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Primeur weekly 2020-06-29

Quantum computing

Atos takes the most powerful quantum simulator in the world to the next level with Atos QLM E ...

New model helps to describe defects and errors in quantum computers ...

Research and Markets to issue 2020 Revenue Assessment for Post-Quantum Cryptography (PQC) report ...

Focus on Europe

Iceland joined the LUMI consortium ...

LRZ to deploy HPE's Cray CS500 system to bring innovative architecture to the science of its users ...

Outcome of the e-IRG Webinar Series organized in the framework of the Croatian EU Presidency on 25-26 May 2020: Grand challenges of e-infrastructures within the new ERA ...

Spring 2020 edition of the e-IRG Magazine available ...

MareNostrum will generate a language model in Spanish based on millions of digital contents from the National Library of Spain ...

A team of bioengineering and computing experts outlines how the creation of text mining and Artificial Intelligence tools could advance biomaterials research and development ...

Barcelona Supercomputing Center releases OmpSs-2 version 2020.06 ...

Barcelona Supercomputing Center releases COMPSs version 2.7 ...

Ghent University engages Atos to build third Tier1 VSC supercomputer supporting research in Flanders ...

Dell Technologies high performance computing customers drive breakthroughs for global impact ...

Hardware

NCSA and Southern Methodist University announce new strategic partnership ...

TYAN brings the latest server advancements at its 2020 Server Solutions Online Exhibition ...

WekaIO awarded a patent for Flash Registry with Write Leveling ...

Western Digital's New NVMe SSDs and NVMe-oF solutions provide the foundation for next-generation, agile data infrastructures ...

CW-WDM MSA Group forms to drive new industry standard for optical laser sources ...

Battelle awarded contract to enable Arctic research ...

Applications

Project to calculate emissions reductions across Europe during the COVID-19 pandemic ...

Supercomputer simulations show how DNA prepares itself for repair ...

Georgia Tech engineers simulate solar cell work using supercomputers ...

A new way of designing global satellite missions ...

Process for 'two-faced' nanomaterials may aid energy, information tech ...

New transatlantic lab decodes the brain with AI ...

Ion conducting polymer crucial to improving neuromorphic devices ...

Scientists develop new tool to design better fusion devices ...

C3.ai Digital Transformation Institute announces COVID-19 awards ...

UCF Consortium announces OpenSNAPI project to develop an open, standard application programming interface for smart networking adapters ...

The Cloud

SDSC's Sherlock Cloud announces Skylab ...

Dell Technologies brings IT infrastructure and Cloud capabilities to Edge environments ...

New technique may enable all-optical data-centre networks ...

Schrödinger expands discovery efforts for COVID-19 Alliance with advanced molecular simulation leveraging high-powered parallel computing on Google Cloud ...

Nebulon emerges from stealth and announces Cloud-Defined Storage ...

Repertoire Immune Medicines receives funding from COVID-19 High Performance Computing Consortium ...

W3BCLOUD raises $20,5 million to roll out a network of data centres dedicated for the blockchain economy ...

Supercomputer simulations show how DNA prepares itself for repair


The Comet supercomputer at the San Diego Supercomputer Center and other XSEDE resources generated this plot of free energy to bring two parallel DNA double helices together as a function of distance and rotation of one around the other. This illustration aids researchers in better understanding the mechanism of replication and repair of DNA. Credit: University of Texas Medical Branch Department of Biochemistry and Molecular Biology, Harvard University Department of Physics.
25 Jun 2020 San Diego - It's common knowledge that the human body consists of trillions of cells. The cell nucleus, which houses DNA, is under attack every second of every day by environmental and behavioural factors. Researchers from Harvard University and the University of Texas Medical Branch at Galveston (UTMB) recently used the Comet supercomputer at the San Diego Supercomputer Center (SDSC) at the University of California San Diego to uncover the novel ways in which DNA prepares itself for repair.

Published in the Physical Review E journal, the study started with two DNA strands soaked in saltwater solution. The scientists watched as the DNA strands twisted and moved toward one another, due to water molecules and nearby sodium ions. The study was unique in that the research team used Comet to show specifics on how the molecules interacted with one another in order to line up before repair. While previous experiments primarily focused on potential mechanisms to demonstrate the interactions of larger DNA strands, these calculations used shorter models to get a closer look at the actual details of the process.

"The interactions or free energies found in our study were proven to be caused by certain structures in the surrounding water molecules and sodium ions", stated Monte Pettitt, who directs the Sealy Center for Structural Biology and Molecular Biophysics at the University of Texas Medical Branch at Galveston. Monte Pettitt is also the Robert A. Welch Distinguished University Chair in Chemistry and further explained that the charges and electrostatics in solution of these molecules allowed them to interact with the phosphates within the DNA.

Before being placed in the solution, the DNA strands repelled one another. Once placed in the solution, the free energy allowed the molecules to sometimes locally attract one another in a geometrically and sequence-specific way. Using Comet to conduct highly detailed simulations allowed the researchers to calculate the exact amount of free energy needed for these two DNA double helices to interact with one another.

"Our simulations showed the free energy available relative to the specific rotation angle of the DNA strands as well as the distance between the strands", stated Monte Pettitt. "This now helps researchers to understand how DNA interacts with itself in order to condense or separate during certain cellular processes."

More specifically, the study showed how the local attraction of DNA to itself only occurs for certain geometries. Although this research is basic, it contributes to an important fundamental science discovery of how DNA is aligned before it is repaired. DNA strands within a cell are not protected from environmental factors such as UV radiation and carcinogens. This makes the DNA vulnerable in the sense that it can be damaged in a spot where repair enzymes will need a roadmap to repair it - that is, another piece of DNA with the same sequence that is geometrically lined up as a template for repair.

"We still need more work to understand the sequence specificity", noted Monte Pettitt. "The calculations to illustrate these concepts would not have been possible without Comet and we are appreciative of the ability it gave us to achieve our goal of furthering basic DNA research."

This research was supported in part by the National Institutes of Health (NIH) (GM066813) and the Robert A. Welch Foundation. Computational time was allocated by the National Science Foundation's Extreme Science and Engineering Discovery Environment (TG-MCA93S001).
Source: San Diego Supercomputer Center - SDSC

Back to Table of contents

Primeur weekly 2020-06-29

Quantum computing

Atos takes the most powerful quantum simulator in the world to the next level with Atos QLM E ...

New model helps to describe defects and errors in quantum computers ...

Research and Markets to issue 2020 Revenue Assessment for Post-Quantum Cryptography (PQC) report ...

Focus on Europe

Iceland joined the LUMI consortium ...

LRZ to deploy HPE's Cray CS500 system to bring innovative architecture to the science of its users ...

Outcome of the e-IRG Webinar Series organized in the framework of the Croatian EU Presidency on 25-26 May 2020: Grand challenges of e-infrastructures within the new ERA ...

Spring 2020 edition of the e-IRG Magazine available ...

MareNostrum will generate a language model in Spanish based on millions of digital contents from the National Library of Spain ...

A team of bioengineering and computing experts outlines how the creation of text mining and Artificial Intelligence tools could advance biomaterials research and development ...

Barcelona Supercomputing Center releases OmpSs-2 version 2020.06 ...

Barcelona Supercomputing Center releases COMPSs version 2.7 ...

Ghent University engages Atos to build third Tier1 VSC supercomputer supporting research in Flanders ...

Dell Technologies high performance computing customers drive breakthroughs for global impact ...

Hardware

NCSA and Southern Methodist University announce new strategic partnership ...

TYAN brings the latest server advancements at its 2020 Server Solutions Online Exhibition ...

WekaIO awarded a patent for Flash Registry with Write Leveling ...

Western Digital's New NVMe SSDs and NVMe-oF solutions provide the foundation for next-generation, agile data infrastructures ...

CW-WDM MSA Group forms to drive new industry standard for optical laser sources ...

Battelle awarded contract to enable Arctic research ...

Applications

Project to calculate emissions reductions across Europe during the COVID-19 pandemic ...

Supercomputer simulations show how DNA prepares itself for repair ...

Georgia Tech engineers simulate solar cell work using supercomputers ...

A new way of designing global satellite missions ...

Process for 'two-faced' nanomaterials may aid energy, information tech ...

New transatlantic lab decodes the brain with AI ...

Ion conducting polymer crucial to improving neuromorphic devices ...

Scientists develop new tool to design better fusion devices ...

C3.ai Digital Transformation Institute announces COVID-19 awards ...

UCF Consortium announces OpenSNAPI project to develop an open, standard application programming interface for smart networking adapters ...

The Cloud

SDSC's Sherlock Cloud announces Skylab ...

Dell Technologies brings IT infrastructure and Cloud capabilities to Edge environments ...

New technique may enable all-optical data-centre networks ...

Schrödinger expands discovery efforts for COVID-19 Alliance with advanced molecular simulation leveraging high-powered parallel computing on Google Cloud ...

Nebulon emerges from stealth and announces Cloud-Defined Storage ...

Repertoire Immune Medicines receives funding from COVID-19 High Performance Computing Consortium ...

W3BCLOUD raises $20,5 million to roll out a network of data centres dedicated for the blockchain economy ...