Tag Archives: Roger D. Kornberg

Nobel Laureates write science articles for children

Caption: Frontiers for Young Minds Nobel Collection. Credit: Frontiers Media

A September 7, 2021 Frontiers news release (also on EurekAlert) describes the company’s latest initiative to engage children in science (Note: I have a bit more about one of the Nobel Laureates, Dan [Daniel] Schechtman at the end of this posting),

Young people everywhere now have access to a free collection of scientific articles written by winners of science’s most coveted honor, the Nobel Prize. The Nobel Collection, published by Frontiers, aims to improve young people’s access to learning material about science’s role in addressing today’s global challenges. The collection will connect young minds with some of today’s most distinguished scientists through engaging learning material steeped in some of the most groundbreaking research from over the last twenty years.

Written for young people aged eight to 15, the collection has been published in the journal Frontiers for Young Minds. With the help of a science mentor, each article in the Nobel Collection has been reviewed by kids themselves to ensure it is understandable, fun, and engaging before publication. By sparking an interest in science from a young age, the Nobel Collection aims to improve young people’s scientific worldview. Its objective is to equip them with a scientific mindset and appreciation of the central role of science in finding solutions to today’s growing catalogue of global challenges.

A keen 13-year-old reviewer from Switzerland shared his experience, “I’m very interested in science and it is fascinating to review papers from the real scientists who know so much about their specialized fields! Many of the papers explain dangerous illnesses to children, and I think such information is so important!”

May-Britt Moser, awarded The Nobel Prize in Physiology or Medicine 2014, said, “I’m honored to contribute to the journal Frontiers for Young Minds. Children are born curious, with passion for questions and with light in their eyes. As a scientist, I feel privileged to be able to ask questions that I think are important. I hope the papers in this journal may help nurture and reinforce children’s passion and curiosity for science – what a gift to humanity that would be!”

Commenting on the Collection, Aaron Ciechanover who was awarded The Nobel Prize in Chemistry 2004, said, “Prizes and recognition are not targets that one should aim for. Breakthrough achievements that expand our knowledge of the world and benefit mankind are. Reading about science was my hobby as a kid and, doubtless, the seed of my curiosity into scientific discovery.”

Currently, the Nobel Collection comprises of contributions including:

How do we find our way? Grid cells in the brain, written by May-Britt Moser, awarded The Nobel Prize in Physiology or Medicine 2014.

Computer Simulations in Service of Biology, written by Michael Levitt, awarded The Nobel Prize in Chemistry 2013.

Quasi-Crystal, Not Quasi-Scientist, written by Dan Shechtman, awarded The Nobel Prize in Chemistry 2011.

The Transcription of Life: from DNA to RNA, written by Roger D. Kornberg, awarded The Nobel Prize in Chemistry 2006.

Targeted Degradation of Proteins – the Ubiquitin System, written by Aaron Ciechanover, The Nobel Prize in Chemistry 2004.

The Nobel Collection’s co-editor Idan Segev, professor of computational neuroscience at the Hebrew University, said: “What we want to achieve with this collection, beyond improving kids’ understanding of the scientific process and the particular Nobel recognized breakthroughs, is to acquaint kids with scientific role models – someone for young people to look up to. The beauty of these articles is that the Nobel Laureates share their life experience with kids, their failures and passions, and provide personal advice for the young minds.

“The kids that we worked with to review the articles were amazed by what they were reading and left the classes with a real sense of admiration for the humanistic as well as the scientific facet of Nobel prize winners. It is an incredible learning resource that can be accessed by anyone with an internet connection worldwide, which in context of the disruption created by the COVID-19 pandemic makes it particularly important.”  

UN Sustainable Development Goals – Quality Education

The initiative is also part of Frontiers’ commitment to the United Nations Sustainable Development Goals [SDGs], particularly Goal 4 – Quality Education. Disruption to access to quality education has been exacerbated by the COVID-19 pandemic, potentially jeopardizing some of the hard-won gains in recent years.

Frontiers, who funds the Frontiers for Young Minds journal as part of its philanthropy program, intends to work with at least five more Nobel Laureates later this year to grow the resource. All the articles are free to read, download, and share. Plans are also in place to translate the Nobel Collection into a portfolio of languages so even more young people from around the world can make use of it.

Dr. Fred Fenter, chief executive editor of Frontiers, said: “From fighting climate change to disease to poverty, science saves lives. What better role models to inspire future generations of scientists than Nobel Prize winners themselves. Our hope is the Nobel Collection will act as a catalyst, both motivating young people and improving their appreciation of the central role science will play in creating a sustainable future for people and planet.”

The Frontiers for Young Minds initiative

The Frontiers for Young Minds journal launched in 2013. Since then, Frontiers has engaged with around 3,500 young reviewers, each of whom has been guided by one of around 600 science mentors. To date, the journal has received more than ten million views and downloads of its 750 articles, which include English, Hebrew, and Arabic versions. The Frontiers for Young Minds editorial board currently consists of scientists and researchers from more than 64 countries.

Topics included in the journal range from astronomy and space science to biodiversity, neuroscience, pollution prevention, and mental health. Although written and edited for a younger audience, all the research published in Frontiers for Young Minds is based on solid evidence-based scientific research. 

I found the Schechtman story in my December 24, 2013 posting,

I suggested earlier that this achievement has a fabulous quality and the Daniel Schechtman backstory is the reason. The winner of the 2011 Nobel Prize for Chemistry, Schechtman was reviled for years within his scientific community as Ian Sample notes in his Oct. 5, 2011 article on the announcement of Schechtman’s Nobel win written for the Guardian newspaper (Note: A link has been removed),

“A scientist whose work was so controversial he was ridiculed and asked to leave his research group has won the Nobel Prize in Chemistry.

Daniel Shechtman, 70, a researcher at Technion-Israel Institute of Technology in Haifa, received the award for discovering seemingly impossible crystal structures in frozen gobbets of metal that resembled the beautiful patterns seen in Islamic mosaics.

Images of the metals showed their atoms were arranged in a way that broke well-establised rules of how crystals formed, a finding that fundamentally altered how chemists view solid matter.

On the morning of 8 April 1982, Shechtman saw something quite different while gazing at electron microscope images of a rapidly cooled metal alloy. The atoms were packed in a pattern that could not be repeated. Shechtman said to himself in Hebrew, “Eyn chaya kazo,” which means “There can be no such creature.”

The bizarre structures are now known as “quasicrystals” and have been seen in a wide variety of materials. Their uneven structure means they do not have obvious cleavage planes, making them particularly hard.

In an interview this year with the Israeli newspaper, Haaretz, Shechtman said: “People just laughed at me.” He recalled how Linus Pauling, a colossus of science and a double Nobel laureate, mounted a frightening “crusade” against him. After telling Shechtman to go back and read a crystallography textbook, the head of his research group asked him to leave for “bringing disgrace” on the team. “I felt rejected,” Shachtman said.”

It takes a lot to persevere when most, if not all, of your colleagues are mocking and rejecting your work so bravo to Schechtman! And,bravo to the Japan-UK project researchers who have persevered to help solve at least part of a complex problem requiring that our basic notions of matter be rethought.

I encourage you to read Sample’s article in its entirety as it is well written and I’ve excerpted only bits of the story as it relates to a point I’m making in this post, i.e., perseverance in the face of extreme resistance.

Shechtman’s quasi-crystal story for Frontiers provides clear explanations and a little inspiration while not flinching away from the difficulties posed when shaking up established theories.

BTW, I like reading material written for children as there are often useful explanations that aren’t included in material intended for adults.

Novel self-assembly at 102 atoms

A Jan. 13, 2017 news item on ScienceDaily announces a discovery about self-assembly of 102-atom gold nanoclusters,

Self-assembly of matter is one of the fundamental principles of nature, directing the growth of larger ordered and functional systems from smaller building blocks. Self-assembly can be observed in all length scales from molecules to galaxies. Now, researchers at the Nanoscience Centre of the University of Jyväskylä and the HYBER Centre of Excellence of Aalto University in Finland report a novel discovery of self-assembling two- and three-dimensional materials that are formed by tiny gold nanoclusters of just a couple of nanometres in size, each having 102 gold atoms and a surface layer of 44 thiol molecules. The study, conducted with funding from the Academy of Finland and the European Research Council, has been published in Angewandte Chemie.

A Jan. 13, 2017 Academy of Finland press release, which originated the news item, provides more technical information about the work,

The atomic structure of the 102-atom gold nanocluster was first resolved by the group of Roger D Kornberg at Stanford University in 2007 (2). Since then, several further studies of its properties have been conducted in the Jyväskylä Nanoscience Centre, where it has also been used for electron microscopy imaging of virus structures (3). The thiol surface of the nanocluster has a large number of acidic groups that can form directed hydrogen bonds to neighbouring nanoclusters and initiate directed self-assembly.

The self-assembly of gold nanoclusters took place in a water-methanol mixture and produced two distinctly different superstructures that were imaged in a high-resolution electron microscope at Aalto University. In one of the structures, two-dimensional hexagonally ordered layers of gold nanoclusters were stacked together, each layer being just one nanocluster thick. Modifying the synthesis conditions, also three-dimensional spherical, hollow capsid structures were observed, where the thickness of the capsid wall corresponds again to just one nanocluster size (see figure).

While the details of the formation mechanisms of these superstructures warrant further systemic investigations, the initial observations open several new views into synthetically made self-assembling nanomaterials.

“Today, we know of several tens of different types of atomistically precise gold nanoclusters, and I believe they can exhibit a wide variety of self-assembling growth patterns that could produce a range of new meta-materials,” said Academy Professor Hannu Häkkinen, who coordinated the research at the Nanoscience Centre. “In biology, typical examples of self-assembling functional systems are viruses and vesicles. Biological self-assembled structures can also be de-assembled by gentle changes in the surrounding biochemical conditions. It’ll be of great interest to see whether these gold-based materials can be de-assembled and then re-assembled to different structures by changing something in the chemistry of the surrounding solvent.”

“The free-standing two-dimensional nanosheets will bring opportunities towards new-generation functional materials, and the hollow capsids will pave the way for highly lightweight colloidal framework materials,” Postdoctoral Researcher Nonappa (Aalto University) said.

Professor Olli Ikkala of Aalto University said: “In a broader framework, it has remained as a grand challenge to master the self-assemblies through all length scales to tune the functional properties of materials in a rational way. So far, it has been commonly considered sufficient to achieve sufficiently narrow size distributions of the constituent nanoscale structural units to achieve well-defined structures. The present findings suggest a paradigm change to pursue strictly defined nanoscale units for self-assemblies.”

References:

(1)    Nonappa, T. Lahtinen, J.S. Haataja, T.-R. Tero, H. Häkkinen and O. Ikkala, “Template-Free Supracolloidal Self-Assembly of Atomically Precise Gold Nanoclusters: From 2D Colloidal Crystals to Spherical Capsids”, Angewandte Chemie International Edition, published online 23 November 2016, DOI: 10.1002/anie.201609036

(2)    P. Jadzinsky et al., “Structure of a thiol-monolayer protected gold nanoparticle at 1.1Å resolution”, Science 318, 430 (2007)

(3)    V. Marjomäki et al., “Site-specific targeting of enterovirus capsid by functionalized monodispersed gold nanoclusters”, PNAS 111, 1277 (2014)

Here’s the figure mentioned in the news release,

Figure: 2D hexagonal sheet-like and 3D capsid structures based on atomically precise gold nanoclusters as guided by hydrogen bonding between the ligands. The inset in the top left corner shows the atomic structure of one gold nanocluster.

Here’s a link to and a citation for the paper,

Template-Free Supracolloidal Self-Assembly of Atomically Precise Gold Nanoclusters: From 2D Colloidal Crystals to Spherical Capsids by Dr. Nonappa, Dr. Tanja Lahtinen, M. Sc. Johannes. S. Haataja, Dr. Tiia-Riikka Tero, Prof. Hannu Häkkinen, and Prof. Olli Ikkala. Angewandte Chemie International Edition Volume 55, Issue 52, pages 16035–16038, December 23, 2016 Version of Record online: 23 NOV 2016 DOI: 10.1002/anie.201609036

© 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim

This paper is behind a paywall.

Gold nanoparticle clusters: four new models

This research is being done at the University of Nebraska-Lincoln (UNL) which seems to be on a publishing tear lately. From an April 27, 2015 news item on Nanowerk, here’s the latest,

They may deal in gold, atomic staples and electron volts rather than cement, support beams and kilowatt-hours, but chemists have drafted new nanoscale blueprints for low-energy structures capable of housing pharmaceuticals and oxygen atoms.

Led by UNL’s Xiao Cheng Zeng and former visiting professor Yi Gao, new research has revealed four atomic arrangements of a gold nanoparticle cluster. The arrangements exhibit much lower potential energy and greater stability than a standard-setting configuration reported last year by a Nobel Prize-winning team from Stanford University.

The modeling of these arrangements could inform the cluster’s use as a transporter of pharmaceutical drugs and as a catalyst for removing pollutants from vehicular emissions or other industrial byproducts, Zeng said.

An April 24, 2015 UNL news release (also on EurekAlert), which originated the news item, provides more technical details about the work,

Led by UNL’s Xiao Cheng Zeng and former visiting professor Yi Gao, new research has revealed four atomic arrangements of a gold nanoparticle cluster. The arrangements exhibit much lower potential energy and greater stability than a standard-setting configuration reported last year by a Nobel Prize-winning team from Stanford University.

The modeling of these arrangements could inform the cluster’s use as a transporter of pharmaceutical drugs and as a catalyst for removing pollutants from vehicular emissions or other industrial byproducts, Zeng said.

Zeng and his colleagues unveiled the arrangements for a molecule featuring 68 gold atoms and 32 pairs of bonded sulfur-hydrogen atoms. Sixteen of the gold atoms form the molecule’s core; the remainder bond with the sulfur and hydrogen to form a protective coating that stems from the core.

Differences in atomic arrangements can alter molecular energy and stability, with less potential energy making for a more stable molecule. The team calculates that one of the arrangements may represent the most stable possible structure in a molecule with its composition.

“Our group has helped lead the front on nano-gold research over the past 10 years,” said Zeng, an Ameritas University Professor of chemistry. “We’ve now found new coating structures of much lower energy, meaning they are closer to the reality than (previous) analyses. So the deciphering of this coating structure is major progress.”

The structure of the molecule’s gold core was previously detailed by the Stanford team. Building on this, Zeng and his colleagues used a computational framework dubbed “divide-and-protect” to configure potential arrangements of the remaining gold atoms and sulfur-hydrogen pairs surrounding the core.

The researchers already knew that the atomic coating features staple-shaped linkages of various lengths. They also knew the potential atomic composition of each short, medium and long staple — such as the fact that a short staple consists of two sulfur atoms bonded with one gold.

By combining this information with their knowledge of how many atoms reside outside the core, the team reduced the number of potential arrangements from millions to mere hundreds.

“We divided 32 into the short, middle and long (permutations),” said Zeng, who helped develop the divide-and-protect approach in 2008. “We lined up all those possible arrangements, and then we computed their energies to find the most stable ones.

“Without those rules, it’s like finding a needle in the Platte River. With them, it’s like finding a needle in the fountain outside the Nebraska Union. It’s still hard, but it’s much more manageable. You have a much narrower range.”

The researchers resorted to the computational approach because of the difficulty of capturing the structure via X-ray crystallography or single-particle transmission electron microscopy, two of the most common imaging methods at the atomic scale.

Knowing the nanoparticle’s most stable configurations, Zeng said, could allow biomedical engineers to identify appropriate binding sites for drugs used to treat cancer and other diseases. The findings could also optimize the use of gold nanoparticles in catalyzing the oxidation process that transforms dangerous carbon monoxide emissions into the less noxious carbon dioxide, he said.

Here’s an image illustrating the work,

This rendering shows the atomic arrangements of a gold nanocluster as reported in a new study led by UNL chemist Xiao Cheng Zeng. The cluster measures about 1.7 nanometers long -- roughly the same length that a human fingernail grows in two seconds. (Joel Brehm/Office of Research and Economic Development)

This rendering shows the atomic arrangements of a gold nanocluster as reported in a new study led by UNL chemist Xiao Cheng Zeng. The cluster measures about 1.7 nanometers long — roughly the same length that a human fingernail grows in two seconds. (Joel Brehm/Office of Research and Economic Development)

Here’s a link to and a citation for the paper,

Unraveling structures of protection ligands on gold nanoparticle Au68(SH)32 by Wen Wu Xu, Yi Gao, and Xiao Cheng Zeng. Science Advances 24 Apr 2015: Vol. 1 no. 3 e1400211 DOI: 10.1126/sciadv.1400211

This is an open access article.

As for the Stanford University team’s work mentioned in the news release, I believe it’s from the Roger Kornberg (Nobel laureate) Laboratory. There’s more about that team’s work in an Aug. 21, 2014 article (A new gold standard for nano; Note: A link has been removed) by David Bradley for Chemistry World,

Characterising gold nanoparticles at atomic resolution might improve our understanding of the catalytic activity of these materials, according to an international team. These researchers have now demonstrated that it is possible to use electron microscopy to obtain data on at least one gold cluster of greater than 1nm diameter and to validate the results by comparison with small-angle x-ray scattering data, infrared absorption spectra and density functional theory calculations.

Here’s a link to and a citation for the 2014 paper,

Electron microscopy of gold nanoparticles at atomic resolution by Maia Azubel, Jaakko Koivisto, Sami Malola, David Bushnell, Greg L. Hura, Ai Leen Koh, Hironori Tsunoyama, Tatsuya Tsukuda, Mika Pettersson, Hannu Häkkinen, & Roger D. Kornberg. Science 22 August 2014: Vol. 345 no. 6199 pp. 909-912 DOI: 10.1126/science.1251959

This paper is behind a paywall.

The most recent posting here about gold nanoparticles is an April 14, 2015 piece titled: Gold atoms: sometimes they’re a metal and sometimes they’re a molecule.