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Computers Excel in Chemistry Class – Lab Manager Magazine

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KAUST researchers are converging machine learning with generating thermodynamic data.

© 2020 KAUST

Creating computers that can teach themselves how chemical structure dictates the fundamental properties of molecules and then using that knowledge to predict the properties of novel molecules could help to design cleaner energy and industrial systems.

KAUST researchers have developed a machine learning model that can analyze the structure of hydrocarbon molecules and accurately predict a property called enthalpy of formation. When it comes to estimating this property, the model already makes better predictions than conventional approaches, and its accuracy will only improve as more data is collected for the model to learn from.

“Data on molecular properties, such as enthalpy of formation, are essential for engineers modeling the kinetic mechanisms, or energy flows, of chemical reactions,” says Kiran Yalamanchi, a PhD student in the research group of Mani Sarathy, who led the research. “Kinetic mechanisms for hydrocarbon fuels are important for the development and optimization of engine designs and chemical reactors,” Yalamanchi says.

Generating the large sets of thermodynamics data required for kinetic mechanism modeling typically uses an approach called group additivity, which has limited accuracy. “Group additivity was developed in the mid-20th century, and the field of data science has advanced a lot in the last few decades,” Yalamanchi says.

So Yalamanchi and Sarathy approached KAUST computer scientist, Xin Gao, to apply machine learning to the problem. “Our initial study gave very promising results,” Yalamanchi says. “This potential helped us to push toward converging machine learning with generating thermodynamic data.”

Machine learning offers a way to take enthalpy of formation data—measured experimentally, or calculated for a small number of molecules using highly accurate but slow quantum chemistry computations—and then extrapolate to a much broader range of molecules.


Related Article: The Power of Algorithms in Analytical Chemistry


The machine learning program analyzed a “training” dataset of molecule structures and their enthalpies of formation. It then used the patterns it detected to predict the enthalpy of formation of molecules it had not seen before.

Machine learning proved to be much more accurate than the traditional group additivity approach. “We got better estimates of enthalpy of formation of chemical species using machine learning methods compared to traditional methods,” Yalamanchi says.

For example, although traditional group additivity can make relatively good predictions for simple molecules with linear structures, its accuracy decreases with more complex molecules, such as those that incorporate carbon rings in their structure. “The improvement we saw in estimates of enthalpy of formation, compared with traditional group additivity, was even more significant in the case of cyclic species,” Yalamanchi adds.

“The results suggest that machine learning will become an increasingly important tool in the field,” Sarathy says. “The ability to accurately predict important thermodynamic properties from molecular descriptors is an important step toward developing fully automated algorithms for predicting more complex chemical phenomenon,” he adds.

The team is now running high accuracy quantum chemistry calculations to expand the machine learning models’ training dataset. “In this way, we are developing a hybrid first-principles artificial intelligence framework for more accurate predictions of many physical-chemical properties,” says Sarathy.

This press release was originally published on KAUST Discovery

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Dozens of McGill students living in student neighbourhood test positive for COVID-19 – Yahoo News Canada

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Dozens of students at McGill University are testing positive for COVID-19 according to their peers, but the university is not counting most of those cases in its official tally, because they happened off-campus.

Jacob Rothery, a student living in the so-called McGill ghetto in Montreal’s Milton Park neighbourhood next to the university, tested positive for COVID-19 this week. So did his three roommates.

Rothery says he knows of at least 20 other students who tested positive, and suspects more numbers are going to come from the popular and crowded student neighbourhood.

“There were a decent amount of students going to student bars,” he said. “And then on top of that, you don’t necessarily know who the people that you think you’re in your bubble with are seeing, so they could be seeing a bunch of other people, who are putting themselves in riskier situations.” 

Rothery says he and his friends did not violate public health guidelines, but that didn’t stop an outbreak in his group of friends.

“People may have had it, but had no symptoms. So they had no reason to get tested. And then you have gatherings that aren’t that big, maybe fifteen people or 10, but those 10 people see other people and their bubbles are a lot bigger than they think they are,” he said. 

Submitted by Jacob Rothery

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Submitted by Jacob Rothery

Thom Haghighat is another McGill student who is self-isolating, after he and his roommate tested positive for COVID-19.

He figures he caught the virus from one of the students returning to the “ghetto” from Toronto or elsewhere in Montreal.

Haghighat says he also knows of at least 25 students living in the area who tested positive, with a dozen in his immediate group of friends.

Like Rothery, Haghighat says he and his friends were limiting personal gatherings and keeping a small circle of people to interact with.

Despite this, he said, he still saw cases rise among his peers in the past week. He believes false negatives are part of the problem. 

“The first time we got tested, we tested negative. We still self-isolated, but I know a lot of people who would think they were in the clear to go see other people,” he said, noting that he knew others who also got false negatives. 

Rothery had also received a false negative test result earlier this week, before testing positive.

<p class="canvas-atom canvas-text Mb(1.0em) Mb(0)–sm Mt(0.8em)–sm" type="text" content="Only "on-campus" numbers” data-reactid=”45″>Only “on-campus” numbers

Despite these anecdotal reports, McGill University has officially recorded just six COVID-19 cases this week on campus, and says there is no evidence of community transmission on its campuses.

McGill’s main campus is downtown. The Macdonald campus, which houses agricultural and nutrition programs among others, is in Sainte-Anne-de-Bellevue in the West Island.

A spokesperson for the university said the number includes staff and students who were present on campus in the week preceding their positive COVID test. 

Most classes at McGill have moved online, which means far fewer people are frequenting the campus. 

Justin Hayward/CBCJustin Hayward/CBC

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Justin Hayward/CBC

Some students say the university should include the numbers of students who test positive off-campus, as well.

“It’s important for them to at least take responsibility for the things that are going on in their student body, whether or not they’re technically on campus, because I think that distinction is pretty useless,” said Rothery.

For its part, McGill says it is working with public health authorities on strict protocols to limit the spread.

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NASA astronaut plans to cast her ballot from space station – 570 News

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ATLANTA — NASA astronaut Kate Rubins told The Associated Press on Friday that she plans to cast her next vote from space – more than 200 miles above Earth.

Rubins is just outside Moscow in Star City, Russia, preparing with two cosmonauts for a mid-October launch and a six-month stay at the International Space Station.

“I think it’s really important for everybody to vote,” Rubins said. “If we can do it from space, then I believe folks can do it from the ground, too.”

Most U.S. astronauts live in Houston. Texas law allows them to vote from space using a secure electronic ballot. Mission Control forwards the ballot to the space station and relays the completed ballot back to the county clerk.

“It’s critical to participate in our democracy,” Rubins said. “We consider it an honour to be able to vote from space.”

NASA astronauts have voted from space before. Rubins and Shane Kimbrough cast their votes from the International Space Station.

Rubins, the first person to sequence DNA in space, plans to work on a cardiovascular experiment and conduct research using the space station’s Cold Atom Lab.

While she’s there, she’ll celebrate the 20th anniversary of continuous human presence on the space station, and welcome the crew of the second SpaceX commercial crew mission, expected to arrive in late October.

_____

Follow Alex Sanz on Twitter at @AlexSanz.

Alex Sanz, The Associated Press

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Teenage British activist stages climate protest on Arctic ice floe – TheChronicleHerald.ca

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By Natalie Thomas

ABOARD ‘ARCTIC SUNRISE’ (Reuters) – Like many of her generation, Mya-Rose Craig feels strongly that adults have failed to take the urgent action needed to tackle global warming and so she has headed to the Arctic Ocean to protest.

Armed with a placard reading ‘Youth Strike for Climate”, the 18-year-old British activist is staging the most northerly protest in a series of youth strikes worldwide.

The strikes, made famous by Swedish campaigner Greta Thunberg, are resuming after a lull caused by the global coronavirus pandemic to draw public attention back to the threat posed by climate change.

“I’m here to… try and make a statement about how temporary this amazing landscape is and how our leaders have to make a decision now in order to save it,” she told Reuters Television as she stood with her placard on the edge of the Arctic sea ice.

“I absolutely think that my generation has always had to think about climate change… which is why as we’ve got older there’s been this massive wave of just this need for change, this demand for change when we realised the grown-ups aren’t going to solve this so we have to do it ourselves.”

Craig, from southwest England, is known as “Birdgirl” online, where her blog chronicling her bird-watching experiences has attracted thousands of followers.

She has travelled hundreds of miles above the Arctic Circle aboard a Greenpeace ship, Arctic Sunrise.

Climate data shows the Arctic is one of the fastest changing ecosystems on the planet, with serious consequences for wildlife from polar bears and seals to plankton and algae, while the melting sea ice contributes to rising sea levels worldwide.

Warming in the Arctic shrank the ice covering the polar ocean this year to its second-lowest extent in four decades, scientists said on Monday.

For Craig, getting to the ice floe involved a two-week quarantine in Germany, followed by a three-week voyage to the edge of the sea ice.

Craig said those who dismiss the youth protests as just a rebellious phase by her generation are wrong, and she wants those in power to stop treating climate change as a low-priority issue, raised only to appease “the lefties in the corner”.

“It’s everything now and it has to be treated like that,” she said.  

(Reporting by Reuters Television; Writing by Gareth Jones; Editing by Janet Lawrence)

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