Tag Archives: McGill University

Interconnected performance analysis music hub shared by McGill University and Université de Montréal announced* June 2, 2016

The press releases promise the Centre for Interdisciplinary Research in Music Media and Technology (CIRMMT) will shape the future of music. The CIRMMT June 2, 2016 (Future of Music) press release (received via email) describes the funding support,

A significant investment of public and private support that will redefine the future of music research in Canada by transforming the way musicians compose,listen and perform music.

The Centre for Interdisciplinary Research in Music Media and Technology (CIRMMT), the Schulich School of Music of McGill University and the Faculty of Music of l’Université de Montréal are creating a unique interconnected research hub that will quite literally link two exceptional spaces at two of Canada’s most renowned music schools.

Imagine a new space and community where musicians, scientists and engineers join forces to gain a better understanding of the influence that music plays on individuals as well as their physical, psychological and even neurological conditions; experience the acoustics of an 18th century Viennese concert hall created with the touch of a fingertip; or attending an orchestral performance in one concert hall but hearing and seeing musicians performing from a completely different venue across town… All this and more will soon become possible here in Montreal!

The combination of public and private gifts will broaden our musical horizons exponentially thanks to significant investment for music research in Canada. With over $14.5 million in grants from the Canada Foundation for Innovation (CFI), the Government of Quebec and the Fonds de Recherche du Québec (FRQ), and a substantial contribution of an additional $2.5million gift from private philanthropy.

“We are grateful for this exceptional investment in music research from both the federal and provincial governments and from our generous donors,” says McGill Principal Suzanne Fortier. “This will further the collaboration between these two outstanding music schools and support the training of the next generation of music researchers and artists. For anyone who loves music, this is very exciting news.”

There’s not much technical detail in this one but here it is,

Digital channels coupling McGill University’s Music Multimedia Room (MMR – a large, sound-isolated performance lab) and l’Université de Montréal’s Salle Claude Champagne ([SCC -] a superb concert hall) will transform these two exceptional spaces into the world’s leading research facility for the scientific study of live performance, movement of recorded sound in space, and distributed performance (where musicians in different locations perform together).

“The interaction between scientific/technological research and artistic practice is one of the most fruitful avenues for future developments in both fields. This remarkable investment in music research is a wonderful recognition of the important contributions of the arts to Canadian society”, says Sean Ferguson, Dean of Schulich School of Music

The other CIRMMT June 2, 2016 (Collaborative hub) press  release (received via email) elaborates somewhat on the technology,

The MMR (McGill University’s Music Multimedia Room) will undergo complete renovations which include the addition of high quality variable acoustical treatment and a state-of-the-art rigging system. An active enhancement and sound spatialization system, together with stereoscopic projectors and displays, will provide virtual acoustic and immersive environments. At the SCC (l’Université de Montréal’s Salle Claude Champagne), the creation of a laboratory, a control room and a customizable rigging system will enable the installation and utilization of new research equipment’s in this acoustically-rich environment. These improvements will drastically augment the research possibilities in the hall, making it a unique hub in Canada for researchers to validate their experiments in a real concert hall.

“This infrastructure will provide exceptional spaces for performance analysis of multiple performers and audience members simultaneously, with equipment such as markerless motion-capture equipment and eye trackers. It will also connect both spaces for experimentations on distributed performances and will make possible new kinds of multimedia artworks.

The research and benefits

The research program includes looking at audio recording technologies, audio and video in immersive environments, and ultra-videoconferencing, leading to the development of new technologies for audio recording, film, television, distance education, and multi-media artworks; as well as a focus on cognition and perception in musical performance by large ensembles and on the rhythmical synchronization and sound blending of performers.

Social benefits include distance learning, videoconferencing, and improvements to the quality of both recorded music and live performance. Health benefits include improved hearing aids, noise reduction in airplanes and public spaces, and science-based music pedagogies and therapy. Economic benefits include innovations in sound recording, film and video games, and the training of highly qualified personnel across disciplines.

Amongst other activities they will be exploring data sonification as it relates to performance.

Hopefully, I’ll have more after the livestreamed press conference being held this afternoon, June 2, 2016,  (2:30 pm EST) at the CIRMMT.

*’opens’ changed to ‘announced’ on June 2, 2016 at 1335 hours PST.

ETA June 8, 2016: I did attend the press conference via livestream. There was some lovely violin played and the piece proved to be a demonstration of the work they’re hoping to expand on now that there will be a CIRMMT (pronounced kermit). There was a lot of excitement and I think that’s largely due to the number of years it’s taken to get to this point. One of the speakers reminisced about being a music student at McGill in the 1970s when they first started talking about getting a new music building.

They did get their building but have unable to complete it until these 2016 funds were awarded. Honestly, all the speakers seemed a bit giddy with delight. I wish them all congratulations!

The song is you: a McGill University, University of Cambridge, and Stanford University research collaboration

These days I’m thinking about sound, music, spoken word, and more as I prepare for a new art/science piece. It’s very early stages so I don’t have much more to say about it but along those lines of thought, there’s a recent piece of research on music and personality that caught my eye. From a May 11, 2016 news item on phys.org,

A team of scientists from McGill University, the University of Cambridge, and Stanford Graduate School of Business developed a new method of coding and categorizing music. They found that people’s preference for these musical categories is driven by personality. The researchers say the findings have important implications for industry and health professionals.

A May 10, 2016 McGill University news release, which originated the news item, provides some fascinating suggestions for new categories for music,

There are a multitude of adjectives that people use to describe music, but in a recent study to be published this week in the journal Social Psychological and Personality Science, researchers show that musical attributes can be grouped into three categories. Rather than relying on the genre or style of a song, the team of scientists led by music psychologist David Greenberg with the help of Daniel J. Levitin from McGill University mapped the musical attributes of song excerpts from 26 different genres and subgenres, and then applied a statistical procedure to group them into clusters. The study revealed three clusters, which they labeled Arousal, Valence, and Depth. Arousal describes intensity and energy in music; Valence describes the spectrum of emotions in music (from sad to happy); and Depth describes intellect and sophistication in music. They also found that characteristics describing music from a single genre (both rock and jazz separately) could be grouped in these same three categories.

The findings suggest that this may be a useful alternative to grouping music into genres, which is often based on social connotations rather than the attributes of the actual music. It also suggests that those in academia and industry (e.g. Spotify and Pandora) that are already coding music on a multitude of attributes might save time and money by coding music around these three composite categories instead.

The researchers also conducted a second study of nearly 10,000 Facebook users who indicated their preferences for 50 musical excerpts from different genres. The researchers were then able to map preferences for these three attribute categories onto five personality traits and 30 detailed personality facets. For example, they found people who scored high on Openness to Experience preferred Depth in music, while Extraverted excitement-seekers preferred high Arousal in music. And those who scored high on Neuroticism preferred negative emotions in music, while those who were self-assured preferred positive emotions in music. As the title from the old Kern and Hammerstein song suggests, “The Song is You”. That is, the musical attributes that you like most reflect your personality. It also provides scientific support for what Joni Mitchell said in a 2013 interview with the CBC: “The trick is if you listen to that music and you see me, you’re not getting anything out of it. If you listen to that music and you see yourself, it will probably make you cry and you’ll learn something about yourself and now you’re getting something out of it.”

The researchers hope that this information will not only be helpful to music therapists but also for health care professions and even hospitals. For example, recent evidence has showed that music listening can increase recovery after surgery. The researchers argue that information about music preferences and personality could inform a music listening protocol after surgery to boost recovery rates.

The article is another in a series of studies that Greenberg and his team have published on music and personality. This past July [2015], they published an article in PLOS ONE showing that people’s musical preferences are linked to thinking styles. And in October [2015], they published an article in the Journal of Research in Personality, identifying the personality trait Openness to Experience as a key predictor of musical ability, even in non-musicians. These series of studies tell us that there are close links between our personality and musical behavior that may be beyond our control and awareness.

Readers can find out how they score on the music and personality quizzes at www.musicaluniverse.org.

David M. Greenberg, lead author from Cambridge University and City University of New York said: “Genre labels are informative but we’re trying to transcend them and move in a direction that points to the detailed characteristics in music that are driving people preferences and emotional reactions.”

Greenberg added: “As a musician, I see how vast the powers of music really are, and unfortunately, many of us do not use music to its full potential. Our ultimate goal is to create science that will help enhance the experience of listening to music. We want to use this information about personality and preferences to increase the day-to-day enjoyment and peak experiences people have with music.”

William Hoffman in a May 11, 2016 article for Inverse describes the work in connection with recently released new music from Radiohead and an upcoming release from Chance the Rapper (along with a brief mention of Drake), Note: Links have been removed,

Music critics regularly scour Thesaurus.com for the best adjectives to throw into their perfectly descriptive melodious disquisitions on the latest works from Drake, Radiohead, or whomever. And listeners of all walks have, since the beginning of music itself, been guilty of lazily pigeonholing artists into numerous socially constructed genres. But all of that can be (and should be) thrown out the window now, because new research suggests that, to perfectly match music to a listener’s personality, all you need are these three scientific measurables [arousal, valence, depth].

This suggests that a slow, introspective gospel song from Chance The Rapper’s upcoming album could have the same depth as a track from Radiohead’s A Moon Shaped Pool. So a system of categorization based on Greenberg’s research would, surprisingly but rightfully, place the rap and rock works in the same bin.

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

The Song Is You: Preferences for Musical Attribute Dimensions Reflect Personality by David M. Greenberg, Michal Kosinski, David J. Stillwell, Brian L. Monteiro, Daniel J. Levitin, and Peter J. Rentfrow. Social Psychological and Personality Science, 1948550616641473, first published on May 9, 2016

This paper is behind a paywall.

Here’s a link to and a citation for the October 2015 paper

Personality predicts musical sophistication by David M. Greenberg, Daniel Müllensiefen, Michael E. Lamb, Peter J. Rentfrow. Journal of Research in Personality Volume 58, October 2015, Pages 154–158 doi:10.1016/j.jrp.2015.06.002 Note: A Feb. 2016 erratum is also listed.

The paper is behind a paywall and it looks as if you will have to pay for it and for the erratum separately.

Here’s a link to and a citation for the July 2015 paper,

Musical Preferences are Linked to Cognitive Styles by David M. Greenberg, Simon Baron-Cohen, David J. Stillwell, Michal Kosinski, Peter J. Rentfrow. PLOS [Public Library of Science ONE]  http://dx.doi.org/10.1371/journal.pone.0131151 Published: July 22, 2015

This paper is open access.

I tried out the research project’s website: The Musical Universe. by filling out the Musical Taste questionnaire. Unfortunately, I did not receive my results. Since the team’s latest research has just been reported, I imagine there are many people trying do the same thing. It might be worth your while to wait a bit if you want to try this out or you can fill out one of their other questionnaires. Oh, and you might want to allot at least 20 mins.

Nanosafety Cluster newsletter—excerpts from the Spring 2016 issue

The European Commission’s NanoSafety Cluster Newsletter (no.7) Spring 2016 edition is some 50 pp. long and it provides a roundup of activities and forthcoming events. Here are a few excerpts,

“Closer to the Market” Roadmap (CTTM) now finalised

Hot off the press! the Cluster’s “Closer to the Market” Roadmap (CTTM)  is  a  multi-dimensional,  stepwise  plan  targeting  a framework to deliver safe nano-enabled products to the market. After some years of discussions, several consultations of a huge number of experts in the nanosafety-field, conferences at which the issue of market implementation of nanotechnologies was talked  about,  writing  hours/days,  and  finally  two public consultation rounds, the CTTM is now finalized.

As stated in the Executive Summary: “Nano-products and nano-enabled applications need a clear and easy-to-follow human and environmental safety framework for the development along the innovation chain from initial idea to market and beyond that facilitates  navigation  through  the  complex  regulatory and approval processes under which different product categories fall.

Download it here, and get involved in its implementation through the Cluster!
Authors: Andreas Falk* 1, Christa Schimpel1, Andrea Haase3, Benoît Hazebrouck4, Carlos Fito López5, Adriele Prina-Mello6, Kai Savolainen7, Adriënne Sips8, Jesús M. Lopez de Ipiña10, Iseult Lynch11, Costas Charitidis12, Visser Germ13

NanoDefine hosts Synergy Workshop with NSC projects

NanoDefine  organised  the  2nd Nanosafety  Cluster  (NSC)  Synergy Workshop  at  the  Netherlands  House  for Education  and  Research  in Brussels  on  2nd  February  2016. The  aim  was  to  identify  overlaps and synergies existing between different projects that could develop into
outstanding cooperation opportunities.

One central issue was the building of a common ontology and a European framework for data management and analysis, as planned within eNanoMapper, to facilitate a closer interdisciplinary collaboration between  NSC projects and to better address the need for proper data storage, analysis and sharing (Open Access).

Unexpectedly, there’s a Canadian connection,

Discovering protocols for nanoparticles: the soils case
NanoFASE WP7 & NanoSafety Cluster WG3 Exposure

In NanoFASE, of course, we focus on the exposure to nanomaterials. Having consistent and meaningful protocols to characterize the fate of nanomaterials in different environments is therefore of great interest to us. Soils and sediments are in this respect very cumbersome. Also in the case of conventional chemicals has the development of  protocols for fate description in terrestrial systems been a long route.

The special considerations of nanomaterials make this job even harder. For instance, how does one handle the fact that the interaction between soils and nanoparticles is always out of equilibrium? How does one distinguish between the nanoparticles that are still mobile and those that are attached to soil?

In the case of conventional chemicals, a single measurement of a filtered soil suspension often suffices to find the mobile fraction, as long one is sure that equilibrium has been attained. Equilibrium never occurs in the case of  nanoparticles, and the distinction between attached/suspended particles is analytically less clear to do.

Current activity in NanoFASE is focusing at finding protocols to characterize this interaction. Not only does the protocol have to provide meaningful parameters that can be used, e.g. in modelling, but also the method itself should be fast and cheap enough so that a lot of data can be collected in a reasonable amount of time. NanoFASE is  in a good position to do this, because of its focus on fate and because of the many international collaborators.

For  instance,  the Swedish  Agricultural  University (Uppsala)  is  collaborating  with  McGill  University (Montreal, Canada [emphasis mine]), an advisory partner to NanoFASE, in developing the OECD [Organization for Economic Cooperation and Development] protocol for column tests (OECD test nr 312:  “Leaching in soil columns”). The effort is led by Yasir Sultan from Environment Canada and by Karlheinz Weinfurtner from the Frauenhofer institute in Germany. Initial results show the transport of nanomaterials in soil columns to be very limited.

The OECD protocol therefore does not often lead to measurable breakthrough curves that can be modelled to provide information about  nanomaterial  mobility  in  soils  and  most  likely  requires adaptations  to  account  for  the  relatively  low mobility  of  typical pristine nanomaterials.

OECD 312 prescribes to use 40 cm columns, which is most likely too long to show a breakthrough in the case of nanoparticles. Testing in NanoFASE will therefore focus on working with shorter columns and also investigating the effect of the flow speed.

The progress and the results of this action will be reported on our website (www.nanofase.eu).

ENM [engineered nanomaterial] Transformation in and Release from Managed Waste Streams (WP5): The NanoFASE pilot Wastewater Treatment Plant is up and running and producing sludge – soon we’ll be dosing with nanoparticles to test “real world” aging.

Now, wastewater,

ENM [engineered nanomaterial] Transformation in and Release from Managed Waste Streams (WP5): The NanoFASE pilot Wastewater Treatment Plant is up and running and producing sludge – soon we’ll be dosing with nanoparticles to test “real world” aging.

WP5 led by Ralf Kaegi of EAWAG [Swiss Federal Institute of Aquatic Science and Technology] (Switzerland) will establish transformation and release rates of ENM during their passage through different reactors. We are focusing on wastewater treatment plants (WWTPs), solid waste and dedicated sewage sludge incinerators as well as landfills (see figure below). Additionally, lab-scale experiments using pristine and well characterized materials, representing the realistic fate relevant forms at each stage, will allow us to obtain a mechanistic understanding of the transformation processes in waste treatment reactors. Our experimental results will feed directly into the development of a mathematical model describing the transformation and transfer of ENMs through the investigated reactors.

I’m including this since I’ve been following the ‘silver nanoparticle story’ for some time,

NanoMILE publication update: NanoMILE on the air and on the cover

Dramatic  differences  in  behavior  of  nano-silver during  the  initial  wash  cycle  and  for  its  further dissolution/transformation potential over time depending on detergent composition and form.

In an effort to better relate nanomaterial aging procedures to those which they are most likely to undergo during the life cycle of nano-enhanced products, in this paper we describe the various transformations which are possible when exposing Ag engineered nanoparticles (ENPs) to a suite of commercially available washing detergents (Figure 1). While Ag ENP transformation and washing of textiles has received considerable attention in recent years, our study is novel in that we (1) used several commercially available detergents allowing us to estimate the various changes possible in individual homes and commercial washing settings; (2) we have continued  method  development  of  state  of  the  art nanometrology techniques, including single particle ICP-MS, for the detection and characterization of ENPs in complex media; and (3) we were able to provide novel additions to the knowledge base of the environmental nanotechnology research community both in terms of the analytical methods (e.g. the first time ENP aggregates have been definitively analyzed via single particle ICP-MS) and broadening the scope of “real world” conditions that should be considered when understanding AgENP through their life cycle.

Our findings, which were recently published in Environmental Science and Toxicology (2015, 49: 9665), indicate that the washing detergent chemistry causes dramatic differences in ENP behavior during the initial wash cycle and has ramifications for the dissolution/transformation potential of the Ag ENPs over time (see Figure 2). The use of silver as an  antimicrobial  treatment  in  textiles  continues  to garner  considerable  attention.  Last  year  we  published  a manuscript in ACS Nano that considered how various silver treatments to textiles (conventional and nano) both release  nano-sized  material  after  the  wash  cycle  with  similar chemical  characteristics.  That  study  essentially conveyed that multiple silver treatments would become more similar through the product life cycle. Our newest  work expands this by investigating one silver ENP under various washing conditions thereby creating more varied silver products as an end result.

Fascinating stuff if you’ve been following the issues around nanotechnology and safety.

Towards the end of the newsletter on pp. 46-48, they list opportunities for partnerships, collaboration, and research posts and they list websites where you can check out job opportunities. Good Luck!

Islamic art inspires stretchy metamaterials

A March 16, 2016 article by Jonathan Webb for BBC (British Broadcasting Corporation) News Online describes research on metamaterials from McGill University (Montréal, Canada),

Metamaterials are engineered to have properties that don’t occur naturally, such as getting wider when stretched instead of just longer and thinner.

These perforated rubber sheets made by a Canadian team do just that – and then remain stable in their expanded state until they are squeezed back again.

Such designs could help make expandable stents or spacecraft components.

“In conventional materials, when you pull in one direction it will contract in other directions,” said Dr Ahmad Rafsanjani, from McGill University in Montreal.

“But with ‘auxetic’ materials, due to their internal architecture, when you pull in one direction they expand in the lateral direction.”

A March 16, 2016 article by Shannon Hall in the New Scientist provides more details,

This property comes from their geometric substructure, which when stationary looks like a series of connected squares. When the squares turn relative to each other, however, the material’s density lowers but its thickness increases, allowing it to grow when stretched.

But this twisting means that the materials lose their original shape as they expand. So Ahmad Rafsanjani and Damiano Pasini of McGill University in Montreal, Canada, set out to create a material that would grow when stretched yet keep its form.

To do this, they turned to a beautiful kind of geometry.

“There is a huge library of geometries when you look at Islamic architectures,” says Rafsanjani. The team picked their design from the walls of the Kharraqan towers, two mausoleums built in 1067 and 1093 in the plains in northern Iran.

Both Webb’s and Hall’s articles are embedded with images of the architecture. There’s also a New Scientist video demonstrating stretchability,

The researchers discussed this work in a presentation titled:  Multistable Compliant Auxetic Metamaterials Inspired by Geometric Patterns in Islamic Arts at the American Physical Society’s March 2016 meeting (March 14 – 18, 2016).

Disinfectant for backyard pools could be key to new nanomaterials

Research from McGill University (Québec, Canada) focuses on cyanuric acid, one of the chemicals used to disinfect backyard pools. according to a March 1, 2016 McGill University news release (received by email; it can also be found in a March 1, 2016 news item on Nanowerk *and on EurekAlert*),

Cyanuric acid is commonly used to stabilize chlorine in backyard pools; it binds to free chlorine and releases it slowly in the water. But researchers at McGill University have now discovered that this same small, inexpensive molecule can also be used to coax DNA into forming a brand new structure: instead of forming the familiar double helix, DNA’s nucleobases — which normally form rungs in the DNA ladder — associate with cyanuric acid molecules to form a triple helix.

The discovery “demonstrates a fundamentally new way to make DNA assemblies,” says Hanadi Sleiman, Canada Research Chair in DNA Nanoscience at McGill and senior author of the study, published in Nature Chemistry. “This concept may apply to many other molecules, and the resulting DNA assemblies could have applications in a range of technologies.”

The DNA alphabet, composed of the four letters A, T, G and C, is the underlying code that gives rise to the double helix famously discovered by Watson and Crick more than 60 years ago. The letters, or bases, of DNA can also interact in other ways to form a variety of DNA structures used by scientists in nanotechnology applications – quite apart from DNA’s biological role in living cells.

For years, scientists have sought to develop a larger, designer alphabet of DNA bases that would enable the creation of more DNA structures with unique, new properties. For the most part, however, devising these new molecules has involved costly and complex procedures.

The road to the McGill team’s discovery began some eight years ago, when Sleiman mentioned to others in her lab that cyanuric acid might be worth experimenting with because of its properties. The molecule has three faces with the same binding features as thymine (T in the DNA alphabet), the natural complement to adenine (A).  “One of my grad students tried it,” she recalls, “and came back and said he saw fibres” through an atomic force microscope.

The researchers later discovered that these fibres have a unique underlying structure. Cyanuric acid is able to coax strands composed of adenine bases into forming a novel motif in DNA assembly. The adenine and cyanuric acid units associate into flower-like rosettes; these form the cross-section of a triple helix.  The strands then combine to form long fibres.

“The nanofibre material formed in this way is easy to access, abundant and highly structured,” says Nicole Avakyan, a PhD student in Sleiman’s lab and first author of the study. “With further development, we can envisage a variety of applications of this material, from medicinal chemistry to tissue engineering and materials science.”

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

Reprogramming the assembly of unmodified DNA with a small molecule by Nicole Avakyan, Andrea A. Greschner, Faisal Aldaye, Christopher J. Serpell, Violeta Toader,    Anne Petitjean, & Hanadi F. Sleiman. Nature Chemistry (2016) doi:10.1038/nchem.2451 Published online 22 February 2016

This paper is behind a paywall.

*’also on EurekAlert’ added on March 2, 2016.

Biological supercomputers (living, breathing supercomputers) and an international collaboration spearheaded by Canadian scientists

A living, breathing supercomputer is a bit mind-boggling but scientists at McGill University (Canada) and their international colleagues have created a working model according to a Feb. 26, 2016 McGill University news release on EurekAlert (and received via email), Note: A link has been removed,

The substance that provides energy to all the cells in our bodies, Adenosine triphosphate (ATP), may also be able to power the next generation of supercomputers. That is what an international team of researchers led by Prof. Nicolau, the Chair of the Department of Bioengineering at McGill, believe. They’ve published an article on the subject earlier this week in the Proceedings of the National Academy of Sciences (PNAS), in which they describe a model of a biological computer that they have created that is able to process information very quickly and accurately using parallel networks in the same way that massive electronic super computers do.

Except that the model bio supercomputer they have created is a whole lot smaller than current supercomputers, uses much less energy, and uses proteins present in all living cells to function.

Doodling on the back of an envelope

“We’ve managed to create a very complex network in a very small area,” says Dan Nicolau, Sr. with a laugh. He began working on the idea with his son, Dan Jr., more than a decade ago and was then joined by colleagues from Germany, Sweden and The Netherlands, some 7 years ago [there is also one collaborator from the US according the journal’s [PNAS] list of author affiliations, read on for the link to the paper]. “This started as a back of an envelope idea, after too much rum I think, with drawings of what looked like small worms exploring mazes.”

The model bio-supercomputer that the Nicolaus (father and son) and their colleagues have created came about thanks to a combination of geometrical modelling and engineering knowhow (on the nano scale). It is a first step, in showing that this kind of biological supercomputer can actually work.

The circuit the researchers have created looks a bit like a road map of a busy and very organized city as seen from a plane. Just as in a city, cars and trucks of different sizes, powered by motors of different kinds, navigate through channels that have been created for them, consuming the fuel they need to keep moving.

More sustainable computing

But in the case of the biocomputer, the city is a chip measuring about 1.5 cm square in which channels have been etched. Instead of the electrons that are propelled by an electrical charge and move around within a traditional microchip, short strings of proteins (which the researchers call biological agents) travel around the circuit in a controlled way, their movements powered by ATP, the chemical that is, in some ways, the juice of life for everything from plants to politicians.

Because it is run by biological agents, and as a result hardly heats up at all, the model bio-supercomputer that the researchers have developed uses far less energy than standard electronic supercomputers do, making it more sustainable. Traditional supercomputers use so much electricity that they heat up a lot and then need to be cooled down, often requiring their own power plant to function.

Moving from model to reality

Although the model bio supercomputer was able to very efficiently tackle a complex classical mathematical problem by using parallel computing of the kind used by supercomputers, the researchers recognize that there is still a lot of work ahead to move from the model they have created to a full-scale functional computer.

”Now that this model exists as a way of successfully dealing with a single problem, there are going to be many others who will follow up and try to push it further, using different biological agents, for example,” says Nicolau. “It’s hard to say how soon it will be before we see a full scale bio super-computer. One option for dealing with larger and more complex problems may be to combine our device with a conventional computer to form a hybrid device. Right now we’re working on a variety of ways to push the research further.”

What was once the stuff of science fiction, is now just science.

The funding for this project is interesting,

This research was funded by: The European Union Seventh Framework Programme; [US] Defense Advanced Research Projects Agency [DARPA]; NanoLund; The Miller Foundation; The Swedish Research Council; The Carl Trygger Foundation; the German Research Foundation; and by Linnaeus University.

I don’t see a single Canadian funding agency listed.

In any event, here’s a link to and a citation for the paper,

Parallel computation with molecular-motor-propelled agents in nanofabricated networks by Dan V. Nicolau, Jr., Mercy Lard, Till Kortend, Falco C. M. J. M. van Delft, Malin Persson, Elina Bengtsson, Alf Månsson, Stefan Diez, Heiner Linke, and Dan V. Nicolau. Proceedings of the National Academy of Sciences (PNAS): http://www.pnas.org/content/early/2016/02/17/1510825113

This paper appears to be open access.

Finally, the researchers have provided an image illustrating their work,

Caption: Strands of proteins of different lengths move around the chip in the bio computer in directed patterns, a bit like cars and trucks navigating the streets of a city. Credit: Till Korten

Caption: Strands of proteins of different lengths move around the chip in the bio computer in directed patterns, a bit like cars and trucks navigating the streets of a city. Credit: Till Korten

ETA Feb. 29 2016: Technical University Dresden’s Feb. 26, 2016 press release on EurekAlert also announces the bio-computer albeit from a rather different perspective,

The pioneering achievement was developed by researchers from the Technische Universität Dresden and the Max Planck Institute of Molecular Cell Biology and Genetics, Dresden in collaboration with international partners from Canada, England, Sweden, the US, and the Netherlands.

Conventional electronic computers have led to remarkable technological advances in the past decades, but their sequential nature -they process only one computational task at a time- prevents them from solving problems of combinatorial nature such as protein design and folding, and optimal network routing. This is because the number of calculations required to solve such problems grows exponentially with the size of the problem, rendering them intractable with sequential computing. Parallel computing approaches can in principle tackle such problems, but the approaches developed so far have suffered from drawbacks that have made up-scaling and practical implementation very difficult. The recently reported parallel-computing approach aims to address these issues by combining well established nanofabrication technology with molecular motors which are highly energy efficient and inherently work in parallel.

In this approach, which the researchers demonstrate on a benchmark combinatorial problem that is notoriously hard to solve with sequential computers, the problem to be solved is ‘encoded’ into a network of nanoscale channels (Fig. 1a). This is done, on the one hand by mathematically designing a geometrical network that is capable of representing the problem, and on the other hand by fabricating a physical network based on this design using so-called lithography, a standard chip-manufacturing technique.

The network is then explored in parallel by many protein filaments (here actin filaments or microtubules) that are self-propelled by a molecular layer of motor proteins (here myosin or kinesin) covering the bottom of the channels (Fig. 3a). The design of the network using different types of junctions automatically guides the filaments to the correct solutions to the problem (Fig. 1b). This is realized by different types of junctions, causing the filaments to behave in two different ways. As the filaments are rather rigid structures, turning to the left or right is only possible for certain angles of the crossing channels. By defining these options (‘split junctions’ Fig. 2a + 3b and ‘pass junctions’, Fig. 2b + 3c) the scientists achieved an ‘intelligent’ network giving the filaments the opportunity either to cross only straight or to decide between two possible channels with a 50/50 probability.

The time to solve combinatorial problems of size N using this parallel-computing approach scales approximately as N2, which is a dramatic improvement over the exponential (2N) time scales required by conventional, sequential computers. Importantly, the approach is fully scalable with existing technologies and uses orders of magnitude less energy than conventional computers, thus circumventing the heating issues that are currently limiting the performance of conventional computing.

The diagrams mentioned were not included with the press release.

Montreal Neuro goes open science

The Montreal Neurological Institute (MNI) in Québec, Canada, known informally and widely as Montreal Neuro, has ‘opened’ its science research to the world. David Bruggeman tells the story in a Jan. 21, 2016 posting on his Pasco Phronesis blog (Note: Links have been removed),

The Montreal Neurological Institute (MNI) at McGill University announced that it will be the first academic research institute to become what it calls ‘Open Science.’  As Science is reporting, the MNI will make available all research results and research data at the time of publication.  Additionally it will not seek patents on any of the discoveries made on research at the Institute.

Will this catch on?  I have no idea if this particular combination of open access research data and results with no patents will spread to other university research institutes.  But I do believe that those elements will continue to spread.  More universities and federal agencies are pursuing open access options for research they support.  Elon Musk has opted to not pursue patent litigation for any of Tesla Motors’ patents, and has not pursued patents for SpaceX technology (though it has pursued litigation over patents in rocket technology). …

Montreal Neuro and its place in Canadian and world history

Before pursuing this announcement a little more closely, you might be interested in some of the institute’s research history (from the Montreal Neurological Institute Wikipedia entry and Note: Links have been removed),

The MNI was founded in 1934 by the neurosurgeon Dr. Wilder Penfield (1891–1976), with a $1.2 million grant from the Rockefeller Foundation of New York and the support of the government of Quebec, the city of Montreal, and private donors such as Izaak Walton Killam. In the years since the MNI’s first structure, the Rockefeller Pavilion was opened, several major structures were added to expand the scope of the MNI’s research and clinical activities. The MNI is the site of many Canadian “firsts.” Electroencephalography (EEG) was largely introduced and developed in Canada by MNI scientist Herbert Jasper, and all of the major new neuroimaging techniques—computer axial tomography (CAT), positron emission tomography (PET), and magnetic resonance imaging (MRI) were first used in Canada at the MNI. Working under the same roof, the Neuro’s scientists and physicians made discoveries that drew world attention. Penfield’s technique for epilepsy neurosurgery became known as the Montreal procedure. K.A.C. Elliott identified γ-aminobutyric acid (GABA) as the first inhibitory neurotransmitter. Brenda Milner revealed new aspects of brain function and ushered in the field of neuropsychology as a result of her groundbreaking study of the most famous neuroscience patient of the 20th century, H.M., who had anterograde amnesia and was unable to form new memories. In 2007, the Canadian government recognized the innovation and work of the MNI by naming it one of seven national Centres of Excellence in Commercialization and Research.

For those with the time and the interest, here’s a link to an interview (early 2015?) with Brenda Milner (and a bonus, related second link) as part of a science podcast series (from my March 6, 2015 posting),

Dr. Wendy Suzuki, a Professor of Neural Science and Psychology in the Center for Neural Science at New York University, whose research focuses on understanding how our brains form and retain new long-term memories and the effects of aerobic exercise on memory. Her book Healthy Brain, Happy Life will be published by Harper Collins in the Spring of 2015.

  • Totally Cerebral: Untangling the Mystery of Memory: Neuroscientist Wendy Suzuki introduces us to scientists who have uncovered some of the deepest secrets about our brains. She begins by talking with experimental psychologist Brenda Milner [interviewed in her office at McGill University, Montréal, Quebéc], who in the 1950s, completely changed our understanding of the parts of the brain important for forming new long-term memories.
  • Totally Cerebral: The Man Without a Memory: Imagine never being able to form a new long term memory after the age of 27. Welcome to the life of the famous amnesic patient “HM”. Neuroscientist Suzanne Corkin studied HM for almost half a century, and gives us a glimpse of what daily life was like for him, and his tremendous contribution to our understanding of how our memories work.

Brief personal anecdote
For those who just want the science, you may want to skip this section.

About 15 years ago, I had the privilege of talking with Mary Filer, a former surgical nurse and artist in glass. Originally from Saskatchewan, she, a former member of Wilder Penfield’s surgical team, was then in her 80s living in Vancouver and still associated with Montreal Neuro, albeit as an artist rather than a surgical nurse.

Penfield had encouraged her to pursue her interest in the arts (he was an art/science aficionado) and at this point her work could be seen many places throughout the world and, if memory serves, she had just been asked to go MNI for the unveiling of one of her latest pieces.

Her husband, then in his 90s, had founded the School of Architecture at McGill University. This couple had known all the ‘movers and shakers’ in Montreal society for decades and retired to Vancouver where their home was in a former chocolate factory.

It was one of those conversations, you just don’t forget.

More about ‘open science’ at Montreal Neuro

Brian Owens’ Jan. 21, 2016 article for Science Magazine offers some insight into the reason for the move to ‘open science’,

Guy Rouleau, the director of McGill University’s Montreal Neurological Institute (MNI) and Hospital in Canada, is frustrated with how slowly neuroscience research translates into treatments. “We’re doing a really shitty job,” he says. “It’s not because we’re not trying; it has to do with the complexity of the problem.”

So he and his colleagues at the renowned institute decided to try a radical solution. Starting this year, any work done there will conform to the principles of the “open-
science” movement—all results and data will be made freely available at the time of publication, for example, and the institute will not pursue patents on any of its discoveries. …

“It’s an experiment; no one has ever done this before,” he says. The intent is that neuroscience research will become more efficient if duplication is reduced and data are shared more widely and earlier. …”

After a year of consultations among the institute’s staff, pretty much everyone—about 70 principal investigators and 600 other scientific faculty and staff—has agreed to take part, Rouleau says. Over the next 6 months, individual units will hash out the details of how each will ensure that its work lives up to guiding principles for openness that the institute has developed. …

Owens’ article provides more information about implementation and issues about sharing. I encourage you to read it in its entirety.

As for getting more research to the patient, there’s a Jan. 26, 2016 Cafe Scientifique talk in Vancouver (my Jan. 22, 2016 ‘Events’ posting; scroll down about 40% of the way) regarding that issue although there’s no hint that the speakers will be discussing ‘open science’.

A nanoparticle ‘printing press’

This research comes from Montréal, Canada via a Jan. 7, 2016 McGill University news release (also on EurekAlert*),

Gold nanoparticles have unusual optical, electronic and chemical properties, which scientists are seeking to put to use in a range of new technologies, from nanoelectronics to cancer treatments.

Some of the most interesting properties of nanoparticles emerge when they are brought close together – either in clusters of just a few particles or in crystals made up of millions of them. Yet particles that are just millionths of an inch in size are too small to be manipulated by conventional lab tools, so a major challenge has been finding ways to assemble these bits of gold while controlling the three-dimensional shape of their arrangement.

One approach that researchers have developed has been to use tiny structures made from synthetic strands of DNA to help organize nanoparticles. Since DNA strands are programmed to pair with other strands in certain patterns, scientists have attached individual strands of DNA to gold particle surfaces to create a variety of assemblies. But these hybrid gold-DNA nanostructures are intricate and expensive to generate, limiting their potential for use in practical materials. The process is similar, in a sense, to producing books by hand.

Enter the nanoparticle equivalent of the printing press. It’s efficient, re-usable and carries more information than previously possible. In results reported online in Nature Chemistry, researchers from McGill’s Department of Chemistry outline a procedure for making a DNA [deoxyribonucleic acid] structure with a specific pattern of strands coming out of it; at the end of each strand is a chemical “sticky patch.”  When a gold nanoparticle is brought into contact to the DNA nanostructure, it sticks to the patches. The scientists then dissolve the assembly in distilled water, separating the DNA nanostructure into its component strands and leaving behind the DNA imprint on the gold nanoparticle. …

The researchers have made an illustration of their concept available,

Credit: Thomas Edwardson

Credit: Thomas Edwardson

“These encoded gold nanoparticles are unprecedented in their information content,” says senior author Hanadi Sleiman, who holds the Canada Research Chair in DNA Nanoscience. “The DNA nanostructures, for their part, can be re-used, much like stamps in an old printing press.”

The news release includes suggestions for possible future applications,

From stained glass to optoelectronics

Some of the properties of gold nanoparticles have been recognized for centuries.  Medieval artisans added gold chloride to molten glass to create the ruby-red colour in stained-glass windows – the result, as chemists figured out much later, of the light-scattering properties of tiny gold particles.

Now, the McGill researchers hope their new production technique will help pave the way for use of DNA-encoded nanoparticles in a range of cutting-edge technologies. First author Thomas Edwardson says the next step for the lab will be to investigate the properties of structures made from these new building blocks. “In much the same way that atoms combine to form complex molecules, patterned DNA gold particles can connect to neighbouring particles to form well-defined nanoparticle assemblies.”

These could be put to use in areas including optoelectronic nanodevices and biomedical sciences, the researchers say. The patterns of DNA strands could, for example, be engineered to target specific proteins on cancer cells, and thus serve to detect cancer or to selectively destroy cancer cells.

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

Transfer of molecular recognition information from DNA nanostructures to gold nanoparticles by Thomas G. W. Edwardson, Kai Lin Lau, Danny Bousmail, Christopher J. Serpell, & Hanadi F. Sleiman. Nature Chemistry (2016)  doi:10.1038/nchem.2420 Published online 04 January 2016

This paper is behind a paywall.

*’also on EurekAlert’ added on Jan. 8, 2016.

Promising new technique for controlled fabrication of nanowires

This research is the result of a collaboration between French, Italian, Australian, and Canadian researchers. From a Jan. 5, 2016 news item on *phys.org,

An international team of researchers including Professor Federico Rosei and members of his group at INRS (Institut national de la recherche scientifique) has developed a new strategy for fabricating atomically controlled carbon nanostructures used in molecular carbon-based electronics. An article just published in the prestigious journal Nature Communications presents their findings: the complete electronic structure of a conjugated organic polymer, and the influence of the substrate on its electronic properties.

A Jan. 5, 2016 INRS news release by Gisèle Bolduc, which originated the news item, indicates this is the beginning rather than an endpoint (Note: A link has been removed),

The researchers combined two procedures previously developed in Professor Rosei’s lab—molecular self-assembly and chain polymerization—to produce a network of long-range poly(para-phenylene) (PPP) nanowires on a copper (Cu) surface. Using advanced technologies such as scanning tunneling microscopy and photoelectron spectroscopy as well as theoretical models, they were able to describe the morphology and electronic structure of these nanostructures.

“We provide a complete description of the band structure and also highlight the strong interaction between the polymer and the substrate, which explains both the decreased bandgap and the metallic nature of the new chains. Even with this hybridization, the PPP bands display a quasi one-dimensional dispersion in conductive polymeric nanowires,” said Professor Federico Rosei, one of the authors of the study.

Although further research is needed to fully describe the electronic properties of these nanostructures, the polymer’s dispersion provides a spectroscopic record of the polymerization process of certain types of molecules on gold, silver, copper, and other surfaces. It’s a promising approach for similar semiconductor studies—an essential step in the development of actual devices.

The results of the study could be used in designing organic nanostructures, with significant potential applications in nanoelectronics, including photovoltaic devices, field-effect transistors, light-emitting diodes, and sensors.

About the article

This study was designed by Yannick Fagot-Revurat and Daniel Malterre of Université de Lorraine/CNRS, Federico Rosei of INRS, Josh Lipton-Duffin of the Institute for Future Environments (Australia), Giorgio Contini of the Italian National Research Council, and Dmytro F. Perepichka of McGill University. […]The researchers were generously supported by Conseil Franco-Québécois de coopération universitaire, the France–Italy International Program for Scientific Cooperation, the Natural Sciences and Engineering Research Council of Canada, Fonds québécois de recherche – Nature et technologies, and a Québec MEIE grant (in collaboration with Belgium).

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

Quasi one-dimensional band dispersion and surface metallization in long-range ordered polymeric wires by Guillaume Vasseur, Yannick Fagot-Revurat, Muriel Sicot, Bertrand Kierren, Luc Moreau, Daniel Malterre, Luis Cardenas, Gianluca Galeotti, Josh Lipton-Duffin, Federico Rosei, Marco Di Giovannantonio, Giorgio Contini, Patrick Le Fèvre, François Bertran, Liangbo Liang, Vincent Meunier, Dmitrii F. Perepichka. Nature Communications 7, Article number:  10235 doi:10.1038/ncomms10235 Published 04 January 2016

This is an open access paper.

*’ScienceDaily’ corrected to ‘phys.org’ on Tues., Jan. 5, 2016 at 1615 PST.