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Primeur weekly 2015-11-30

Focus

Turkey to prepare itself for European Open Science Cloud ...

Quantum computing

Quantum computer coding in silicon now possible ...

Middleware

Open Science Grid using SDSC's Comet supercomputer virtual clusters ...

IBM and OpenPOWER members deliver accelerated technologies to break Big Data speed barriers ...

Hardware

Hewlett Packard Enterprise sees significant momentum in high-performance computing ...

Mellanox announces ConnectX-4 Lx Programmable adapter with onboard Xilinx FPGA acceleration ...

Mellanox introduces the Switch-IB 2, world's first 100Gb/s smart switch ...

Supermicro debuts new 4U 90/60-bay storage server alongside 1U 4x GPU, NVMe, high-density server and storage solutions ...

Los Alamos National Labs selects Aeon Computing's next generation of supercomputing infrastructure ...

Dell innovation to democratize high performance computing and accelerate mainstream adoption ...

State grant enables energy-saving retrofit of Lawrence Livermore computing clusters ...

Applications

NSF-supported supercomputing resources enable research that would otherwise be impossible ...

New supercomputer simulations enhance understanding of protein motion and function ...

Scientists use supercomputer to model plasma turbulence, and solve a 50-year-old mystery ...

IBM Research and Rensselaer Polytechnic Institute pioneer next-generation cognitive environments for business decision making ...

How DNA and a supercomputer can help sustain honey bee populations ...

IRB Barcelona develops an advanced method and the first platform of DNA simulations ...

INCITE grants awarded to 56 computational research projects ...

OLCF supercomputer's GPUs advance earthquake simulations for high-frequency seismic hazard map ...

Researchers trains Watson AI to 'chat' and spark more creativity in humans ...

TOP500

HPC system Hazel Hen of High Performance Computing Center Stuttgart captures position 8 on new TOP500 list ...

HPCG-Benchmark: GCS Centre HLRS runs Europe's fastest supercomputer ...

The Cloud

ICGC brings more genomic health data to researchers on the Amazon Web Services Cloud ...

Penguin Computing increases customer compute capacity with availability of the Tundra platform on its Penguin Computing on Demand HPC Cloud service ...

Hewlett Packard Enterprise delivers Docker solutions from the data centre to the Cloud ...

New supercomputer simulations enhance understanding of protein motion and function


This is an illustration of the structure of a phosphoglycerate kinase protein that was subjected to molecular dynamics simulations. The relative motions of the red and blue domains of the proteins are highly complex, and can be described in terms of motion of a configurational point on a rough energy landscape (illustrated). The transitions of the structure between energy minima on the landscape can be described in terms of a network (illustrated), which is found to be fractal (self-similar) on every timescale. Credit: Thomas Splettstoesser
23 Nov 2015 Oak Ridge - Supercomputing simulations at the Department of Energy's Oak Ridge National Laboratory could change how researchers understand the internal motions of proteins that play functional, structural and regulatory roles in all living organisms. The team's results are featured inNature Physics.

"Proteins have never been seen this way before", stated co-author Jeremy Smith, director of ORNL's Center for Molecular Biophysics and a Governor's Chair at the University of Tennessee (UT). "We used considerable computer power to provide a unified conceptual picture of the motions in proteins over a huge range of timescales, from the very shortest lengths of time at which atoms move (picoseconds) right up to the lifetimes of proteins in cells (roughly 1000 seconds). It changes what we think a protein fundamentally is."

Studying proteins - their structure and function - is essential to advancing understanding of biological systems relevant to different energy and medical sciences, from bio-energy research and subsurface biogeochemistry to drug design.

Results obtained by Jeremy Smith's UT graduate student, Xiaohu Hu, revealed that the dynamics of single protein molecules are "self-similar" and out of equilibrium over an enormous range of timescales.

With the help of Titan - the fastest supercomputer in the U.S., located at the DOE Office of Science's Oak Ridge Leadership Computing Facility - Jeremy Smith's team developed a complete picture of protein dynamics, revealing that the structural fluctuations within any two identical protein molecules, even if coded from the same gene, turn out to be different.

"A gene is a code for a protein, producing different copies of the protein that should be the same, but the internal fluctuations of these individual protein molecules may never reach equilibrium, or converge", Jeremy Smith stated. "This is because the fluctuations themselves are continually aging and don't have enough time to settle down before the protein molecules are eaten up in the cell and replaced."

Understanding the out-of-equilibrium phenomenon has biological implications because the function of a protein depends on its motions. Two individual protein molecules, even though they come from the same gene, will not function precisely the same way within the cell.

"You may have, for example, two identical enzyme molecules that catalyze the same reaction", stated Jeremy Smith. "But due to the absence of equilibrium, the rate at which the catalysis happens will be slightly different for the two proteins. This affects the biological function of the protein."

The team also discovered that the dynamics of single protein molecules are self-similar, or fractal over the whole range of timescales. In other words, the motions in a single protein molecule look the same however long you look at them for, from picoseconds to hundreds of seconds.

"The motions in a protein, how the bits of the protein wiggle and jiggle relative to each other, resemble one another on all these timescales", Jeremy Smith stated. "We represent the shape of a protein as a point. If it changes its shape due to motions, it goes to a different point, and so on. We joined these points, drawing pictures, and we found that these pictures are the same when you look at them on whatever timescale, whether it's nanoseconds, microseconds, or milliseconds."

By building a more complete picture of protein dynamics, the team's research reveals that motions of a single protein molecule on very fast timescales resemble those that govern the protein's function.

To complete all of the simulations, the team combined the power of Titan with two other supercomputers - Anton, a specialty parallel computer built by D.E. Shaw Research, and Hopper, the National Energy Research Scientific Computing Center's Cray XE6 supercomputer located at Lawrence Berkeley National Laboratory.

"Titan was especially useful for us to get accurate statistics", Jeremy Smith stated. "It allowed us to do a lot of simulations in order to reduce the errors and get more confident results."

The title of theNature Physicspaper is "The Dynamics of Single Protein Molecules is Non-Equilibrium and Self-Similar Over Thirteen Decades in Time".

This research was supported by the DOE Office of Science through an Advanced Scientific Computing Research (ASCR) Leadership Computing Challenge (ALCC) allocation and funded in part by a DOE Experimental Programme to Stimulate Competitive Research (EPSCoR) award. The Oak Ridge Leadership Computing Facility and National Energy Research Scientific Computing Center are DOE Office of Science User Facilities.
Source: DOE/Oak Ridge National Laboratory

Back to Table of contents

Primeur weekly 2015-11-30

Focus

Turkey to prepare itself for European Open Science Cloud ...

Quantum computing

Quantum computer coding in silicon now possible ...

Middleware

Open Science Grid using SDSC's Comet supercomputer virtual clusters ...

IBM and OpenPOWER members deliver accelerated technologies to break Big Data speed barriers ...

Hardware

Hewlett Packard Enterprise sees significant momentum in high-performance computing ...

Mellanox announces ConnectX-4 Lx Programmable adapter with onboard Xilinx FPGA acceleration ...

Mellanox introduces the Switch-IB 2, world's first 100Gb/s smart switch ...

Supermicro debuts new 4U 90/60-bay storage server alongside 1U 4x GPU, NVMe, high-density server and storage solutions ...

Los Alamos National Labs selects Aeon Computing's next generation of supercomputing infrastructure ...

Dell innovation to democratize high performance computing and accelerate mainstream adoption ...

State grant enables energy-saving retrofit of Lawrence Livermore computing clusters ...

Applications

NSF-supported supercomputing resources enable research that would otherwise be impossible ...

New supercomputer simulations enhance understanding of protein motion and function ...

Scientists use supercomputer to model plasma turbulence, and solve a 50-year-old mystery ...

IBM Research and Rensselaer Polytechnic Institute pioneer next-generation cognitive environments for business decision making ...

How DNA and a supercomputer can help sustain honey bee populations ...

IRB Barcelona develops an advanced method and the first platform of DNA simulations ...

INCITE grants awarded to 56 computational research projects ...

OLCF supercomputer's GPUs advance earthquake simulations for high-frequency seismic hazard map ...

Researchers trains Watson AI to 'chat' and spark more creativity in humans ...

TOP500

HPC system Hazel Hen of High Performance Computing Center Stuttgart captures position 8 on new TOP500 list ...

HPCG-Benchmark: GCS Centre HLRS runs Europe's fastest supercomputer ...

The Cloud

ICGC brings more genomic health data to researchers on the Amazon Web Services Cloud ...

Penguin Computing increases customer compute capacity with availability of the Tundra platform on its Penguin Computing on Demand HPC Cloud service ...

Hewlett Packard Enterprise delivers Docker solutions from the data centre to the Cloud ...