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Primeur weekly 2020-09-14

Focus

Some RISC-V high performance implementations presented at RISC-V Global Forum by European Processor Initiative, NSITEXE, OpenBLAS, and SemiDynamics ...

Exascale supercomputing

Combustion pioneer named Department of Energy fellow ...

Quantum computing

New method prevents quantum computers from crashing ...

Q-CTRL and Quantum Machines announce partnership to accelerate quantum computing development ...

Cambridge Quantum Computing welcomes Mehdi Bozzo-Rey ...

Focus on Europe

Researchers develop molecule to store solar energy ...

First release of PROCESS software now available ...

From artificial intelligence to nanomaterials and astrophysics - Seven Irish research projects to benefit from EuroHPC Academic Flagship Programme ...

Middleware

SDSC to help create science gateway for new materials discovery ...

Hardware

NCSA's Donna J. Cox honoured with rare IPS Technology Innovation Award ...

Advanced NVMe controller technology for next generation memory devices ...

Credo announces the DOVE platform, its second generation of low power PAM4 DSPs for 100G/200G/400G data networks ...

Tachyum opens U.S., EU and NATO Government Business Unit ...

National Science Foundation awards CENIC an international networking grant for operation of Pacific Wave ...

UCF Consortium receives open source contribution from Arm to speed access to persistent memory storage ...

Liqid announces agreement with Arrow Electronics to bring composable disaggregated infrastructure solutions to data centres worldwide ...

Research and Markets to issue Global Hybrid Memory Cube (HMC) and High-Bandwidth Memory (HBM) Suppliers Strategic Positioning and Leadership Quadrant Report 2020 ...

Genomics England scales up genomic sequencing with Quantum ActiveScale object storage ...

NVIDIA to acquire Arm for $40 billion, creating world's premier computing company for the age of AI ...

Applications

NCSA and University of Illinois announce new Center for AstroPhysical Surveys ...

Lead lab selected for next-generation cosmic microwave background experiment ...

Insilico announces the launch of AI-powered COVIDomic to support COVID-19 research worldwide ...

Model shows that the speed neurons fire impacts their ability to synchronize ...

Physicists achieve tunable spin wave excitation ...

EBRAINS makes bid to enter the European Research Infrastructure Roadmap with ten-country strong coalition and France as lead country ...

Mysterious cellular droplets come into focus ...

The presence of resonating cavities above sunspots has been confirmed ...

The Hospital Clínic and BSC will use artificial intelligence to predict the evolution of patients with COVID-19 ...

ORIGINS - answers to existential questions ...

Altair announces 2020 Global Technology Conference to explore "The Future of..." ...

The Cloud

National Science Foundation-funded CloudBank now operational ...

Schlumberger, IBM and Red Hat announce major hybrid Cloud collaboration for the energy industry ...

Red Hat Marketplace aims to accelerate open hybrid Cloud innovation with certified software solutions ready to run on any Cloud ...

Renesas introduces DDR5 data buffer for high-performance server and Cloud service applications ...

NETINT deploys video transcoding technology in the Nimbix Cloud ...

Mysterious cellular droplets come into focus


Individual protein molecules comprising the condensate are highlighted using colour. Credit: Han-Yi Chou, University of Illinois, Urbana-Champaign.
9 Sep 2020 Austin - The world inside the human cell grew a bit more interesting in recent years as the role of a new biological structure became clearer.

It was long believed that most important operations in the cell occur within organelles. "They're there to do certain functions. For instance, mitochondria generate the energy that everything runs on", explained Aleksei Aksimentiev, a professor of physics at the University of Illinois at Urbana-Champaign. "What is common to all of them is that they're surrounded by a lipid membrane. What people recently discovered is there are organelles that don't have lipid bilayers. They assemble spontaneously in the form of droplets. And those organelles have particular functions."

In recent years, with improved imaging capabilities, the roles, occurrence, and behavior of these membrane-less organelles have become clearer. In 2017 they were given a name: biological condensates. They are thought to play a role in DNA repair and aging, and researchers believe a number of neurological diseases are related to the condensate not working properly, including Amyotrophic lateral sclerosis, or ALS, where nerve cells break down, leading to loss of muscular function.

"Let's say you have DNA and it suddenly has a break. It's usually a really bad thing, because it cannot replicate, but there's a machinery that will come and repair it", he explained. "A bubble of condensate forms that miraculously attracts only the molecules that are required to repair the DNA. There are all kinds of different condensates and they all recruit the right molecules somehow."

How do these membrane-less organelles spontaneously form? And how do they recruit other molecules to help them?

The physics of this process appears similar to phase separation, like how oil and water spontaneously form droplets in the right conditions, but with some differences. In normal phase separation, temperature usually motivates the separation. In biology, it is a change in concentrations.

"We don't know exactly how it works", Aleksei Aksimentiev stated. "I'm specifically interested in how this recruitment happens, and how molecules recognize other molecules."

Aleksei Aksimentiev is using the Frontera supercomputer at the Texas Advanced Computing Center (TACC), one of the fastest in the world, to better understand this process. Over the last decade, he and others developed the tools and methods to explore the behavior of biological systems at the atomic level using molecular dynamics simulations.

Aleksei Aksimentiev is able to simulate biological systems with millions of interacting atoms in a realistic environment for microseconds or even milliseconds - the timescales at which biological systems operate. Today's supercomputers allow larger, faster simulations, and permit scientists to ask and answer new questions.

Even by the standards of the field, biological condensates are challenging to study computationally. Unlike other ordered systems like proteins with known rigid structures, or disordered systems like water, biological condensates are what's known as 'partially disordered' - a particularly hard type of structure to simulate.

Writing in the Journal of Physical Chemistry Letters in May 2020, Aleksei Aksimentiev and graduate student Han-Yi Chou described coarse-grained molecular dynamics simulations on Frontera that charted the phase diagram - a graphical representation of the physical states of a substance under different conditions of temperature and pressure - of one particular biomolecular condensate - fused in sarcoma (FUS). A nuclear DNA/RNA binding protein, FUS regulates different steps of gene expression, including transcription, splicing and mRNA transport. The research was supported by grants from the National Science Foundation and the National Institutes of Health.

The researchers showed that a particle-based molecular dynamics model can reproduce known phase separation properties of a FUS condensate, including its critical concentration and susceptibility to mutations.

They also showed that they could use chain collapse theory to determine the thermodynamic properties of the condensate and to link them to changes in the shape of individual condensate molecules.

The behaviour of a biological condensate, with all its complex inter- and intramolecular interactions, can be described by a polymer physics model, they found. This makes computer modelling a useful tool for uncovering the behavior of these still-mysterious cellular actors.

Aleksei Aksimentiev's research sets the stage for future studies that will elucidate the molecular mechanisms driving the formation of droplets in more complex biological condensates, like those that repair RNA. The work is one step on a long path to fully elucidate the mystery of biological condensates in cells - another trick of nature slowly uncovered.

Source: University of Texas at Austin, Texas Advanced Computing Center - TACC

Back to Table of contents

Primeur weekly 2020-09-14

Focus

Some RISC-V high performance implementations presented at RISC-V Global Forum by European Processor Initiative, NSITEXE, OpenBLAS, and SemiDynamics ...

Exascale supercomputing

Combustion pioneer named Department of Energy fellow ...

Quantum computing

New method prevents quantum computers from crashing ...

Q-CTRL and Quantum Machines announce partnership to accelerate quantum computing development ...

Cambridge Quantum Computing welcomes Mehdi Bozzo-Rey ...

Focus on Europe

Researchers develop molecule to store solar energy ...

First release of PROCESS software now available ...

From artificial intelligence to nanomaterials and astrophysics - Seven Irish research projects to benefit from EuroHPC Academic Flagship Programme ...

Middleware

SDSC to help create science gateway for new materials discovery ...

Hardware

NCSA's Donna J. Cox honoured with rare IPS Technology Innovation Award ...

Advanced NVMe controller technology for next generation memory devices ...

Credo announces the DOVE platform, its second generation of low power PAM4 DSPs for 100G/200G/400G data networks ...

Tachyum opens U.S., EU and NATO Government Business Unit ...

National Science Foundation awards CENIC an international networking grant for operation of Pacific Wave ...

UCF Consortium receives open source contribution from Arm to speed access to persistent memory storage ...

Liqid announces agreement with Arrow Electronics to bring composable disaggregated infrastructure solutions to data centres worldwide ...

Research and Markets to issue Global Hybrid Memory Cube (HMC) and High-Bandwidth Memory (HBM) Suppliers Strategic Positioning and Leadership Quadrant Report 2020 ...

Genomics England scales up genomic sequencing with Quantum ActiveScale object storage ...

NVIDIA to acquire Arm for $40 billion, creating world's premier computing company for the age of AI ...

Applications

NCSA and University of Illinois announce new Center for AstroPhysical Surveys ...

Lead lab selected for next-generation cosmic microwave background experiment ...

Insilico announces the launch of AI-powered COVIDomic to support COVID-19 research worldwide ...

Model shows that the speed neurons fire impacts their ability to synchronize ...

Physicists achieve tunable spin wave excitation ...

EBRAINS makes bid to enter the European Research Infrastructure Roadmap with ten-country strong coalition and France as lead country ...

Mysterious cellular droplets come into focus ...

The presence of resonating cavities above sunspots has been confirmed ...

The Hospital Clínic and BSC will use artificial intelligence to predict the evolution of patients with COVID-19 ...

ORIGINS - answers to existential questions ...

Altair announces 2020 Global Technology Conference to explore "The Future of..." ...

The Cloud

National Science Foundation-funded CloudBank now operational ...

Schlumberger, IBM and Red Hat announce major hybrid Cloud collaboration for the energy industry ...

Red Hat Marketplace aims to accelerate open hybrid Cloud innovation with certified software solutions ready to run on any Cloud ...

Renesas introduces DDR5 data buffer for high-performance server and Cloud service applications ...

NETINT deploys video transcoding technology in the Nimbix Cloud ...