Prize for Physics was awarded to Carlo Rubbia and Simon van der Meer for the developments that resulted in the discoveries of the W and Z bosons. The 1992 Nobel Prize for Physics was awarded to CERN staff researcher Georges Charpak “for his invention and development of particle detectors, in particular the multiwire proportional chamber”. The 2013 Nobel Prize for Physics was awarded to François Englert and Peter Higgs for the theoretical description of the Higgs mechanism in the year after the Higgs boson was found by CERN experiments.

Computer science

The World Wide Web began as a CERN project named ENQUIRE, initiated by Tim Berners-Lee in 1989 and Robert Cailliau in 1990. Berners-Lee and Cailliau were jointly honoured by the Association for Computing Machinery in 1995 for their contributions to the development of the World Wide Web.

Current complex

CERN operates a network of six accelerators and a decelerator. Each machine in the chain increases the energy of particle beams before delivering them to experiments or to the next more powerful accelerator. Currently (as of 2019) active machines are:

The LINAC 3 linear accelerator generating low energy particles. It provides heavy ions at 4.2 MeV/u for injection into the Low Energy Ion Ring (LEIR).
The Proton Synchrotron Booster increases the energy of particles generated by the proton linear accelerator before they are transferred to the other accelerators.
The Low Energy Ion Ring (LEIR) accelerates the ions from the ion linear accelerator LINAC 3, before transferring them to the Proton Synchrotron (PS). This accelerator was commissioned in 2005, after having been reconfigured from the previous Low Energy Antiproton Ring (LEAR).
The 28 GeV Proton Synchrotron (PS), built during 1954—1959 and still operating as a feeder to the more powerful SPS.
The Super Proton Synchrotron (SPS), a circular accelerator with a diameter of 2 kilometres built in a tunnel, which started operation in 1976. It was designed to deliver an energy of 300 GeV and was gradually upgraded to 450 GeV. As well as having its own beamlines for fixed-target experiments (currently COMPASS and NA62), it has been operated as a proton–antiproton collider (the SppS collider), and for accelerating high energy electrons and positrons which were injected into the Large Electron–Positron Collider (LEP). Since 2008, it has been used to inject protons and heavy ions into the Large Hadron Collider (LHC).
The On-Line Isotope Mass Separator (ISOLDE), which is used to study unstable nuclei. The radioactive ions are produced by the impact of protons at an energy of 1.0–1.4 GeV from the Proton Synchrotron Booster. It was first commissioned in 1967 and was rebuilt with major upgrades in 1974 and 1992.
The Antiproton Decelerator (AD), which reduces the velocity of antiprotons to about 10% of the speed of light for research of antimatter.[50] The AD machine was reconfigured from the previous Antiproton Collector (AC) machine.
The AWAKE experiment, which is a proof-of-principle plasma wakefield accelerator.
The CERN Linear Electron Accelerator for Research (CLEAR) accelerator research and development facility.

Large Hadron Collider

Many activities at CERN currently involve operating the Large Hadron Collider (LHC) and the experiments for it. The LHC represents a large-scale, worldwide scientific cooperation project.

The LHC tunnel is located 100 metres underground, in the region between the Geneva International Airport and the nearby Jura mountains. The majority of its length is on the French side of the border. It uses the 27 km circumference circular tunnel previously occupied by the Large Electron–Positron Collider (LEP), which was shut down in November 2000. CERN’s existing PS/SPS accelerator complexes are used to pre-accelerate protons and lead ions which are then injected into the LHC.

Eight experiments (CMS, ATLAS, LHCb, MoEDAL, TOTEM, LHCf, FASER and ALICE) are located along the collider; each of them studies particle collisions from a different aspect, and with different technologies. Construction for these experiments required an extraordinary engineering effort. For example, a special crane was rented from Belgium to lower pieces of the CMS detector into its cavern, since each piece weighed nearly 2,000 tons. The first of the approximately 5,000 magnets necessary for construction was lowered down a special shaft at 13:00 GMT on 7 March 2005.

The LHC has begun to generate vast quantities of data, which CERN streams to laboratories around the world for distributed processing (making use of a specialized grid infrastructure, the LHC Computing Grid). During April 2005, a trial successfully streamed 600 MB/s to seven different sites across the world.

The initial particle beams were injected into the LHC August 2008. The first beam was circulated through the entire LHC on 10 September 2008, but the system failed 10 days later because of a faulty magnet connection, and it was stopped for repairs on 19 September 2008.

The LHC resumed operation on 20 November 2009 by successfully circulating two beams, each with an energy of 3.5 teraelectronvolts (TeV). The challenge for the engineers was then to try to line up the two beams so that they smashed into each other. This is like “firing two needles across the Atlantic and getting them to hit each other” according to Steve Myers, director for accelerators and technology.

On 30 March 2010, the LHC successfully collided two proton beams with 3.5 TeV of energy per proton, resulting in a 7 TeV collision energy. However, this was just the start of what was needed for the expected discovery of the Higgs boson. When the 7 TeV experimental period ended, the LHC revved to 8 TeV (4 TeV per proton) starting March 2012, and soon began particle collisions at that energy. In July 2012, CERN scientists announced the discovery of a new sub-atomic particle that was later confirmed to be the Higgs boson.

In March 2013, CERN announced that the measurements performed on the newly found particle allowed it to conclude that this is a Higgs boson. In early 2013, the LHC was deactivated for a two-year maintenance period, to strengthen the electrical connections between magnets inside the accelerator and for other upgrades.

On 5 April 2015, after two years of maintenance and consolidation, the LHC restarted for a second run. The first ramp to the record-breaking energy of 6.5 TeV was performed on 10 April 2015. In 2016, the design collision rate was exceeded for the first time. A second two-year period of shutdown begun at the end of 2018.

Accelerators under construction

As of October 2019, the construction is on-going to upgrade the LHC’s luminosity in a project called High Luminosity LHC (HL-LHC).

This project should see the LHC accelerator upgraded by 2026 to an order of magnitude higher luminosity.

As part of the HL-LHC upgrade project, also other CERN accelerators and their subsystems are receiving upgrades. Among other work, the LINAC 2 linear accelerator injector was decommissioned, to be replaced by a new injector accelerator, the LINAC4 in 2020.

Possible future accelerators

CERN, in collaboration with groups worldwide, is investigating two main concepts for future accelerators: A linear electron-positron collider with a new acceleration concept to increase the energy (CLIC) and a larger version of the LHC, a project currently named Future Circular Collider.

Not discussed or described, but worthy of consideration is the ILC, International Linear Collider in the planning stages for construction in Japan.

Participation

Since its foundation by 12 members in 1954, CERN regularly accepted new members. All new members have remained in the organization continuously since their accession, except Spain and Yugoslavia. Spain first joined CERN in 1961, withdrew in 1969, and rejoined in 1983. Yugoslavia was a founding member of CERN but quit in 1961. Of the 23 members, Israel joined CERN as a full member on 6 January 2014, becoming the first (and currently only) non-European full member.

Enlargement

Associate Members, Candidates:

Turkey signed an association agreement on 12 May 2014 and became an associate member on 6 May 2015.
Pakistan signed an association agreement on 19 December 2014 and became an associate member on 31 July 2015.
Cyprus signed an association agreement on 5 October 2012 and became an associate Member in the pre-stage to membership on 1 April 2016.
Ukraine signed an association agreement on 3 October 2013. The agreement was ratified on 5 October 2016.
India signed an association agreement on 21 November 2016. The agreement was ratified on 16 January 2017.
Slovenia was approved for admission as an Associate Member state in the pre-stage to membership on 16 December 2016. The agreement was ratified on 4 July 2017.
Lithuania was approved for admission as an Associate Member state on 16 June 2017. The association agreement was signed on 27 June 2017 and ratified on 8 January 2018.
Croatia was approved for admission as an Associate Member state on 28 February 2019. The agreement was ratified on 10 October 2019.
Estonia was approved for admission as an Associate Member in the pre-stage to membership state on 19 June 2020. The agreement was ratified on 1 February 2021.