Lifeboat Foundation

The DeepMind team has made probably the most ambitious attempt yet to deploy AI to calculate electron density, the end result of DFT calculations. “It’s sort of the ideal problem for machine learning: you know the answer, but not the formula you want to apply,” says Aron Cohen, a theoretical chemist who has long worked on DFT and who is now at DeepMind.

A team led by scientists at the London-based artificial-intelligence company DeepMind has developed a machine-learning model that suggests a molecule’s characteristics by predicting the distribution of electrons within it. The approach, described in the 10 December issue of Science¹, can calculate the properties of some molecules more accurately than existing techniques.

“To make it as accurate as they have done is a feat,” says Anatole von Lilienfeld, a materials scientist at the University of Vienna.

Continue reading “DeepMind AI tackles one of chemistry’s most valuable techniques” »

Atom ’s electrons are arranged in energy shells. Like concertgoers in an arena, each electron occupies a single chair and cannot drop to a lower tier if all its chairs are occupied. This fundamental property of atomic physics is known as the Pauli exclusion principle, and it explains the shell structure of atoms, the diversity of the periodic table of elements, and the stability of the material universe.

Now, MIT

MIT is an acronym for the Massachusetts Institute of Technology. It is a prestigious private research university in Cambridge, Massachusetts that was founded in 1861. It is organized into five Schools: architecture and planning; engineering; humanities, arts, and social sciences; management; and science. MIT’s impact includes many scientific breakthroughs and technological advances.

Many intractable diseases are the result of a genetic mutation. Genome editing technology promises to correct the mutation and thus new treatments for patients. However, getting the technology to the cells that need the correction remains a major challenge. A new study led by CiRA Junior Associate Professor Akitsu Hotta and in collaboration with Takeda Pharmaceutical Company Limited as part of the T-CiRA Joint Research Program reports how lipid nanoparticles provide an effective means for the delivery to treat Duchenne muscular dystrophy (DMD) in mice.

Last year’s Nobel Prize for Chemistry to the discoverers of CRISPR-Cas9 cemented the impact of genome editing technology. While CRISPR-Cas9 can be applied to agriculture and livestock for more nutritious food and robust crops, most media attention is on its medical potential. DMD is just one of the many diseases that researchers foresee a treatment using CRISPR-Cas9.

“Oligonucleotide drugs are now available for DMD, but their effects are transient, so the patient has to undergo weekly treatments. On the other hand, CRISPR-Cas9 effects are long lasting,” said Hotta.

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In a paper published today in the scientific journal Science, DeepMind demonstrates how neural networks can be used to describe electron interactions in chemical systems more accurately than existing methods.

Density Functional Theory, established in the 1960s, describes the mapping between electron density and interaction energy. For more than 50 years, the exact nature of mapping between electron density and interaction energy—the so-called density functional—has remained unknown. In a significant advancement for the field, DeepMind has shown that neural networks can be used to build a more accurate map of the density and interaction between electrons than was previously attainable.

Continue reading “Simulating matter on the nanoscale with AI” »

Launched in 2010, DARPA’s Living Foundries program aimed to enable adaptable, scalable, and on-demand production of critical, high-value molecules by programming the fundamental metabolic processes of biological systems to generate a vast number of complex molecules. These molecules were often prohibitively expensive, unable to be domestically sourced, and/or impossible to manufacture using traditional synthetic chemistry approaches. As a proof of concept, DARPA intended to produce 1,000 molecules and material precursors spanning a wide range of defense-relevant applications including industrial chemicals, fuels, coatings, and adhesives.

Divided into two parts – Advanced Tools and Capabilities for Generalizable Platforms (ATCG) and 1,000 Molecules – the Living Foundries program succeeded not only in meeting its programmatic goals of producing 1,000 molecules as a proof-of-concept, but pivoted in 2019 to expand program objectives to working with military mission partners to test molecules for military applications. The performer teams collectively have produced over 1,630 molecules and materials to-date, and more importantly, DARPA is transitioning a subset of these technologies to five military research teams from Army, Navy, and Air Force labs who partnered with the agency on testing and evaluation over the course of the program.

“Biologically-produced molecules offer orders-of-magnitude greater diversity in chemical functionality compared to traditional approaches, enabling scientists to produce new bioreachable molecules faster than ever before,” noted Dr. Anne Cheever, Living Foundries program manager. “Through Living Foundries, DARPA has transformed synthetic biomanufacturing into a predictable engineering practice supportive of a broad range of national security objectives.”

A team of researchers affiliated with a host of institutions in China and the U.S. has found that injecting procyanidin C1 (PCC1), a chemical found in grape seed extract, into older mice extended their lifespan. In their paper published in the journal Nature Metabolism, the group describes the link between PCC1 and extended lifespan in mice and the experiments they carried out with the material.

Scientists have been trying for many years to understand the aging process. The hope is that once it is understood, mitigation efforts can slow or stop the process to allow people to live longer or to live in a more healthy way as they age. In this new effort, the researchers screened 46 plant extracts looking for anti-aging capabilities. They came across PCC1. Initial tests during screening showed it reduced the number of senescent cells in the human prostate. Such cells are known to contribute to aging. Intrigued with their results, the researchers tested it further. They found that at low doses it prevented senescent cells from contributing to inflammation, and at higher doses killed them outright without harming other cells.

The team then injected 171 mice with PCC1, 91 of whom were considered to be old. They found that this increased the overall lifespan of the mice by 9 percent and their remaining lifespans by 60 percent, on average. The researchers also injected younger mice with the extract chemical over a period of four months and found it improved their physical fitness. They then injected mice that had cancerous tumors with the chemical and found that doing so helped to shrink tumors when given in conjunction with chemotherapy. They also found it did the same with human tumor cells implanted into mice.

A scientist who loves to write, can do it well, and can share the excitement of the scientific pursuit is incredibly rare. Kevin Peter Hand 0, Deputy Project Scientist, Europa and Director of the JPL Ocean Worlds Lab is that rare person who can do all these things. In his incredible book Alien Oceans: The Search for Life in the Depths of Space 0, he explains that “We know that the laws of physics, the principles of chemistry, and the principles of geology all work beyond Earth. We’ve explored other worlds and observed that these sciences are universal. When it comes to biology, however, we have yet to make that leap.”

If you want to learn about how the intersection of numerous areas of science are helping inform our understanding of the oceans, space, and ourselves, Alien Oceans is by far one of the most clearly written books on the topic. As Kevin notes, he wrote the book he wishes he could have read in college. Kevin will teach you and inspire you and explain complicated scientific topics in ways nearly anyone can understand. Not only is it a book about his areas of expertise, it is also a wonderful window into the way scientists and engineers think about solving real world problems and applying basic knowledge. For example, Kevin notes in this interview that “Making measurements is where the creativity of science meets the hard reality of engineering.” I read a lot of books on science written for a broad audience, and this book, by far is among the very best I have ever read. More than anything else what came through in Kevin’s writing is excitement about finding out what is true.

What inspired you to write this book?

Combining knowledge of chemistry, physics, biology, and engineering, scientists from McGill University develop a biomaterial tough enough to repair the heart, muscles, and vocal cords, representing a major advance in regenerative medicine.

“People recovering from heart damage often face a long and tricky journey. Healing is challenging because of the constant movement tissues must withstand as the heart beats. The same is true for vocal cords. Until now there was no injectable material strong enough for the job,” says Guangyu Bao, a PhD candidate in the Department of Mechanical Engineering at McGill University.

The team, led by Professor Luc Mongeau and Assistant Professor Jianyu Li, developed a new injectable hydrogel for wound repair. The hydrogel is a type of biomaterial that provides room for cells to live and grow. Once injected into the body, the biomaterial forms a stable, porous structure allowing live cells to grow or pass through to repair the injured organs.

Graphene consists of a planar structure, with carbon atoms connected in a hexagonal shape that resembles a beehive. When graphene is reduced to several nanometers (nm) in size, it becomes a graphene quantum dot that exhibits fluorescent and semiconductor properties. Graphene quantum dots can be used in various applications as a novel material, including display screens, solar cells, secondary batteries, bioimaging, lighting, photocatalysis, and sensors. Interest in graphene quantum dots is growing, because recent research has demonstrated that controlling the proportion of heteroatoms (such as nitrogen, sulfur, and phosphorous) within the carbon structures of certain materials enhances their optical, electrical, and catalytic properties.

The Korea Institute of Science and Technology (KIST, President Seok-Jin Yoon) reported that the research team led by Dr. Byung-Joon Moon and Dr. Sukang Bae of the Functional Composite Materials Research Center have developed a technique to precisely control the bonding structure of single heteroatoms in the graphene quantum dot, which is a zero-dimensional carbon nanomaterial, through simple chemical reaction control; and that they identified the relevant reaction mechanisms.

With the aim of controlling heteroatom incorporation within the graphene quantum dot, researchers have previously investigated using additives that introduce the heteroatom into the dot after the dot itself has already been synthesized. The dot then had to be purified further, so this method added several steps to the overall fabrication process. Another method that was studied involved the simultaneous use of multiple organic precursors (which are the main ingredients for dot synthesis), along with the additives that contain the heteroatom. However, these methods had significant disadvantages, including reduced crystallinity in the final product and lower overall reaction yield, since several additional purification steps had to be implemented. Furthermore, in order to obtain quantum dots with the chemical compositions desired by manufacturers, various reaction conditions, such as the proportion of additives, would have to be optimized.