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Primeur weekly 2017-04-03

Focus

Luxembourg capital of supercomputing in Europe ...

Quantum computing

Quantum communication: How to outwit noise ...

Rigetti Computing raises $64 million in Series A and B funding, led by Andreessen Horowitz and Vy Capital ...

Focus on Europe

HPC Summit Week 2017 in Barcelona to gather main HPC stakeholders in Europe ...

Six High Performance Computing centres in the UK to be officially launched ...

It is easier for a DNA knot ...

Prof. Dieter Kranzlmüller is new Chairman of the Board of Directors at Leibniz Supercomputing Centre ...

GW4 world-first ARM based production supercomputer launched at national exhibition in the UK ...

Middleware

New version of Univa Grid Engine 2x faster than Sun Grid Engine 6.2u5 ...

Huawei and Altair sign MoU to jointly pursue High-Performance Computing (HPC) opportunities and build industrial simulation Cloud solutions ...

Hardware

New HPC installation to deploy Asetek liquid cooling solution ...

HPE to acquire Nimble Storage to strengthen leadership in hybrid IT ...

New Supermicro rack scale design brings open management for on-demand Cloud scale data centres ...

Supermicro launches new Intel Optane SSD optimized platforms ...

GBP 3 million awarded to Oxford-led consortium for national machine learning computing facility ...

EPCC invests GB 2.4 million in Tier-2 Cirrus system ...

Eurotech continues to lead innovation in embedded and high-performance computing: New designs featuring 2nd generation Intel Xeon Phi and Intel Atom E39XX ...

Officials dedicate Ohio OSC's newest, most powerful supercomputer ...

USC's Information Sciences Institute tapped to produce computing chips technology ...

Applications

Supercomputer puts Colombia on fast track to designing new HIV drugs, science and engineering discovery ...

SDSC announces Annual Supercomputing & Data Science Workshop ...

IBM patents cognitive system to manage self-driving vehicles ...

Cryo-electron microscopy achieves unprecedented resolution using new computational methods ...

Psychologists enlist machine learning to help diagnose depression ...

A seismic mapping milestone ...

Information storage with a nanoscale twist ...

Nanomagnets for future data storage ...

Researchers shoot for success with simulations of laser pulse-material interactions ...

A system based on data science to predict student dropouts ...

The Cloud

Oracle unveils industry-first Cloud Converged Storage to help organisations bridge on-premises and Oracle Cloud storage ...

Cryo-electron microscopy achieves unprecedented resolution using new computational methods


Complete capsid of bacteriophage P22 generated with validated atomic models that were derived from a high-resolution cryo-electron microscopy density map. C. Hryc and the Chiu Lab, Baylor College of Medicine.
23 May 2017 Berkeley - Cryo-electron microscopy (cryo-EM) - which enables the visualization of viruses, proteins, and other biological structures at the molecular level - is a critical tool used to advance biochemical knowledge. Now Lawrence Berkeley National Laboratory researchers have extended cryo-EM's impact further by developing a new computational algorithm that was instrumental in constructing a 3D atomic-scale model of bacteriophage P22 for the first time.

Over 20,000 two-dimensional cryo-EM images of bacteriophage P22 - also known as the P22 virus that infects the common bacterium Salmonella - from Baylor College of Medicine were used to make the model. The results were published by researchers from Baylor College of Medicine, Massachusetts Institute of Technology, Purdue University and Berkeley Lab in the Proceedings of the National Academies of Sciences earlier in March.

"This is a great example of how to exploit electron microscopy technology and combine it with new computational methods to determine a bacteriophage's structure", stated Paul Adams, Berkeley Lab's Molecular Biophysics & Integrated Bioimaging division director and a co-author of the paper. "We developed the algorithms - the computational code - to optimize the atomic model so that it best fit the experimental data."

Pavel Afonine, a Berkeley Lab computational research scientist and paper co-author, took the lead in developing the algorithm using Phenix, a software suite used traditionally in X-ray crystallography for determining macromolecular structures.

The successful rendering of bacteriophage P22's 3D atomic-scale model allows researchers to peek inside the virus' protein coats at resolution. It is the culmination of several years of work that previously had enabled Baylor College researchers to trace out most of the protein’s backbone, but not the fine details, according to Corey Hryc, co-first author and a graduate student of Baylor biochemistry professor Wah Chiu.

"Thanks to this exquisite structural detail, we have determined the protein chemistry of the P22 virus", Wah Chiu stated. "I think it is important that we provide detailed annotations with the structure so other researchers can use it for their future experiments", he added. Wah Chiu's lab has been using cryo-EM and computer reconstruction techniques to build 3D molecular structures for almost 30 years.

And the findings could have valuable biological implications as well.

Thanks to the 3D atomic-scale model, it's now "possible to see the interactions between the pieces making up the P22 virus, which are critical to making it stable", Paul Adams stated. This helps researchers figure out how to make chemicals that can bind to certain proteins. Paul Adams underscores that the ability to understand the configuration of atoms in molecular space can be used to generate new insights into drug design and development.

The National Institutes of Health funded this work.
Source: Lawrence Berkeley National Laboratory

Back to Table of contents

Primeur weekly 2017-04-03

Focus

Luxembourg capital of supercomputing in Europe ...

Quantum computing

Quantum communication: How to outwit noise ...

Rigetti Computing raises $64 million in Series A and B funding, led by Andreessen Horowitz and Vy Capital ...

Focus on Europe

HPC Summit Week 2017 in Barcelona to gather main HPC stakeholders in Europe ...

Six High Performance Computing centres in the UK to be officially launched ...

It is easier for a DNA knot ...

Prof. Dieter Kranzlmüller is new Chairman of the Board of Directors at Leibniz Supercomputing Centre ...

GW4 world-first ARM based production supercomputer launched at national exhibition in the UK ...

Middleware

New version of Univa Grid Engine 2x faster than Sun Grid Engine 6.2u5 ...

Huawei and Altair sign MoU to jointly pursue High-Performance Computing (HPC) opportunities and build industrial simulation Cloud solutions ...

Hardware

New HPC installation to deploy Asetek liquid cooling solution ...

HPE to acquire Nimble Storage to strengthen leadership in hybrid IT ...

New Supermicro rack scale design brings open management for on-demand Cloud scale data centres ...

Supermicro launches new Intel Optane SSD optimized platforms ...

GBP 3 million awarded to Oxford-led consortium for national machine learning computing facility ...

EPCC invests GB 2.4 million in Tier-2 Cirrus system ...

Eurotech continues to lead innovation in embedded and high-performance computing: New designs featuring 2nd generation Intel Xeon Phi and Intel Atom E39XX ...

Officials dedicate Ohio OSC's newest, most powerful supercomputer ...

USC's Information Sciences Institute tapped to produce computing chips technology ...

Applications

Supercomputer puts Colombia on fast track to designing new HIV drugs, science and engineering discovery ...

SDSC announces Annual Supercomputing & Data Science Workshop ...

IBM patents cognitive system to manage self-driving vehicles ...

Cryo-electron microscopy achieves unprecedented resolution using new computational methods ...

Psychologists enlist machine learning to help diagnose depression ...

A seismic mapping milestone ...

Information storage with a nanoscale twist ...

Nanomagnets for future data storage ...

Researchers shoot for success with simulations of laser pulse-material interactions ...

A system based on data science to predict student dropouts ...

The Cloud

Oracle unveils industry-first Cloud Converged Storage to help organisations bridge on-premises and Oracle Cloud storage ...