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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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The body of a Ugandan Olympic athlete who was set on fire by her partner is received by family

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NAIROBI, Kenya (AP) — The body of Ugandan Olympic athlete Rebecca Cheptegei — who died after being set on fire by her partner in Kenya — was received Friday by family and anti-femicide crusaders, ahead of her burial a day later.

Cheptegei’s family met with dozens of activists Friday who had marched to the Moi Teaching and Referral Hospital’s morgue in the western city of Eldoret while chanting anti-femicide slogans.

She is the fourth female athlete to have been killed by her partner in Kenya in yet another case of gender-based violence in recent years.

Viola Cheptoo, the founder of Tirop Angels – an organization that was formed in honor of athlete Agnes Tirop, who was stabbed to death in 2021, said stakeholders need to ensure this is the last death of an athlete due to gender-based violence.

“We are here to say that enough is enough, we are tired of burying our sisters due to GBV,” she said.

It was a somber mood at the morgue as athletes and family members viewed Cheptegei’s body which sustained 80% of burns after she was doused with gasoline by her partner Dickson Ndiema. Ndiema sustained 30% burns on his body and later succumbed.

Ndiema and Cheptegei were said to have quarreled over a piece of land that the athlete bought in Kenya, according to a report filed by the local chief.

Cheptegei competed in the women’s marathon at the Paris Olympics less than a month before the attack. She finished in 44th place.

Cheptegei’s father, Joseph, said that the body will make a brief stop at their home in the Endebess area before proceeding to Bukwo in eastern Uganda for a night vigil and burial on Saturday.

“We are in the final part of giving my daughter the last respect,” a visibly distraught Joseph said.

He told reporters last week that Ndiema was stalking and threatening Cheptegei and the family had informed police.

Kenya’s high rates of violence against women have prompted marches by ordinary citizens in towns and cities this year.

Four in 10 women or an estimated 41% of dating or married Kenyan women have experienced physical or sexual violence perpetrated by their current or most recent partner, according to the Kenya Demographic and Health Survey 2022.

The Canadian Press. All rights reserved.

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The ancient jar smashed by a 4-year-old is back on display at an Israeli museum after repair

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TEL AVIV, Israel (AP) — A rare Bronze-Era jar accidentally smashed by a 4-year-old visiting a museum was back on display Wednesday after restoration experts were able to carefully piece the artifact back together.

Last month, a family from northern Israel was visiting the museum when their youngest son tipped over the jar, which smashed into pieces.

Alex Geller, the boy’s father, said his son — the youngest of three — is exceptionally curious, and that the moment he heard the crash, “please let that not be my child” was the first thought that raced through his head.

The jar has been on display at the Hecht Museum in Haifa for 35 years. It was one of the only containers of its size and from that period still complete when it was discovered.

The Bronze Age jar is one of many artifacts exhibited out in the open, part of the Hecht Museum’s vision of letting visitors explore history without glass barriers, said Inbal Rivlin, the director of the museum, which is associated with Haifa University in northern Israel.

It was likely used to hold wine or oil, and dates back to between 2200 and 1500 B.C.

Rivlin and the museum decided to turn the moment, which captured international attention, into a teaching moment, inviting the Geller family back for a special visit and hands-on activity to illustrate the restoration process.

Rivlin added that the incident provided a welcome distraction from the ongoing war in Gaza. “Well, he’s just a kid. So I think that somehow it touches the heart of the people in Israel and around the world,“ said Rivlin.

Roee Shafir, a restoration expert at the museum, said the repairs would be fairly simple, as the pieces were from a single, complete jar. Archaeologists often face the more daunting task of sifting through piles of shards from multiple objects and trying to piece them together.

Experts used 3D technology, hi-resolution videos, and special glue to painstakingly reconstruct the large jar.

Less than two weeks after it broke, the jar went back on display at the museum. The gluing process left small hairline cracks, and a few pieces are missing, but the jar’s impressive size remains.

The only noticeable difference in the exhibit was a new sign reading “please don’t touch.”

The Canadian Press. All rights reserved.

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B.C. sets up a panel on bear deaths, will review conservation officer training

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VICTORIA – The British Columbia government is partnering with a bear welfare group to reduce the number of bears being euthanized in the province.

Nicholas Scapillati, executive director of Grizzly Bear Foundation, said Monday that it comes after months-long discussions with the province on how to protect bears, with the goal to give the animals a “better and second chance at life in the wild.”

Scapillati said what’s exciting about the project is that the government is open to working with outside experts and the public.

“So, they’ll be working through Indigenous knowledge and scientific understanding, bringing in the latest techniques and training expertise from leading experts,” he said in an interview.

B.C. government data show conservation officers destroyed 603 black bears and 23 grizzly bears in 2023, while 154 black bears were killed by officers in the first six months of this year.

Scapillati said the group will publish a report with recommendations by next spring, while an independent oversight committee will be set up to review all bear encounters with conservation officers to provide advice to the government.

Environment Minister George Heyman said in a statement that they are looking for new ways to ensure conservation officers “have the trust of the communities they serve,” and the panel will make recommendations to enhance officer training and improve policies.

Lesley Fox, with the wildlife protection group The Fur-Bearers, said they’ve been calling for such a committee for decades.

“This move demonstrates the government is listening,” said Fox. “I suspect, because of the impending election, their listening skills are potentially a little sharper than they normally are.”

Fox said the partnership came from “a place of long frustration” as provincial conservation officers kill more than 500 black bears every year on average, and the public is “no longer tolerating this kind of approach.”

“I think that the conservation officer service and the B.C. government are aware they need to change, and certainly the public has been asking for it,” said Fox.

Fox said there’s a lot of optimism about the new partnership, but, as with any government, there will likely be a lot of red tape to get through.

“I think speed is going to be important, whether or not the committee has the ability to make change and make change relatively quickly without having to study an issue to death, ” said Fox.

This report by The Canadian Press was first published Sept. 9, 2024.

The Canadian Press. All rights reserved.

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