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Primeur weekly 2020-01-06

Focus

The LUMI supercomputer is not just a very fast supercomputer, it is first of all a competence development platform - Interview with Kimmo Koski, CSC, Finland ...

Quantum computing

ORNL researchers advance performance benchmark for quantum computers ...

In leap for quantum computing, silicon quantum bits establish a long-distance relationship ...

The Quantum Information Edge launches to accelerate quantum computing R&D ...

Focus on Europe

The coolest LEGO in the universe ...

Middleware

BP looks to ORNL and ADIOS to help rein in data ...

Hardware

New year brings new directory structure for OLCF's high-performance storage system ...

GIGABYTE brings AI, Cloud solutions and smart applications to CES 2020 to enable future today ...

During its final hours of operation, the Titan supercomputer simulated the birth of supernovae ...

Big iron afterlife: How ORNL's Titan supercomputer was recycled ...

Applications

Stanford researchers build a particle accelerator that fits on a chip ...

Brain-like functions emerging in a metallic nanowire network ...

Award-winning engineer helps keep US nuclear deterrent safe from radiation ...

New algorithm could mean more efficient, accurate equipment for Army ...

Paul Ginsparg named winner of the 2020 AIP Karl Compton Medal ...

'Super' simulations offer fresh insight into serotonin receptors ...

Researchers accelerate plasma turbulence simulations on Oak Ridge supercomputers to improve fusion design models ...

'Super' simulations offer fresh insight into serotonin receptors


Credit: A. James Clark School of Engineering, University of Maryland.
23 Dec 2019 College Park - Scientists at the University of Maryland (UMD) and the National Institute of Standards and Technology (NIST) have discovered a way to detect the molecular mechanism by which 5HT3A, a serotonin receptor located at the neuron synapse, is activated. Having a molecular model of this activation will allow the testing of pharmaceuticals inhibitors using computer models instead of traditional experiments, potentially reducing the cost and time of screening new drugs.

The study led by Jeffery Klauda, a professor of Chemical and Biomolecular Engineering (ChBE) at the University of Maryland (UMD), has been published in theProceedings of the National Academy of Sciences(PNAS). Nicholas Guros, a ChBE graduate research assistant, served as first author on the study and was co-advised by Arvind Balijepalli, a mechanical engineer at NIST.

5HT3Ais a type of protein known as an ion channel, implicated in depression, anxiety and targeted to reduce chemotherapy-induced nausea. It regulates the flow of ions at the post-synaptic cleft of neurons. The authors performed computer simulations of 5HT3Afor up to 20 microseconds - much longer than past simulations performed.

"If you think of molecular dynamics (MD) as a molecular microscope, this means we're able to observe the mechanism of activation for 10x longer than past", stated Nicholas Guros. "New computational capabilities can provide the power to observe the molecular activation of complex proteins at significantly greater timescales. The longer this timescale, the better validation we can have of experimental results to demonstrate MD models are a robust method to study protein and test pharmaceuticals."

The activation and desensitization of proteins like 5HT3Aoccur over milliseconds, so while closer to the true timescale, scientists are still somewhat behind observing the entire transport cycle of the protein. This study, however, was able to provide insight into the effects of serotonin binding on developing a preactive state of 5HT3Aand how membrane lipids diversity influences protein structure and function.

Much simulation space to explore with these models remains, and it's only been made possible in the past few years with strides in computational power. Specifically, this study was performed using a grant-based allocation on the Anton2 supercomputer maintained by the Pittsburgh Supercomuting Center (PSC) and sponsored by DE Shaw research. Traditional high-performance computing resources would not be capable of reaching the timescales of this study.

As computing speed and power increases in the future, the group hopes to study the effects of pharmaceuticals, such as granisetron or ondansetron, in an effort to accurately model their effects on the protein and investigate other targeted therapies.

Guros, N.B., Balijepalli, A. and Klauda, J.B. are the authors of the paper titled " Microsecond Timescale Simulations Suggests 5-HT mediated Pre-activation of the 5-HT<sub>3A</sub> Serotonin Receptor ", published inProceedings of the National Academy of Sciences- DOI: 10.1073/pnas.1908848117.
Source: University of Maryland

Back to Table of contents

Primeur weekly 2020-01-06

Focus

The LUMI supercomputer is not just a very fast supercomputer, it is first of all a competence development platform - Interview with Kimmo Koski, CSC, Finland ...

Quantum computing

ORNL researchers advance performance benchmark for quantum computers ...

In leap for quantum computing, silicon quantum bits establish a long-distance relationship ...

The Quantum Information Edge launches to accelerate quantum computing R&D ...

Focus on Europe

The coolest LEGO in the universe ...

Middleware

BP looks to ORNL and ADIOS to help rein in data ...

Hardware

New year brings new directory structure for OLCF's high-performance storage system ...

GIGABYTE brings AI, Cloud solutions and smart applications to CES 2020 to enable future today ...

During its final hours of operation, the Titan supercomputer simulated the birth of supernovae ...

Big iron afterlife: How ORNL's Titan supercomputer was recycled ...

Applications

Stanford researchers build a particle accelerator that fits on a chip ...

Brain-like functions emerging in a metallic nanowire network ...

Award-winning engineer helps keep US nuclear deterrent safe from radiation ...

New algorithm could mean more efficient, accurate equipment for Army ...

Paul Ginsparg named winner of the 2020 AIP Karl Compton Medal ...

'Super' simulations offer fresh insight into serotonin receptors ...

Researchers accelerate plasma turbulence simulations on Oak Ridge supercomputers to improve fusion design models ...