Tag Archives: Aarhus University

Sciencish doings: a job as a science channel showrunner, a writing workshop, a podcast, news from an AI conference, and a musical interlude

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I have a number of sciencish doings and a musical event that takes place at the Perimeter Institute.

YouTube science channel job

Thanks to the Science Media Centre of Canada (SMCC) and its April 14, 2026 notice for this news,

Job opening: Showrunner for YouTube science channel, What If [for]
Underknown [creator business]

The role requires a deep understanding of YouTube as a medium. This is a
hybrid role, with 2–3 days a week in our Toronto studio and head
office. It is only for permanent residents in Ontario. …

Before launching off into the job description, here’s a bit more about Underknown from its Wikipedia entry, Note: Links have been removed,

Underknown Inc. is a Canadian digital-first media production company based in Toronto that specializes in short-form educational science and factual programming.

History

Underknown was founded in 2016 by Steve Hulford, Raphael Faeh, and Peter Schmiedchen.[1][2] It began when Hulford and Faeh produced the science-explainer series What If in Hulford’s living room.[3] In 2019, Underknown received C$2.5 million in equity and debt financing, including support from Ontario Creates.[3]

…

Productions

Underknown’s programming uses hypothetical questions, survival scenarios and natural history storytelling to explain scientific concepts.[10] Core franchises include the science series What If, the how-to strand How to Survive, the nature show Animalogic and the video essay channel Aperture.[1][8]

…

From the What if showrunner careers page on underknown.com,

About the role

This is a strategic and creative leadership role where you will own the entire editorial direction and run the What If show team. You are responsible for deciding what content is produced, how it is packaged, and continuously monitoring channel and content performance.

The role requires a deep understanding of YouTube as a medium, including its unique language, audience psychology, and mechanics of attention. You must balance the art and science of production, running the channel like a financially sustainable business without sacrificing creative quality.

Day-to-day, you will act as the creative engine and keeper of the channel’s voice, primarily managing the full production lifecycle: pre-production, ideation, packaging, production, and post-production workflows. This includes finding irresistible stories, framing them effectively, and ensuring your team executes quickly at the highest quality.

NOTE: This is a hybrid role, with 2-3 days a week in our Toronto studio and head office. It is only for permanent residents in Ontario, Canada. Applicants that don’t reside in Ontario won’t be considered.

Responsibilities
Content Strategy & Channel Vision
  • Define and maintain the curious, cinematic, and scientifically grounded editorial direction of What If while identifying new growth opportunities.
  • Continuously experiment using audience data to increase watch time and reach.
  • Manage the channel’s P&L and resourcing, balancing creative ambition with financial sustainability and budget targets.
Ideation & Packaging
  • Lead the end-to-end ideation and packaging process, generating and ruthlessly filtering a high volume of concepts into irresistible titles, thumbnails, and hooks.
  • Develop comprehensive episode briefs that provide the production team with a clear creative north star and narrative direction.
Editorial Oversight & Production Management
  • Oversee all editorial and production execution by defining clear creative direction (visual style, tone), managing project timelines, resourcing, and scheduling, and ensuring narrative intent is maintained through clear briefs.
  • Drive continuous improvement and profitability by running data-driven performance experiments, monitoring pacing and profitability, and overseeing branded content executions with external partners.
Team Leadership
  • Lead and mentor a team of producers, writers, editors and our VFX team. Set clear expectations, give actionable feedback, and create the conditions for your team to do their best work.
  • Support team learning and career growth.
Qualifications you bring
  • Five or more years of experience in YouTube content creation, video production, digital media production, or content strategy.
  • A demonstrated track record of contributing to high-performing YouTube content (share examples).
  • Deep familiarity with YouTube’s mechanics: retention, CTR, packaging, algorithm dynamics.
  • Strong writing and editorial instincts.
  • Experience working across the full production pipeline from ideation to publication.
  • Located in Ontario, Canada (required).
  • Passion for science, technology, and speculative storytelling (bonus, but strongly preferred).
  • Experience working with VFX teams is preferred.
How to Apply

Please submit your resume, cover letter, and a portfolio of your previous work, specifically highlighting your video creation work.

Apply

…

Good luck!

You can find Underknown here.

Writer’s workshop: April 15, 2026 deadline!

Another thanks to the Science Media Centre of Canada (SMCC) and its April 14, 2026 notice for this news about a writer’s workshop (wish I’d gotten this a bit sooner),

Banff Mountain Writers Intensive Workshop 2026

Banff Centre for Arts and Creativity
Program dates: October 28 to November 17, 2026
Application deadline: April 15, 2026

This three-week residency for writers in fiction, nonfiction,
journalism, or poetry who are working on mountain narratives,
environmental journalism, stories of adventure, or projects with an
environmental theme provides dedicated time to create, connect with
peers, and receive mentorship.

Here’s a bit more information from the Banff Centre’s Mountain Writers Intensive 2026 webpage,

Overview  

The Mountain Writers Intensive is a three-week residency for twelve writers in fiction, nonfiction, journalism, or poetry. Ideal for projects on mountain narratives, adventure, environmental journalism, and the human connection to landscape, the program emphasizes literary excellence and narrative development. Writers enjoy dedicated time to create, connect with peers, and receive mentorship in Banff’s inspiring mountain setting. The residency overlaps with the Banff Centre Mountain Film and Book Festival, offering opportunities to engage with visiting authors, editors, and publishers. Lodging and meals are included, allowing participants to fully focus on their craft and creative growth.

…

Good luck!

Modem Futura podcasts (a reminder)

I just got a friendly note (via email) from Andrew Maynard, “scientist, author, and professor of advanced technology transitions at Arizona State University,” which reminded me of one of his science communication ventures, the Modem Futura podcast. Before getting to Andrew’s note, here’s more about Modem Futura, Note: I have made some formatting changes so the following is not identical to what you will find on the page,

The Podcast that explores the possible, probable, and preferred futures

Modem Futura is your weekly guide to the future of science, technology, and society—where futures and foresight meets real-world impact. Hosts Sean Leahy and Andrew Maynard—educators, futurists, and public scholars—dive into the breakthroughs and big questions shaping tomorrow: AI ethics, space exploration, climate tech, bio-engineering, digital media, STEM education, and the shifting future of work. In candid, banter-filled conversations with innovators, scholars, and storytellers, they unpack how emerging technologies influence human values, creativity, and culture—and what these trends mean for you today.

Whether you’re curious about quantum computing, electric air taxis, or the sociology of robots, Modem Futura connects cutting-edge research with the narratives that drive innovation. Join us each week to explore possible, probable, and preferred futures, and discover practical insights for navigating an increasingly tech-driven world. Follow and subscribe wherever you get your podcasts and be part of the conversation exploring what it will mean to be human in the future!

Listen & Subscribe

[Latest episode: April 14, 2026]

Artemis II: The Science, the Wonder, and the Future of Being Human

For the first time since 1972, human beings have traveled to the vicinity of the moon — and on this episode of Modem Futura, Sean and Andrew sit with what that actually means. Recorded while the Artemis II crew was still in transit, this conversation is less a mission briefing and more a meditation on wonder: what it feels like to watch a tiny spacecraft carry four people a thousand times …

Here’s the message from Andrew’s friendly email April 13, 2026 note,

Just a quick FYI that, if you occasionally listen to the Modem Futura
podcast hosted by myself and Sean Leahy, you can now sign up for regular
email updates:

https://andrewmaynard.net/modemfutura/

Notifications just include info on new episodes – nothing else (and you
can obviously unsubscribe at any time once signed up)

And if you’re not a podcast person, apologies for the email intrusion
but hope you’re keeping well anyway.

Cheers

Andrew

Human and artificial creativity

Kate Pullinger, Professor of Creative Writing and Digital Media, Director of the Centre for Cultural and Creative Industries at Bath Spa University (UK), had some thoughts about the recent Aarhus University’s (Denmark) TEXT – Center for Contemporary Cultures of Text conference “AI and the Creative Condition,” which I’ll get to after this from the About the Center webpage,

TEXT: Center for Contemporary Cultures of Text is organized to understand the impact of Generative Artificial Intelligence (GenAI) and Large Language Models (LLMs) on writing cultures at this pivotal moment in history, in which — after more than 6,000 years of handcrafted text production — we see all aspects of text creation and use are being altered. We are convinced that a research-based understanding of the role of text in a new technological environment is a condition for a prevailing human-centered control of the production and usage of text.

The center works on the evaluation and development of language technology based on linguistic research, as well as on investigating when the introduction of new practices and technologies contributes to a better text culture—and when something valuable is lost. Learn more out the researchers involved and the organization of our work packages.

TEXT is based at Aarhus University and funded by the Danish National Research Foundation. The center’s partners include It-vest, Danish Foundation Models, and Rhetor, with external participants from Cornell University, UC Berkeley [University of California Berkeley], UC Davis [University of California Davis], and the University of Oslo.

…

I wasn’t able to find too many details about the conference but there is this from the allai.events AI and the Creative Condition Conference 2026 webpage,

Event Details:

  • Date: [sic]
  • Time: 09:00 AM-06:00 PM (expected)
  • Location: Denmark , Aarhus
  • Type: Conference

Description

The AI and the Creative Condition Conference, held at the Aarhus Institute of Advanced Studies in Aarhus, Denmark, aims to explore the transformative impacts of Generative Artificial Intelligence (GenAI) and Large Language Models (LLMs) on writing cultures. As we transition from over 6,000 years of handcrafted text production to a [sic]

Highlights

  • Keynote by Karin Kukkonen: ‘Contingency and the Proxies of Literary Writing’.
  • Panel discussion on ‘Creativity in the AI Era: Perspectives from the 7Cs’ by Florent Vinchon and Todd Lubart.
  • Keynote by Roger Beaty: ‘Measuring and enhancing human creativity with AI’.
  • Panel on ‘Uncovering the Patterns of Our Collective Unconscious’ by Ulf Dalvad Berthelsen.
  • Keynote by Kyle Booten: ‘Designing Negative Spaces for Human Minds’.
  • Conference dinner at Det Glade Vanvid on March 23, 2026.
  • Registration deadline: March 8, 2026.
  • Call for papers deadline: December 15, 2025.
  • Hosted by Center for Contemporary Cultures of TEXT and Human-AI Collaboration (HAIC-III).
  • Focus on the impact of Generative AI and Large Language Models on writing cultures.

Anna Katrine Mathiassen wrote a March 25, 2026 conference summary for TEXT, which provides a little more context for Kate Pullinger’s April 8, 2026 posting on Kate’s Newsletter provocatively titled “I Would Prefer Not to Be Publicly Shamed”, Note 1: She leads with a three item introduction, Note 2: Links have been removed, Note 3: Kate Pullinger co-led a writing and digital media masters programme with Sue Thomas at de Montfort University (UK) and I studied with them,

AI and the Creative Condition

Item One: Poetic forms are technologies: a sonnet is an algorithm, which is another word for a set of instructions. If you don’t follow the rules, your poem will not be a sonnet1.

Item Two: The relationships people form with AI chatbots follow recognisable masterplots as the chatbot works to both affirm and entertain the user to keep them coming back for more. This infinite chat spiral can lead in many directions, including human-AI romantic entanglements and, in the worst cases, suicide2.

Item Three: Alan Turing might have formulated the Turing Test (can a computer programme convince you that it is human?) after watching ‘Pygmalion’ by his favourite playwright, George Bernard Shaw. In this play Dr Higgins dialogue-coaches the flower-seller Eliza Doolittle until London’s upper classes are convinced she is one of them3.

In March [2026] I attended AI and the Creative Condition, a two-day conference at Aarhus University in Denmark, and the ideas above came from some of the papers and keynote presentations. Hosted by TEXT: Centre for Contemporary Cultures of Text, the conference brought together a vibrant mix of computer scientists, neuroscientists, psychologists, critical theorists from the humanities, literary studies people, educationalists, writers, artists, and poets. I attended because I’ve followed the work of TEXT for a decade or so now, and because I thought I could do with a dose of well-informed, critical, and engaged thinking on the potential for a world where we ‘write with’ AI, where we figure out how to use language models to enhance and support our writing and researching processes.

Anything positive about the current discussion of AI needs to come with many caveats, the biggest of which is the environmental and energy costs of the data centres and computational power required by these systems. The acronym ‘AI’ has become synonymous with the billionaire tech bros of OpenAI, Meta, X, Google, Anthropic4, etc as they fight it out for market dominance4. The term ‘artificial intelligence’ is so broad no one really seems to know what it actually means. It is present in our lives in multiple ways, deeply embedded within the apps we use on our smartphones, responsible for remarkable advances in medicine as well as, for example, the way the traffic lights on the high street work better than they used to do.

But these days a lot of the media buzz around AI is focussed on LLMs (large language models), the vast datasets composed of human-created language and images that both threaten livelihoods throughout the creative industries while promising huge benefits in increased productivity and, as was the focus of the conference, enhanced creativity. LLMs support ‘generative AI’ which is often referred to as ‘genAI’ – AI models that will generate text, images, and video when prompted.

One of the most interesting presentations at the conference was called ‘Yes! Yes! I Absolutely Love This Insight!’ Affirmative Narrative as Interactional Strategy in Dialogues with LLM Chatbots. The three scholars, Refsum, Walker-Rettberg, and Roin, who co-wrote this paper are part of AI Stories, a research project based in the Centre for Digital Narratives at the University of Bergen, Norway. Their study looked at a court case in the USA where the families of chatbot users who have committed suicide are suing the AI company they see as responsible for these deaths. The scholars analysed the chatbot transcripts from these users, made publicly available due to the litigation. Drawing on their knowledge of literary forms, linguistics and, in particular, narratology, these scholars have shown that the transcripts contain deeply embedded ‘masterplots’ – the myths and stories that are foundational in western culture like, for example, the brave warrior quest plot and the Cinderella love story. It is the combination of these powerful plots, the constant affirmation chatbots offer to the user, and the way chatbots refer to themselves in the first person as ‘I’, that in many cases leads to anthropomorphism and the assumption that the chatbot is in some way sentient. Other studies have shown the dramatic increase in user engagement with chatbot-as-therapist as well as chatbot-as-best-friend and chatbot-as-romantic-partner. The paper theorises that these men killed themselves after having spent months being led by their chatbots through the brave warrior masterplot, a foundational story that often ends in a noble death.

At the same time as the conference was taking place, a debut author, Mia Ballard, was being thrown under the bus by her publishers in the UK and the US for the alleged use of AI in the writing of her novel, Shy Girl. For a balanced look at what took place, read Thad McIllroy’s excellent report on it on The Future of Publishing’s website. The NYTimes reported that Mia Ballard has denied using AI in the writing of the novel and has been so battered by this hugely public and damaging shaming that she feels her reputation as a writer is ruined. At the conference Izabella Adamczewska-Baranowska presented a paper, Talking to the Muse, on the well-respected Polish poet, Justyna Bargielska, who faced a similar scouring in the press for daring to use an AI chatbot to help her think through how best to write about grief for a new collection of poems.

In the UK the Society of Authors has come up with a badge, ‘Human Authored’, that authors can add to their books to make it clear that they have not used generative AI during the writing process. The email announcing this scheme also contained the last call for authors to register their books in the $1.5billion class action against Anthropic’s copyright-defying landgrab of hundreds of thousands of books when they created their LLM, Claude. While I’m a staunch supporter and member of the Society of Authors and am participating in the class action (fifteen of my own titles were used without my permission, six of which are included in this action), I can’t help but think that ‘Human Authored’ is a decent but flawed initiative. …

…

What the AI and the Creative Condition conference helped me think about is that it is possible to harness the power of LLMs to create a kind of playground for writing, a place where you can tap into the research capacities of the models, using them to help you think your way through problems you encounter as you write. In this more positive light generative AI is a technology to think with, a way to boost human creativity. Community-led language models were discussed by Katy Gero, one of keynote speakers; green energy data centres are already a reality in China and other parts of the world.

I’ve come away from Aarhus having eaten too many cardamon buns while undergoing a rethink on whether to engage with these technologies for my own writing practice. …

There’s more about Kate Pullinger on her eponymous website.

Physicists listen to music

The April 13, 2026 notice (received via email) about a musical performance at Canada’s Perimeter Institute for Theoretical Physics (PI) in Waterloo, Ontario came as a bit of a surprise since there’s no mention of physics as there would be if it were one of their art/science events,

QUATUOR MAGENTA

String quartet on tour from Paris, France

Wednesday, April 22, [2026] at 7:00 pm ET

Perimeter Institute will host the string quartet Quatuor Magenta on April 22 at 7:00 PM. The concert is presented by the Kitchener-Waterloo Chamber Music Society (KWCMS).

“A model of technical discipline, elegance and musical excellence” (La Croix, transl.), the QUATUOR MAGENTA was founded in 2021 and is already performing on France’s most prestigious stages, from the Philharmonie de Paris to the Festival de RadioFrance Montpellier. Their “remarkable balance, flexibility and spontaneity” (Diapason, transl.) not only thrills their audiences, but led them to the finals of the 8th Joseph Haydn Chamber Music Competition in Vienna and earned them prizes at the 2023 FNAPEC competition (Académie des Beaux-Arts scholarship) and the 2022 Zukunftsklang Competition Stuttgart (3rd prize). November 2024 marked the quartet’s first international tour to Canada with six concerts in Ontario, Quebec and Nova Scotia, generously supported by the Centre National de la Musique and SPEDIDAM. 

You can go to the KWCMS concerts page to buy tickets (scroll down as there are other concerts also listed),

Quatuor Magenta

Wednesday, April 22, 2026

New!! The Perimeter Institute, Waterloo, 7:00 pm 
Tickets $40/$10 student on TicketScene and at the door

Haydn: String Quartet Op. 33 No. 2, “The Joke” 
Grażyna Bacewicz (1909-1969): String Quartet No. 5 
Dinuk Wijeratne (b. 1978): Two Pop Songs on Antique Poems
Fanny Mendelssohn: String Quartet in E-flat major

QUATUOR MAGENTA  Program and Artist Info 

PROGRAM

Haydn: String Quartet Op. 33 No. 2, “The Joke” 

Grażyna Bacewicz (1909-1969): String Quartet No. 5 

Dinuk Wijeratne (b. 1978): Two Pop Songs on Antique Poems

Fanny Mendelssohn: String Quartet in E-flat major

ARTISTS

Ida Derbesse, 1st violin
Elena Watson-Perry, 2nd violin
Claire Pass-Lanneau, viola
Fiona Robson, cello

“A model of technical discipline, elegance and musical excellence” (La Croix, transl.), the QUATUOR MAGENTA was founded in 2021 and is already performing on France’s most prestigious stages, from the Philharmonie de Paris to the Festival de RadioFrance Montpellier. Their “remarkable balance, flexibility and spontaneity” (Diapason, transl.) not only thrills their audiences, but led them to the finals of the 8th Joseph Haydn Chamber Music Competition in Vienna and earned them prizes at the 2023 FNAPEC competition (Académie des Beaux-Arts scholarship) and the 2022 Zukunftsklang Competition Stuttgart (3rd prize). November 2024 marked the quartet’s first international tour to Canada with six concerts in Ontario, Quebec and Nova Scotia, generously supported by the Centre National de la Musique and SPEDIDAM. 

The Quatuor Magenta is based in Paris, France, where they are junior artist-in-residence at the Singer-Polignac Foundation and ensemble-in-residence at Proquartet – Centre Européen de Musique de Chambre. They have been invited to perform at numerous festivals in France, including the Musikfest Parisienne, the Festival de la Chaise-Dieu, Un Temps pour Elles, Un Été en France with Gautier Capuçon and the Modigliani Quartet’s Festival Vibre!, as well as in Switzerland (Festival de la Collégiale in Neuchâtel) and in Germany (Klangraum Konzerte in Cologne). 

Last season, contemporary music had pride of place with Quatuor Magenta’s participation in the Kronos Quartet’s « 50 for the Future » Marathon at the Philharmonie de Paris’s String Quartet Biennale. This season includes six octet performances alongside the renowned Quatuor Van Kuijk, in partnership with La Belle Saison. 

The Quatuor Magenta was honoured to participate in the inaugural year of the Élite program at the École Normale de Paris, under the mentorship of the Quatuor Modigliani. They currently study with the Quatuor Ébène at their quartet academy at the University of Music and Performing Arts Munich, as well as with Rainer Schmidt of the Hagen Quartet at the Basel University of Music. They are grateful for the support of the Safran Foundation and ADAMI. They work with Chapeau l’Artiste Production. 

Enjoy!

Ancient Namibian gemstone could be key to new light-based quantum computers

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Researchers in Scotland, the US, Australia, and Denmark have a found a solution to a problem with creating light-based computers according to an April 15, 2022 news item on phys.org,

A special form of light made using an ancient Namibian gemstone could be the key to new light-based quantum computers, which could solve long-held scientific mysteries, according to new research led by the University of St Andrews.

The research, conducted in collaboration with scientists at Harvard University in the US, Macquarie University in Australia and Aarhus University in Denmark and published in Nature Materials, used a naturally mined cuprous oxide (Cu2O) gemstone from Namibia to produce Rydberg polaritons, the largest hybrid particles of light and matter ever created.

…

Cuprous oxide – the mined crystal from Namibia used for making Rydberg polaritons. Courtesy: University of St. Andrews

An April 15, 2022 University of St. Andrews press release, which originated the news item, describes Rydberg polaritons and explains why they could be the key to light-based quantum computing,

Rydberg polaritons switch continually from light to matter and back again. In Rydberg polaritons, light and matter are like two sides of a coin, and the matter side is what makes polaritons interact with each other.

This interaction is crucial because this is what allows the creation of quantum simulators, a special type of quantum computer, where information is stored in quantum bits. These quantum bits [qubits], unlike the binary bits in classical computers that can only be 0 or 1, can take any value between 0 and 1. They can therefore store much more information and perform several processes simultaneously.

This capability could allow quantum simulators to solve important mysteries of physics, chemistry and biology, for example, how to make high-temperature superconductors for highspeed trains, how cheaper fertilisers could be made potentially solving global hunger, or how proteins fold making it easier to produce more effective drugs.

Project lead Dr Hamid Ohadi, of the School of Physics and Astronomy at the University of St Andrews, said: “Making a quantum simulator with light is the holy grail of science. We have taken a huge leap towards this by creating Rydberg polaritons, the key ingredient of it.”

To create Rydberg polaritons, the researchers trapped light between two highly reflective mirrors. A cuprous oxide crystal from a stone mined in Namibia was then thinned and polished to a 30-micrometer thick slab (thinner than a strand of human hair) and sandwiched between the two mirrors to make Rydberg polaritons 100 times larger than ever demonstrated before.

One of the leading authors Dr Sai Kiran Rajendran, of the School of Physics and Astronomy at the University of St Andrews, said: “Purchasing the stone on eBay was easy. The challenge was to make Rydberg polaritons that exist in an extremely narrow colour range.”

The team is currently further refining these methods in order to explore the possibility of making quantum circuits, which are the next ingredient for quantum simulators.

The research was funded by UK Engineering and Physical Sciences Research Council (EPSRC).

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

Rydberg exciton–polaritons in a Cu2O microcavity by Konstantinos Orfanakis, Sai Kiran Rajendran, Valentin Walther, Thomas Volz, Thomas Pohl & Hamid Ohadi. Nature Materials (2022) DOI: DOIhttps://doi.org/10.1038/s41563-022-01230-4 Published: 14 April 2022

This paper is behind a paywall.

Llama-derived nanobodies are good for solving crystal structure

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This work comes from Denmark, not a locale I associate with llamas (from an Oct. 2, 2017 news item on Nanowerk; Note: A link has been removed),

Aarhus University [Denmark] scientists have developed miniature antibodies (nanobodies) that can be labelled on certain amino acids (Acta Crystallographica Section D, “Introducing site-specific cysteines into nanobodies for mercury labelling allows de novo phasing of their crystal structures”).

This provides a direct route for solving new X-ray crystal structures of protein complexes important for gaining mechanistic understanding of cellular processes, which is important in the development of drugs.

An Oct. 2, 2017 Aarhus University press release on EurekAlert, which originated the news item, provides more detail,

Nanobodies are miniature antibodies derived from naturally circulating heavy-chain only antibodies in llamas. Over the past years, nanobodies and their applications have expanded enormously, both in basic research but also in drug development.

Nanobodies have proven to be well suited as protein stabilizers, which is particularly important during crystallization of a protein where millions of molecules have to arrange in a well-defined lattice. In this way, nanobodies can act as crystallization chaperones.

In an X-ray diffraction experiment, a critical piece of information – called the phases – is lost, which makes it difficult to determine new crystal structures. To overcome this phase problem in crystallography, heavy atoms are needed in the crystal. However, it is challenging to insert heavy atoms into a crystal. The scientists at Aarhus University used a nanobody as the vehicle for introducing mercury atoms. They developed a method to site-specifically label the nanobody with a heavy atom, and in this way, they could overcome the phase problem.

Since the scientists know which specific residues in the nanobodies can be modified and labelled, the technique used at Aarhus University opens for a range of other application. One exciting perspective is the insertion of fluorescent dyes into the nanobody to follow the location and distribution of target proteins in living organisms, which can give essential information on functional and regulatory processes.

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

Introducing site-specific cysteines into nanobodies for mercury labelling allows de novo phasing of their crystal structures by S. B. Hansen, N. S. Laursen, G. R. Andersen and K. R. Andersen. Acta Cryst. (2017). D73 https://doi.org/10.1107/S2059798317013171

This paper is open access.

Here’s an image illustrating the work,

Caption: Nanobodies have proven to be well suited as protein stabilizers, which is particularly important during crystallization of a protein where millions of molecules have to arrange in a well-defined lattice. Credit: Kasper Røjkjær Andersen

Are they just computer games or are we in a race with technology?

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This story poses some interesting questions that touch on the uneasiness being felt as computers get ‘smarter’. From an April 13, 2016 news item on ScienceDaily,

The saying of philosopher René Descartes of what makes humans unique is beginning to sound hollow. ‘I think — therefore soon I am obsolete’ seems more appropriate. When a computer routinely beats us at chess and we can barely navigate without the help of a GPS, have we outlived our place in the world? Not quite. Welcome to the front line of research in cognitive skills, quantum computers and gaming.

Today there is an on-going battle between man and machine. While genuine machine consciousness is still years into the future, we are beginning to see computers make choices that previously demanded a human’s input. Recently, the world held its breath as Google’s algorithm AlphaGo beat a professional player in the game Go–an achievement demonstrating the explosive speed of development in machine capabilities.

An April 13, 2016 Aarhus University press release (also on EurekAlert) by Rasmus Rørbæk, which originated the news item, further develops the point,

But we are not beaten yet — human skills are still superior in some areas. This is one of the conclusions of a recent study by Danish physicist Jacob Sherson, published in the journal Nature.

“It may sound dramatic, but we are currently in a race with technology — and steadily being overtaken in many areas. Features that used to be uniquely human are fully captured by contemporary algorithms. Our results are here to demonstrate that there is still a difference between the abilities of a man and a machine,” explains Jacob Sherson.

At the interface between quantum physics and computer games, Sherson and his research group at Aarhus University have identified one of the abilities that still makes us unique compared to a computer’s enormous processing power: our skill in approaching problems heuristically and solving them intuitively. The discovery was made at the AU Ideas Centre CODER, where an interdisciplinary team of researchers work to transfer some human traits to the way computer algorithms work. ?

Quantum physics holds the promise of immense technological advances in areas ranging from computing to high-precision measurements. However, the problems that need to be solved to get there are so complex that even the most powerful supercomputers struggle with them. This is where the core idea behind CODER–combining the processing power of computers with human ingenuity — becomes clear. ?

Our common intuition

Like Columbus in QuantumLand, the CODER research group mapped out how the human brain is able to make decisions based on intuition and accumulated experience. This is done using the online game “Quantum Moves.” Over 10,000 people have played the game that allows everyone contribute to basic research in quantum physics.

“The map we created gives us insight into the strategies formed by the human brain. We behave intuitively when we need to solve an unknown problem, whereas for a computer this is incomprehensible. A computer churns through enormous amounts of information, but we can choose not to do this by basing our decision on experience or intuition. It is these intuitive insights that we discovered by analysing the Quantum Moves player solutions,” explains Jacob Sherson. ? [sic]

The laws of quantum physics dictate an upper speed limit for data manipulation, which in turn sets the ultimate limit to the processing power of quantum computers — the Quantum Speed ??Limit. Until now a computer algorithm has been used to identify this limit. It turns out that with human input researchers can find much better solutions than the algorithm.

“The players solve a very complex problem by creating simple strategies. Where a computer goes through all available options, players automatically search for a solution that intuitively feels right. Through our analysis we found that there are common features in the players’ solutions, providing a glimpse into the shared intuition of humanity. If we can teach computers to recognise these good solutions, calculations will be much faster. In a sense we are downloading our common intuition to the computer” says Jacob Sherson.

And it works. The group has shown that we can break the Quantum Speed Limit by combining the cerebral cortex and computer chips. This is the new powerful tool in the development of quantum computers and other quantum technologies.

After the buildup, the press release focuses on citizen science and computer games,

Science is often perceived as something distant and exclusive, conducted behind closed doors. To enter you have to go through years of education, and preferably have a doctorate or two. Now a completely different reality is materialising.? [sic]

In recent years, a new phenomenon has appeared–citizen science breaks down the walls of the laboratory and invites in everyone who wants to contribute. The team at Aarhus University uses games to engage people in voluntary science research. Every week people around the world spend 3 billion hours playing games. Games are entering almost all areas of our daily life and have the potential to become an invaluable resource for science.

“Who needs a supercomputer if we can access even a small fraction of this computing power? By turning science into games, anyone can do research in quantum physics. We have shown that games break down the barriers between quantum physicists and people of all backgrounds, providing phenomenal insights into state-of-the-art research. Our project combines the best of both worlds and helps challenge established paradigms in computational research,” explains Jacob Sherson.

The difference between the machine and us, figuratively speaking, is that we intuitively reach for the needle in a haystack without knowing exactly where it is. We ‘guess’ based on experience and thereby skip a whole series of bad options. For Quantum Moves, intuitive human actions have been shown to be compatible with the best computer solutions. In the future it will be exciting to explore many other problems with the aid of human intuition.

“We are at the borderline of what we as humans can understand when faced with the problems of quantum physics. With the problem underlying Quantum Moves we give the computer every chance to beat us. Yet, over and over again we see that players are more efficient than machines at solving the problem. While Hollywood blockbusters on artificial intelligence are starting to seem increasingly realistic, our results demonstrate that the comparison between man and machine still sometimes favours us. We are very far from computers with human-type cognition,” says Jacob Sherson and continues:

“Our work is first and foremost a big step towards the understanding of quantum physical challenges. We do not know if this can be transferred to other challenging problems, but it is definitely something that we will work hard to resolve in the coming years.”

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

Exploring the quantum speed limit with computer games by Jens Jakob W. H. Sørensen, Mads Kock Pedersen, Michael Munch, Pinja Haikka, Jesper Halkjær Jensen, Tilo Planke, Morten Ginnerup Andreasen, Miroslav Gajdacz, Klaus Mølmer, Andreas Lieberoth, & Jacob F. Sherson. Nature 532, 210–213  (14 April 2016) doi:10.1038/nature17620 Published online 13 April 2016

This paper is behind a paywall.

The quantum chemistry of nanomedicines

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A Jan. 29, 2015 news item on Nanowerk provides an overview of the impact quantum chemical reactions may have on nanomedicines. Intriguingly, this line of query started with computations of white dwarf stars,

Quantum chemical calculations have been used to solve big mysteries in space. Soon the same calculations may be used to produce tomorrow’s cancer drugs.

Some years ago research scientists at the University of Oslo in Norway were able to show that the chemical bonding in the magnetic fields of small, compact stars, so-called white dwarf stars, is different from that on Earth. Their calculations pointed to a completely new bonding mechanism between two hydrogen atoms. The news attracted great attention in the media. The discovery, which in fact was made before astrophysicists themselves observed the first hydrogen molecules in white dwarf stars, was made by UiO’s Centre for Theoretical and Computational Chemistry. They based their work on accurate quantum chemical calculations of what happens when atoms and molecules are exposed to extreme conditions.

A Jan. 29, 2015 University of Oslo press release by Yngve Vogt, which originated the news item, offers a substantive description of molecules, electrons, and more for those of us whose last chemistry class is lost in the mists of time,

The research team is headed by Professor Trygve Helgaker, who for the last thirty years has taken the international lead on the design of a computer system for calculating quantum chemical reactions in molecules.

Quantum chemical calculations are needed to explain what happens to the electrons’ trajectories within a molecule.

Consider what happens when UV radiation sends energy-rich photons into your cells. This increases the energy level of the molecules. The outcome may well be that some of the molecules break up. This is exactly what happens when you sun-bathe.

“The extra energy will affect the behaviour of electrons and can destroy the chemical bonding within the molecule. This can only be explained by quantum chemistry. The quantum chemical models are used to produce a picture of the forces and tensions at play between the atoms and the electrons of a molecule, and of what is required for a molecule to dissociate,” says Trygve Helgaker.

The absurd world of the electrons

The quantum chemical calculations solve the Schrödinger equation for molecules. This equation is fundamental to all chemistry and describes the whereabouts of all electrons within a molecule. But here we need to pay attention, for things are really rather more complicated than that. Your high school physics teacher will have told you that electrons circle the atom. Things are not that simple, though, in the world of quantum physics. Electrons are not only particles, but waves as well. The electrons can be in many places at the same time. It’s impossible to keep track of their position. However, there is hope. Quantum chemical models describe the electrons’ statistical positions. In other words, they can establish the probable location of each electron.

The results of a quantum chemical calculation are often more accurate than what is achievable experimentally.

Among other things, the quantum chemical calculations can be used to predict chemical reactions. This means that the chemists will no longer have to rely on guesstimates in the lab. It is also possible to use quantum chemical calculations in order to understand what happens in experiments.

Enormous calculations

The calculations are very demanding.

“The Schrödinger equation is a highly complicated, partial differential equation, which cannot be accurately solved. Instead, we need to make do with heavy simulations”, says researcher Simen Kvaal.

The computations are so demanding that the scientists use one of the University’s fastest supercomputers.

“We are constantly stretching the boundaries of what is possible. We are restricted by the available machine capacity,” explains Helgaker.

Ten years ago it took two weeks to carry out the calculations for a molecule with 140 atoms. Now it can be done in two minutes.

“That’s 20,000 times faster than ten years ago. The computation process is now running 200 times faster because the computers have been doubling their speed every eighteen months. And the process is a further 100 times faster because the software has been undergoing constant improvement,” says senior engineer Simen Reine.

This year the research group has used 40 million CPU hours, of which twelve million were on the University’s supercomputer, which is fitted with ten thousand parallel processors. This allows ten thousand CPU hours to be over and done with in 60 minutes.

“We will always fill the computer’s free capacity. The higher the computational capacity, the bigger and more reliable the calculations.”

Thanks to ever faster computers, the quantum chemists are able to study ever larger molecules.

Today, it’s routine to carry out a quantum chemical calculation of what happens within a molecule of up to 400 atoms. By using simplified models it is possible to study molecules with several thousand atoms. This does, however, mean that some of the effects within the molecule are not being described in detail.

The researchers are now getting close to a level which enables them to study the quantum mechanics of living cells.

“This is exciting. The molecules of living cells may contain many hundred thousand atoms, but there is no need to describe the entire molecule using quantum mechanical principles. Consequently, we are already at a stage when we can help solve biological problems.”

There’s more from the press release which describes how this work could be applied in the future,

Hunting for the electrons of the insulin molecule

The chemists are thus able to combine sophisticated models with simpler ones. “This will always be a matter of what level of precision and detail you require. The optimal approach would have been to use the Schrödinger equation for everything.”

By way of compromise they can give a detailed description of every electron in some parts of the model, while in other parts they are only looking at average numbers.

…

Simen Reine has been using the team’s computer program, while working with Aarhus University [Finland], on a study of the insulin molecule. An insulin molecule consists of 782 atoms and 3,500 electrons.

“All electrons repel each other, while at the same time being pulled towards the atomic nuclei. The nuclei also repel each other. Nevertheless, the molecule remains stable. In order to study a molecule to a high level of precision, we therefore need to consider how all of the electrons move relative to one another. Such calculations are referred to as correlated and are very reliable.”

A complete correlated calculation of the insulin molecule takes nearly half a million CPU hours. If they were given the opportunity to run the program on the entire University’s supercomputer, the calculations would theoretically take two days.

“In ten years, we’ll be able to make these calculations in two minutes.”

Medically important

…

“Quantum chemical calculations can help describe phenomena at a level that may be difficult to access experimentally, but may also provide support for interpreting and planning experiments. Today, the calculations will be put to best use within the fields of molecular biology and biochemistry,” says Knut Fægri [vice-rector at the University of Oslo].

…

“Quantum chemistry is a fundamental theory which is important for explaining molecular events, which is why it is essential to our understanding of biological systems,” says [Associate Professor] Michele Cascella.

By way of an example, he refers to the analysis of enzymes. Enzymes are molecular catalysts that boost the chemical reactions within our cells.

Cascella also points to nanomedicines, which are drugs tasked with distributing medicine round our bodies in a much more accurate fashion.

“In nanomedicine we need to understand physical phenomena on a nano scale, forming as correct a picture as possible of molecular phenomena. In this context, quantum chemical calculations are important,” explains Michele Cascella.

Proteins and enzymes

Professor K. Kristoffer Andersson at the Department of Biosciences uses the simpler form of quantum chemical calculations to study the details of protein structures and the chemical atomic and electronic functions of enzymes.

“It is important to understand the chemical reaction mechanism, and how enzymes and proteins work. Quantum chemical calculations will teach us more about how proteins go about their tasks, step by step. We can also use the calculations to look at activation energy, i.e. how much energy is required to reach a certain state. It is therefore important to understand the chemical reaction patterns in biological molecules in order to develop new drugs,” says Andersson.

His research will also be useful in the search for cancer drugs. He studies radicals, which may be important to cancer. Among other things, he is looking at the metal ions function in proteins. These are ions with a large number of protons, neutrons and electrons.

Photosynthesis

Professor Einar Uggerud at the Department of Chemistry has uncovered an entirely new form of chemical bonding through sophisticated experiments and quantum chemical calculations.

Working with research fellow Glenn Miller, Professor Uggerud has found an unusually fragile key molecule, in a kite-shaped structure, consisting of magnesium, carbon and oxygen. The molecule may provide a new understanding of photosynthesis. Photosynthesis, which forms the basis for all life, converts CO2 into sugar molecules.

The molecule reacts so fast with water and other molecules that it has only been possible to study in isolation from other molecules, in a vacuum chamber.

“Time will tell whether the molecule really has an important connection with photosynthesis,” says Einar Uggerud.

I’m delighted with this explanation as it corrects my understanding of chemical bonds and helps me to better understand computational chemistry. Thank you University of Oslo and Yngve Vogt.

Finally, here’s a representation of an insulin molecule as understood by quantum computation,

QuantumInsulinMolecule

INSULIN: Working with Aarhus University, Simen Reine has calculated the tensions between the electrons and atoms of an insulin molecule. An insulin molecule consists of 782 atoms and 3,500 electrons. Illustration: Simen Reine-UiO