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Primeur weekly 2017-03-20

Focus

CEO Steve Cotter elaborates on GEANT's backbone infrastructure, service deployment and KPI development ...

Exascale supercomputing

MicroVisor, a new hypervisor technology, paves the way for low-power data centres ...

Crowd computing

iEx.ec announces token crowdsale to launch the first distributed Cloud Crowdcomputing platform ...

Quantum computing

Digital pioneering work: Volkswagen uses quantum computers ...

D-Wave and Virginia Tech join forces to advance quantum computing ...

D-Wave 2000Q system to be installed at Quantum Artificial Intelligence Lab run by Google, NASA, and Universities Space Research Association ...

Focus on Europe

NVIDIA partners with Bosch for system based on next-generation DRIVE PX Xavier platform ...

New supercomputer for RWTH Aachen ...

European 'Big Data' e-infrastructure to support biodiversity research Lifewatch now ERIC legal entity ...

ISC 2017 dedicates a day to deep learning ...

Hardware

Los Alamos National Laboratory donation adding to University of New Mexico supercomputing power ...

BASF selects HPE to build supercomputer for global chemical research ...

Top weather and climate sites rely on DDN storage for more accurate, faster simulations, forecasts and predictions ...

Noodle.ai unveils BEAST Enterprise Artificial Intelligence supercomputing technology - powered by NVIDIA DGX-1 AI supercomputer ...

Simons Foundation's Flatiron Institute to repurpose SDSC's 'Gordon' supercomputer ...

Applications

A scientist and a supercomputer re-create a tornado ...

Arthritis Research UK introduces IBM Watson-powered 'virtual assistant' to provide information and advice to people with arthritis ...

High-precision calculations on supercomputers help reveal the physics of the universe ...

IDx and IBM Watson Health forge alliance for eye health ...

IBM Watson Health to integrate MedyMatch Technology into cognitive imaging offerings to help doctors identify head trauma and stroke ...

Simultaneous detection of multiple spin states in a single quantum dot ...

Computer simulation of protein synthesis reveals awesome complexity of cell machinery ...

Computer simulations first step toward designing more efficient amine chemical scrubbers ...

The prototype of a chemical computer detects a sphere ...

The Cloud

Oracle announces fiscal 2017 Q3 results ...

IBM and Red Hat Collaborate to Accelerate Hybrid Cloud Adoption with OpenStack ...

Computer simulation of protein synthesis reveals awesome complexity of cell machinery

A result of protein synthesis simulation. Concentration changes of 241 components are shown. Credit: Osaka University.16 Mar 2017 Osaka - Life depends on proteins. These molecules are produced continually in our cells, which act as microscopic production lines - but the process is so complex we have barely begun to understand it. Exploring protein synthesis may, however, be the key to revealing how the body controls the thousands of reactions occurring simultaneously inside us.

Now, a Japanese research team led by Osaka University and RIKEN has run a computer simulation of a small protein (peptide) being produced by bacterial translation machinery, confirming a "molecular toolkit" as highly sophisticated even for simple lifeforms.

Full-size proteins are too large to model in detail. However, a tripeptide - made from three amino acids: "Met-Gly-Gly" - can be produced by a set of 27 molecules in the bacteria E. coli. The researchers simulated this process, also known as an in-vitro translation (IVT), by modeling the chemical reactions on a computer.

Even for this simple tripeptide, over 900 reactions were needed, with over 200 chemicals formed as by-products. These reactions occurred at wildly different speeds, and the slowest acted as bottlenecks on the overall process. The researchers found some reaction rates from earlier experiments, while others had to be assumed. Then, they simulated 1000 seconds of the resulting chemical dance.

"We were surprised that even with so many assumptions and simplifications, the simulation accurately described the kinetics of Met-Gly-Gly production", study lead author Tomoaki Matsuura stated. "When we increased the amounts of some initial components, the rate of synthesis increased, in line with real IVT."

By tracking the amount of each chemical present, the researchers found that many chemicals reached a stable level - termed steady-state, however, only to suddenly decrease again later on. In fact, this collapse happened twice - after 0.5 sec and again after 10 sec.

The researchers believe this non-linear behavior, wherein chemicals reach a "stable state" in the system, but are later recruited back to "active state", is typical of biochemistry.

"The peak, collapse, and further peaking of steady states is likely to occur in other processes, such as glucose metabolism", Tomoaki Matsuura stated.

Tomoaki Matsuura added that the simulations could be extended to different proteins, including larger ones. "By comparing our simulations with IVT experiments", he stated, "we can improve the IVT systems - which in turn will help us improve the simulations. The awesome complexity of this 'simple' synthesis reminds us that we are just beginning to understand life at the molecular level."

Source: Osaka University

Back to Table of contents

Primeur weekly 2017-03-20

Focus

CEO Steve Cotter elaborates on GEANT's backbone infrastructure, service deployment and KPI development ...

Exascale supercomputing

MicroVisor, a new hypervisor technology, paves the way for low-power data centres ...

Crowd computing

iEx.ec announces token crowdsale to launch the first distributed Cloud Crowdcomputing platform ...

Quantum computing

Digital pioneering work: Volkswagen uses quantum computers ...

D-Wave and Virginia Tech join forces to advance quantum computing ...

D-Wave 2000Q system to be installed at Quantum Artificial Intelligence Lab run by Google, NASA, and Universities Space Research Association ...

Focus on Europe

NVIDIA partners with Bosch for system based on next-generation DRIVE PX Xavier platform ...

New supercomputer for RWTH Aachen ...

European 'Big Data' e-infrastructure to support biodiversity research Lifewatch now ERIC legal entity ...

ISC 2017 dedicates a day to deep learning ...

Hardware

Los Alamos National Laboratory donation adding to University of New Mexico supercomputing power ...

BASF selects HPE to build supercomputer for global chemical research ...

Top weather and climate sites rely on DDN storage for more accurate, faster simulations, forecasts and predictions ...

Noodle.ai unveils BEAST Enterprise Artificial Intelligence supercomputing technology - powered by NVIDIA DGX-1 AI supercomputer ...

Simons Foundation's Flatiron Institute to repurpose SDSC's 'Gordon' supercomputer ...

Applications

A scientist and a supercomputer re-create a tornado ...

Arthritis Research UK introduces IBM Watson-powered 'virtual assistant' to provide information and advice to people with arthritis ...

High-precision calculations on supercomputers help reveal the physics of the universe ...

IDx and IBM Watson Health forge alliance for eye health ...

IBM Watson Health to integrate MedyMatch Technology into cognitive imaging offerings to help doctors identify head trauma and stroke ...

Simultaneous detection of multiple spin states in a single quantum dot ...

Computer simulation of protein synthesis reveals awesome complexity of cell machinery ...

Computer simulations first step toward designing more efficient amine chemical scrubbers ...

The prototype of a chemical computer detects a sphere ...

The Cloud

Oracle announces fiscal 2017 Q3 results ...

IBM and Red Hat Collaborate to Accelerate Hybrid Cloud Adoption with OpenStack ...