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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 ...

It is easier for a DNA knot


How can long DNA filaments, which have convoluted and highly knotted structure, manage to pass through the tiny pores of various biological systems? This is the fascinating question addressed by Antonio Suma and Cristian Micheletti, researchers at the International School for Advanced Studies (SISSA) in Trieste who used computer simulations to investigate the options available to the genetic material in such situations. The study has just been published in PNAS, the journal of the National Academy of Sciences of the Unites States. Credit: Antonio Suma, SISSA.
28 Mar 2017 Trieste - Anyone who has been on a sailing boat knows that tying a knot is the best way to secure a rope to a hook and prevent its slippage. The same applies to sewing threads where knots are introduced to prevent them slipping through two pieces of fabric. How, then, can long DNA filaments, which have convoluted and highly knotted structure, manage to pass through the tiny pores of various biological systems? This is the fascinating question addressed by Antonio Suma and Cristian Micheletti, researchers at the International School for Advanced Studies (SISSA) in Trieste who used computer simulations to investigate the options available to the genetic material in such situations.

"Our computational study sheds light on the latest experimental breakthroughs on knotted DNA manipulation and adds interesting and unexpected elements", explained Cristian Micheletti. "We first observed how knotted DNA filaments pass through minuscule pores with diameter of about 10 nanometers (10 billionths of a meter). The behaviour observed in our simulations was in good agreement with the experimental measurements obtained by an international research team led by Cees Dekker, which were published only a few months ago inNature Biotechnology. These advanced and sophisticated experiments marked a turning point for understanding DNA knotting. However, current experiments cannot 'see' how DNA knots actually pass through the narrow pore. In fact, the phenomenon occurs over a tiny spatial scale, and therefore inaccessible to microscopes. This is precisely the reason why our group resorted to what the great German biophysicist Klaus Schulten called 'the computational microscope', that is, computer simulations."

Antonio Suma and Cristian Micheletti explained: "The simulations revealed that the passage of the knot can occur in two distinct ways: one where the knot is tight, and the other where the knot is more delocalised. In both cases, the knot not only manages to pass through the pore, but it does so in a very brief time."

Moreover, the knot usually passes in the final stages of the translocation, when most of the DNA strand has already passed. "But there is something more that is counterintuitive", stated the authors. "The size of the knot, be it small or large, does not seem to affect much the pore obstruction time. The latter depends instead on the translocation speed, which, in turn, depends on the initial position of the knot along the filament." These results, said the researchers, ought to help the design of future experiments probing the spontaneous knotting of DNA, a still largely unexplored venue, especially regarding the size of DNA knots.

Advancing our current understanding of knots in biological molecules is important to clarify their implications in biological contexts as well as in applicative ones, such as DNA sequencing using nanopores. Antonio Suma and Cristian Micheletti hope that the promising directions suggested by their study can lead to a more detailed and accurate profiling of entanglement in DNA, RNA and proteins.

The study has just been published in PNAS, the Journal of the National Academy of Sciences of the Unites States .

Source: Scuola Internazionale Superiore di Studi Avanzati

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 ...