Tag Archives: France

Developing cortical implants for future speech neural prostheses

I’m guessing that graphene will feature in these proposed cortical implants since the project leader is a member of the Graphene Flagship’s Biomedical Technologies Work Package. (For those who don’t know, the Graphene Flagship is one of two major funding initiatives each receiving funding of 1B Euros over 10 years from the European Commission as part of their FET [Future and Emerging Technologies)] Initiative.)  A Jan. 12, 2017 news item on Nanowerk announces the new project (Note: A link has been removed),

BrainCom is a FET Proactive project, funded by the European Commission with 8.35M€ [8.3 million Euros] for the next 5 years, holding its Kick-off meeting on January 12-13 at ICN2 (Catalan Institute of Nanoscience and Nanotechnology) and the UAB [ Universitat Autònoma de Barcelona]. This project, coordinated by ICREA [Catalan Institution for Research and Advanced Studies] Research Prof. Jose A. Garrido from ICN2, will permit significant advances in understanding of cortical speech networks and the development of speech rehabilitation solutions using innovative brain-computer interfaces.

A Jan. 12, 2017 ICN2 press release, which originated the news item expands on the theme (it is a bit repetitive),

More than 5 million people worldwide suffer annually from aphasia, an extremely invalidating condition in which patients lose the ability to comprehend and formulate language after brain damage or in the course of neurodegenerative disorders. Brain-computer interfaces (BCIs), enabled by forefront technologies and materials, are a promising approach to treat patients with aphasia. The principle of BCIs is to collect neural activity at its source and decode it by means of electrodes implanted directly in the brain. However, neurorehabilitation of higher cognitive functions such as language raises serious issues. The current challenge is to design neural implants that cover sufficiently large areas of the brain to allow for reliable decoding of detailed neuronal activity distributed in various brain regions that are key for language processing.

BrainCom is a FET Proactive project funded by the European Commission with 8.35M€ for the next 5 years. This interdisciplinary initiative involves 10 partners including technologists, engineers, biologists, clinicians, and ethics experts. They aim to develop a new generation of neuroprosthetic cortical devices enabling large-scale recordings and stimulation of cortical activity to study high level cognitive functions. Ultimately, the BraimCom project will seed a novel line of knowledge and technologies aimed at developing the future generation of speech neural prostheses. It will cover different levels of the value chain: from technology and engineering to basic and language neuroscience, and from preclinical research in animals to clinical studies in humans.

This recently funded project is coordinated by ICREA Prof. Jose A. Garrido, Group Leader of the Advanced Electronic Materials and Devices Group at the Institut Català de Nanociència i Nanotecnologia (Catalan Institute of Nanoscience and Nanotechnology – ICN2) and deputy leader of the Biomedical Technologies Work Package presented last year in Barcelona by the Graphene Flagship. The BrainCom Kick-Off meeting is held on January 12-13 at ICN2 and the Universitat Autònoma de Barcelona (UAB).

Recent developments show that it is possible to record cortical signals from a small region of the motor cortex and decode them to allow tetraplegic [also known as, quadriplegic] people to activate a robotic arm to perform everyday life actions. Brain-computer interfaces have also been successfully used to help tetraplegic patients unable to speak to communicate their thoughts by selecting letters on a computer screen using non-invasive electroencephalographic (EEG) recordings. The performance of such technologies can be dramatically increased using more detailed cortical neural information.

BrainCom project proposes a radically new electrocorticography technology taking advantage of unique mechanical and electrical properties of novel nanomaterials such as graphene, 2D materials and organic semiconductors.  The consortium members will fabricate ultra-flexible cortical and intracortical implants, which will be placed right on the surface of the brain, enabling high density recording and stimulation sites over a large area. This approach will allow the parallel stimulation and decoding of cortical activity with unprecedented spatial and temporal resolution.

These technologies will help to advance the basic understanding of cortical speech networks and to develop rehabilitation solutions to restore speech using innovative brain-computer paradigms. The technology innovations developed in the project will also find applications in the study of other high cognitive functions of the brain such as learning and memory, as well as other clinical applications such as epilepsy monitoring.

The BrainCom project Consortium members are:

  • Catalan Institute of Nanoscience and Nanotechnology (ICN2) – Spain (Coordinator)
  • Institute of Microelectronics of Barcelona (CNM-IMB-CSIC) – Spain
  • University Grenoble Alpes – France
  • ARMINES/ Ecole des Mines de St. Etienne – France
  • Centre Hospitalier Universitaire de Grenoble – France
  • Multichannel Systems – Germany
  • University of Geneva – Switzerland
  • University of Oxford – United Kingdom
  • Ludwig-Maximilians-Universität München – Germany
  • Wavestone – Luxembourg

There doesn’t seem to be a website for the project but there is a BrainCom webpage on the European Commission’s CORDIS (Community Research and Development Information Service) website.

Nanotech business news from Turkey and from Northern Ireland

I have two nanotech business news bits, one from Turkey and one from Northern Ireland.

Turkey

A Turkish company has sold one of its microscopes to the US National Aeronautics and Space Administration (NASA), according to a Jan. 20, 2017 news item on dailysabah.com,

Turkish nanotechnology company Nanomanyetik has begun selling a powerful microscope to the U.S. space agency NASA, the company’s general director told Anadolu Agency on Thursday [Jan. 19, 2017].

Dr. Ahmet Oral, who also teaches physics at Middle East Technical University, said Nanomanyetik developed a microscope that is able to map surfaces on the nanometric and atomic levels, or extremely small particles.

Nanomanyetik’s foreign customers are drawn to the microscope because of its higher quality yet cheaper price compared to its competitors.

“There are almost 30 firms doing this work,” according to Oral. “Ten of them are active and we are among these active firms. Our aim is to be in the top three,” he said, adding that Nanomanyetik jumps to the head of the line because of its after-sell service.

In addition to sales to NASA, the Ankara-based firm exports the microscope to Brazil, Chile, France, Iran, Israel, Italy, Japan, Poland, South Korea and Spain.

Electronics giant Samsung is also a customer.

“Where does Samsung use this product? There are pixels in the smartphones’ displays. These pixels are getting smaller each year. Now the smallest pixel is 15X10 microns,” he said. Human hair is between 10 and 100 microns in diameter.

“They are figuring inner sides of pixels so that these pixels can operate much better. These patterns are on the nanometer level. They are using these microscopes to see the results of their works,” Oral said.

Nanomanyetik’s microscopes produces good quality, high resolution images and can even display an object’s atoms and individual DNA fibers, according to Oral.

You can find the English language version of the Nanomanyetik (NanoMagnetics Instruments) website here . For those with the language skills there is the Turkish language version, here.

Northern Ireland

A Jan. 22, 2017 news article by Dominic Coyle for The Irish Times (Note: Links have been removed) shares this business news and mention of a world first,

MOF Technologies has raised £1.5 million (€1.73 million) from London-based venture capital group Excelsa Ventures and Queen’s University Belfast’s Qubis research commercialisation group.

MOF Technologies chief executive Paschal McCloskey welcomed the Excelsa investment.

Established in part by Qubis in 2012 in partnership with inventor Prof Stuart James, MOF Technologies began life in a lab at the School of Chemistry and Chemical Engineering at Queen’s.

Its metal organic framework (MOF) technology is seen as having significant potential in areas including gas storage, carbon capture, transport, drug delivery and heat transformation. Though still in its infancy, the market is forecast to grow to £2.2 billion by 2022, the company says.

MOF Technologies last year became the first company worldwide to successfully commercialise MOFs when it agreed a deal with US fruit and vegetable storage provider Decco Worldwide to commercialise MOFs for use in a food application.

TruPick, designed by Decco and using MOF Technologies’ environmentally friendly technology, enables nanomaterials control the effects of ethylene on fruit produce so it maintains freshness in storage or transport.

MOFs are crystalline, sponge-like materials composed of two components – metal ions and organic molecules known as linkers.

“We very quickly recognised the market potential of MOFs in terms of their unmatched ability for gas storage,” said Moritz Bolle from Excelsa Ventures. “This technology will revolutionise traditional applications and open countless new opportunities for industry. We are confident MOF Technologies is the company that will lead this seismic shift in materials science.

You can find MOF Technologies here.

Drip dry housing

This piece on new construction materials does have a nanotechnology aspect although it’s not made clear exactly how nanotechnology plays a role.

From a Dec. 28, 2016 news item on phys.org (Note: A link has been removed),

The construction industry is preparing to use textiles from the clothing and footwear industries. Gore-Tex-like membranes, which are usually found in weather-proof jackets and trekking shoes, are now being studied to build breathable, water-resistant walls. Tyvek is one such synthetic textile being used as a “raincoat” for homes.

You can find out more about Tyvek here.on the Dupont website.

A Dec. 21, 2016 press release by Chiara Cecchi for Youris ((European Research Media Center), which originated the news item, proceeds with more about textile-type construction materials,

Camping tents, which have been used for ages to protect against wind, ultra-violet rays and rain, have also inspired the modern construction industry, or “buildtech sector”. This new field of research focuses on the different fibres (animal-based such as wool or silk, plant-based such as linen and cotton and synthetic such as polyester and rayon) in order to develop technical or high-performance materials, thus improving the quality of construction, especially for buildings, dams, bridges, tunnels and roads. This is due to the fibres’ mechanical properties, such as lightness, strength, and also resistance to many factors like creep, deterioration by chemicals and pollutants in the air or rain.

“Textiles play an important role in the modernisation of infrastructure and in sustainable buildings”, explains Andrea Bassi, professor at the Department of Civil and Environmental Engineering (DICA), Politecnico of Milan, “Nylon and fiberglass are mixed with traditional fibres to control thermal and acoustic insulation in walls, façades and roofs. Technological innovation in materials, which includes nanotechnologies [emphasis mine] combined with traditional textiles used in clothes, enables buildings and other constructions to be designed using textiles containing steel polyvinyl chloride (PVC) or ethylene tetrafluoroethylene (ETFE). This gives the materials new antibacterial, antifungal and antimycotic properties in addition to being antistatic, sound-absorbing and water-resistant”.

Rooflys is another example. In this case, coated black woven textiles are placed under the roof to protect roof insulation from mould. These building textiles have also been tested for fire resistance, nail sealability, water and vapour impermeability, wind and UV resistance.

Photo: Production line at the co-operative enterprise CAVAC Biomatériaux, France. Natural fibres processed into a continuous mat (biofib) – Martin Ansell, BRE CICM, University of Bath, UK

In Spain three researchers from the Technical University of Madrid (UPM) have developed a new panel made with textile waste. They claim that it can significantly enhance both the thermal and acoustic conditions of buildings, while reducing greenhouse gas emissions and the energy impact associated with the development of construction materials.

Besides textiles, innovative natural fibre composite materials are a parallel field of the research on insulators that can preserve indoor air quality. These bio-based materials, such as straw and hemp, can reduce the incidence of mould growth because they breathe. The breathability of materials refers to their ability to absorb and desorb moisture naturally”, says expert Finlay White from Modcell, who contributed to the construction of what they claim are the world’s first commercially available straw houses, “For example, highly insulated buildings with poor ventilation can build-up high levels of moisture in the air. If the moisture meets a cool surface it will condensate and producing mould, unless it is managed. Bio-based materials have the means to absorb moisture so that the risk of condensation is reduced, preventing the potential for mould growth”.

The Bristol-based green technology firm [Modcell] is collaborating with the European Isobio project, which is testing bio-based insulators which perform 20% better than conventional materials. “This would lead to a 5% total energy reduction over the lifecycle of a building”, explains Martin Ansell, from BRE Centre for Innovative Construction Materials (BRE CICM), University of Bath, UK, another partner of the project.

“Costs would also be reduced. We are evaluating the thermal and hygroscopic properties of a range of plant-derived by-products including hemp, jute, rape and straw fibres plus corn cob residues. Advanced sol-gel coatings are being deposited on these fibres to optimise these properties in order to produce highly insulating and breathable construction materials”, Ansell concludes.

You can find Modcell here.

Here’s another image, which I believe is a closeup of the processed fibre shown in the above,

Production line at the co-operative enterprise CAVAC Biomatériaux, France. Natural fibres processed into a continuous mat (biofib) – Martin Ansell, BRE CICM, University of Bath, UK [Note: This caption appears to be a copy of the caption for the previous image]

Sniffing out disease (Na-Nose)

The ‘artificial nose’ is not a newcomer to this blog. The most recent post prior to this is a March 15, 2016 piece about Disney using an artificial nose for art conservation. Today’s (Jan. 9, 2016) piece concerns itself with work from Israel and ‘sniffing out’ disease, according to a Dec. 30, 2016 news item in Sputnik News,

A team from the Israel Institute of Technology has developed a device that from a single breath can identify diseases such as multiple forms of cancer, Parkinson’s disease, and multiple sclerosis. While the machine is still in the experimental stages, it has a high degree of promise for use in non-invasive diagnoses of serious illnesses.

The international team demonstrated that a medical theory first proposed by the Greek physician Hippocrates some 2400 years ago is true, certain diseases leave a “breathprint” on the exhalations of those afflicted. The researchers created a prototype for a machine that can pick up on those diseases using the outgoing breath of a patient. The machine, called the Na-Nose, tests breath samples for the presence of trace amounts of chemicals that are indicative of 17 different illnesses.

A Dec. 22, 2016 Technion Israel Institute of Technology press release offers more detail about the work,

An international team of 56 researchers in five countries has confirmed a hypothesis first proposed by the ancient Greeks – that different diseases are characterized by different “chemical signatures” identifiable in breath samples. …

Diagnostic techniques based on breath samples have been demonstrated in the past, but until now, there has not been scientific proof of the hypothesis that different and unrelated diseases are characterized by distinct chemical breath signatures. And technologies developed to date for this type of diagnosis have been limited to detecting a small number of clinical disorders, without differentiation between unrelated diseases.

The study of more than 1,400 patients included 17 different and unrelated diseases: lung cancer, colorectal cancer, head and neck cancer, ovarian cancer, bladder cancer, prostate cancer, kidney cancer, stomach cancer, Crohn’s disease, ulcerative colitis, irritable bowel syndrome, Parkinson’s disease (two types), multiple sclerosis, pulmonary hypertension, preeclampsia and chronic kidney disease. Samples were collected between January 2011 and June 2014 from in 14 departments at 9 medical centers in 5 countries: Israel, France, the USA, Latvia and China.

The researchers tested the chemical composition of the breath samples using an accepted analytical method (mass spectrometry), which enabled accurate quantitative detection of the chemical compounds they contained. 13 chemical components were identified, in different compositions, in all 17 of the diseases.

According to Prof. Haick, “each of these diseases is characterized by a unique fingerprint, meaning a different composition of these 13 chemical components.  Just as each of us has a unique fingerprint that distinguishes us from others, each disease has a chemical signature that distinguishes it from other diseases and from a normal state of health. These odor signatures are what enables us to identify the diseases using the technology that we developed.”

With a new technology called “artificially intelligent nanoarray,” developed by Prof. Haick, the researchers were able to corroborate the clinical efficacy of the diagnostic technology. The array enables fast and inexpensive diagnosis and classification of diseases, based on “smelling” the patient’s breath, and using artificial intelligence to analyze the data obtained from the sensors. Some of the sensors are based on layers of gold nanoscale particles and others contain a random network of carbon nanotubes coated with an organic layer for sensing and identification purposes.

The study also assessed the efficiency of the artificially intelligent nanoarray in detecting and classifying various diseases using breath signatures. To verify the reliability of the system, the team also examined the effect of various factors (such as gender, age, smoking habits and geographic location) on the sample composition, and found their effect to be negligible, and without impairment on the array’s sensitivity.

“Each of the sensors responds to a wide range of exhalation components,” explain Prof. Haick and his previous Ph.D student, Dr. Morad Nakhleh, “and integration of the information provides detailed data about the unique breath signatures characteristic of the various diseases. Our system has detected and classified various diseases with an average accuracy of 86%.

This is a new and promising direction for diagnosis and classification of diseases, which is characterized not only by considerable accuracy but also by low cost, low electricity consumption, miniaturization, comfort and the possibility of repeating the test easily.”

“Breath is an excellent raw material for diagnosis,” said Prof. Haick. “It is available without the need for invasive and unpleasant procedures, it’s not dangerous, and you can sample it again and again if necessary.”

Here’s a schematic of the study, which the researchers have made available,

Diagram: A schematic view of the study. Two breath samples were taken from each subject, one was sent for chemical mapping using mass spectrometry, and the other was analyzed in the new system, which produced a clinical diagnosis based on the chemical fingerprint of the breath sample. Courtesy: Tech;nion

There is also a video, which covers much of the same ground as the press release but also includes information about the possible use of the Na-Nose technology in the European Union’s SniffPhone project,

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

Diagnosis and Classification of 17 Diseases from 1404 Subjects via Pattern Analysis of Exhaled Molecules by Morad K. Nakhleh, Haitham Amal, Raneen Jeries, Yoav Y. Broza, Manal Aboud, Alaa Gharra, Hodaya Ivgi, Salam Khatib, Shifaa Badarneh, Lior Har-Shai, Lea Glass-Marmor, Izabella Lejbkowicz, Ariel Miller, Samih Badarny, Raz Winer, John Finberg, Sylvia Cohen-Kaminsky, Frédéric Perros, David Montani, Barbara Girerd, Gilles Garcia, Gérald Simonneau, Farid Nakhoul, Shira Baram, Raed Salim, Marwan Hakim, Maayan Gruber, Ohad Ronen, Tal Marshak, Ilana Doweck, Ofer Nativ, Zaher Bahouth, Da-you Shi, Wei Zhang, Qing-ling Hua, Yue-yin Pan, Li Tao, Hu Liu, Amir Karban, Eduard Koifman, Tova Rainis, Roberts Skapars, Armands Sivins, Guntis Ancans, Inta Liepniece-Karele, Ilze Kikuste, Ieva Lasina, Ivars Tolmanis, Douglas Johnson, Stuart Z. Millstone, Jennifer Fulton, John W. Wells, Larry H. Wilf, Marc Humbert, Marcis Leja, Nir Peled, and Hossam Haick. ACS Nano, Article ASAP DOI: 10.1021/acsnano.6b04930 Publication Date (Web): December 21, 2016

Copyright © 2017 American Chemical Society

This paper appears to be open access.

As for SniffPhone, they’re hoping that Na-Nose or something like it will allow them to modify smartphones in a way that will allow diseases to be detected.

I can’t help wondering who will own the data if your smartphone detects a disease. If you think that’s an idle question, here’s an excerpt from Sue Halpern’s Dec. 22, 2016 review of two books (“Weapons of Math Destruction: How Big Data Increases Inequality and Threatens Democracy” by Cathy O’Neil and “Virtual Competition: The Promise and Perils of the Algorithm-Driven Economy” by Ariel Ezrachi and Maurice E. Stucke) for the New York Times Review of Books,

We give our data away. We give it away in drips and drops, not thinking that data brokers will collect it and sell it, let alone that it will be used against us. There are now private, unregulated DNA databases culled, in part, from DNA samples people supply to genealogical websites in pursuit of their ancestry. These samples are available online to be compared with crime scene DNA without a warrant or court order. (Police are also amassing their own DNA databases by swabbing cheeks during routine stops.) In the estimation of the Electronic Frontier Foundation, this will make it more likely that people will be implicated in crimes they did not commit.

Or consider the data from fitness trackers, like Fitbit. As reported in The Intercept:

During a 2013 FTC panel on “Connected Health and Fitness,” University of Colorado law professor Scott Peppet said, “I can paint an incredibly detailed and rich picture of who you are based on your Fitbit data,” adding, “That data is so high quality that I can do things like price insurance premiums or I could probably evaluate your credit score incredibly accurately.”

Halpern’s piece is well worth reading in its entirety.

Testing ‘smart’ antibacterial surfaces and eating haute cuisine in space

Housekeeping in space, eh? This seems to be a French initiative. From a Nov. 15, 2016 news item on Nanowerk,

Leti [Laboratoire d’électronique des technologies de l’information (LETI)], an institute of CEA [French Alternative Energies and Atomic Energy Commission or Commissariat a l’Energie Atomique (CEA)] Tech, and three French partners are collaborating in a “house-cleaning” project aboard the International Space Station that will investigate antibacterial properties of new materials in a zero-gravity environment to see if they can improve and simplify cleaning inside spacecraft.

The Matiss experiment, as part of the Proxima Mission sponsored by France’s CNES space agency [Centre national d’études spatiales (CNES); National Centre for Space Studies (CNES)], is based on four identical plaques that European Space Agency (ESA) astronaut Thomas Pesquet, the 10th French citizen to go into space, will take with him and install when he joins the space station in November for a six-month mission. The plaques will be in the European Columbus laboratory in the space station for at least three months, and Pesquet will bring them back to earth for analysis at the conclusion of his mission.

A November 15, 2016 CEA-LETI press release on Business Wire (you may also download it from here), which originated the news item, describes the proposed experiments in more detail,

Leti, in collaboration with the ENS de Lyon, CNRS, the French company Saint Gobain and CNES, selected five advanced materials that could stop bacteria from settling and growing on “smart” surfaces. A sixth material, made of glass, will be used as control material.

The experiment will test the new smart surfaces in a gravity-free, enclosed environment. These surfaces are called “smart” because of their ability to provide an appropriate response to a given stimulus. For example, they may repel bacteria, prevent them from growing on the surface, or create their own biofilms that protect them from the bacteria.

The materials are a mix of advanced technology – from self-assembly monolayers and green polymers to ceramic polymers and water-repellent hybrid silica. By responding protectively to air-borne bacteria they become easier to clean and more hygienic. The experiment will determine which one is most effective and could lead to antibacterial surfaces on elevator buttons and bars in mass-transit cars, for example.

“Leveraging its unique chemistry platform, Leti has been developing gas, liquid and supercritical-phase-collective processes of surface functionalization for more than 10 years,” said Guillaume Nonglaton, Leti’s project manager for surface chemistry for biology and health-care applications. “Three Leti-developed surfaces will be part of the space-station experiment: a fluorinated thin layer, an organic silica and a biocompatible polymer. They were chosen for their hydrophobicity, or lack of attraction properties, their level of reproducibility and their rapid integration within Pesquet’s six-month mission.”

Now, for Haute Cusine

Pesquet is bringing meals from top French chefs Alain Ducasse and Thierry Marx for delectation. The menu includes beef tongue with truffled foie gras and duck breast confit. Here’s more from a Nov. 17, 2016 article by Thibault Marchand (Agence France Presse) ong phys.org,

“We will have food prepared by a Michelin-starred chef at the station. We have food for the big feasts: for Christmas, New Year’s and birthdays. We’ll have two birthdays, mine and Peggy’s,” said the Frenchman, who is also taking a saxophone up with him.

French space rookie Thomas Pesquet, 38, will lift off from the Baikonur cosmodrome in Kazakhstan with veteran US and Russian colleagues Peggy Whitson and Oleg Novitsky, for a six-month mission to the ISS.

Bon appétit! By the way, this is not the first time astronauts have been treated to haute cuisine (see a Dec. 2, 2006 article on the BBC [British Broadcasting Corporation] website.)

The launch

Mark Garcia’s Nov. 17, 2016 posting on one of the NASA (US National Aeronautics and Space Administration) blogs describes this latest launch into space,

The Soyuz MS-03 launched from the Baikonur Cosmodrome in Kazakhstan to the International Space Station at 3:20 p.m. EST Thursday, Nov. 17 (2:20 a.m. Baikonur time, Nov. 18). At the time of launch, the space station was flying about 250 miles over the south Atlantic east of Argentina. NASA astronaut Peggy Whitson, Oleg Novitskiy of Roscosmos and Thomas Pesquet of ESA (European Space Agency) are now safely in orbit.

Over the next two days, the trio will orbit the Earth for approximately two days before docking to the space station’s Rassvet module, at 5:01 p.m. on Saturday, Nov. 19. NASA TV coverage of the docking will begin at 4:15 p.m. Saturday.

Garcia’s post gives you details about how to access more information about the mission. The European Space Agency also offers more information as does Thomas Pesquet on his website.

A computer that intuitively predicts a molecule’s chemical properties

First, we have emotional artificial intelligence from MIT (Massachusetts Institute of Technology) with their Kismet [emotive AI] project and now we have intuitive computers according to an Oct. 14, 2016 news item on Nanowerk,

Scientists from Moscow Institute of Physics and Technology (MIPT)’s Research Center for Molecular Mechanisms of Aging and Age-Related Diseases together with Inria research center, Grenoble, France have developed a software package called Knodle to determine an atom’s hybridization, bond orders and functional groups’ annotation in molecules. The program streamlines one of the stages of developing new drugs.

An Oct. 14, 2016 Moscow Institute of Physics and Technology press release (also on EurekAlert), which originated the news item, expands on the theme,

Imagine that you were to develop a new drug. Designing a drug with predetermined properties is called drug-design. Once a drug has entered the human body, it needs to take effect on the cause of a disease. On a molecular level this is a malfunction of some proteins and their encoding genes. In drug-design these are called targets. If a drug is antiviral, it must somehow prevent the incorporation of viral DNA into human DNA. In this case the target is viral protein. The structure of the incorporating protein is known, and we also even know which area is the most important – the active site. If we insert a molecular “plug” then the viral protein will not be able to incorporate itself into the human genome and the virus will die. It boils down to this: you find the “plug” – you have your drug.

But how can we find the molecules required? Researchers use an enormous database of substances for this. There are special programs capable of finding a needle in a haystack; they use quantum chemistry approximations to predict the place and force of attraction between a molecular “plug” and a protein. However, databases only store the shape of a substance; information about atom and bond states is also needed for an accurate prediction. Determining these states is what Knodle does. With the help of the new technology, the search area can be reduced from hundreds of thousands to just a hundred. These one hundred can then be tested to find drugs such as Reltagravir – which has actively been used for HIV prevention since 2011.

From science lessons at school everyone is used to seeing organic substances as letters with sticks (substance structure), knowing that in actual fact there are no sticks. Every stick is a bond between electrons which obeys the laws of quantum chemistry. In the case of one simple molecule, like the one in the diagram [diagram follows], the experienced chemist intuitively knows the hybridizations of every atom (the number of neighboring atoms which it is connected to) and after a few hours looking at reference books, he or she can reestablish all the bonds. They can do this because they have seen hundreds and hundreds of similar substances and know that if oxygen is “sticking out like this”, it almost certainly has a double bond. In their research, Maria Kadukova, a MIPT student, and Sergei Grudinin, a researcher from Inria research center located in Grenoble, France, decided to pass on this intuition to a computer by using machine learning.

Compare “A solid hollow object with a handle, opening at the top and an elongation at the side, at the end of which there is another opening” and “A vessel for the preparation of tea”. Both of them describe a teapot rather well, but the latter is simpler and more believable. The same is true for machine learning, the best algorithm for learning is the simplest. This is why the researchers chose to use a nonlinear support vector machines (SVM), a method which has proven itself in recognizing handwritten text and images. On the input it was given the positions of neighboring atoms and on the output collected hybridization.

Good learning needs a lot of examples and the scientists did this using 7605 substances with known structures and atom states. “This is the key advantage of the program we have developed, learning from a larger database gives better predictions. Knodle is now one step ahead of similar programs: it has a margin of error of 3.9%, while for the closest competitor this figure is 4.7%”, explains Maria Kadukova. And that is not the only benefit. The software package can easily be modified for a specific problem. For example, Knodle does not currently work with substances containing metals, because those kind of substances are rather rare. But if it turns out that a drug for Alzheimer’s is much more effective if it has metal, the only thing needed to adapt the program is a database with metallic substances. We are now left to wonder what new drug will be found to treat a previously incurable disease.

Scientists from MIPT's Research Center for Molecular Mechanisms of Aging and Age-Related Diseases together with Inria research center, Grenoble, France have developed a software package called Knodle to determine an atom's hybridization, bond orders and functional groups' annotation in molecules. The program streamlines one of the stages of developing new drugs. Credit: MIPT Press Office

Scientists from MIPT’s Research Center for Molecular Mechanisms of Aging and Age-Related Diseases together with Inria research center, Grenoble, France have developed a software package called Knodle to determine an atom’s hybridization, bond orders and functional groups’ annotation in molecules. The program streamlines one of the stages of developing new drugs. Credit: MIPT Press Office

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

Knodle: A Support Vector Machines-Based Automatic Perception of Organic Molecules from 3D Coordinates by Maria Kadukova and Sergei Grudinin. J. Chem. Inf. Model., 2016, 56 (8), pp 1410–1419 DOI: 10.1021/acs.jcim.5b00512 Publication Date (Web): July 13, 2016

Copyright © 2016 American Chemical Society

This paper is behind a paywall.

Phenomen: a future and emerging information technology project

A Sept. 19, 2016 news item on Nanowerk describes a new research project incorporating photonics, phononics, and radio frequency signal processing,

HENOMEN is a ground breaking project designed to harness the potential of combined phononics, photonics and radio-frequency (RF) electronic signals to lay the foundations of a new information technology. This new Project, funded though the highly competitive H2020 [the European Union’s Horizon 2020 science funding programme] FET [Future and Emerging Technologies]-Open call, joins the efforts of three leading research institutes, three internationally recognised universities and a high-tech SME. The Consortium members kick-offed the project with a meeting on Friday September 16, 2016, at the Catalan Institute of Nanoscience and Nanotechnology (ICN2), coordinated by ICREA Research Prof Dr Clivia M. Sotomayor-Torres, of the ICN2’ Phononic and Photonic Nanostructures (P2N) Group.

A Sept. 16, 2016 ICN2 press release, which originated the news item, provides more detail,

Most information is currently transported by electrical charge (electrons) and by light (photons). Phonons are the quanta of lattice vibrations with frequencies covering a wide range up to tens of THz and provide coupling to the surrounding environment. In PHENOMEN the core of the research will be focused on phonon-based signal processing to enable on-chip synchronisation and transfer information carried between optical channels by phonons.

This ambitious prospect could serve as a future scalable platform for, e.g., hybrid information processing with phonons. To achieve it, PHENOMEN proposes to build the first practical optically-driven phonon sources and detectors including the engineering of phonon lasers to deliver coherent phonons to the rest of the chip pumped by a continuous wave optical source. It brings together interdisciplinary scientific and technology oriented partners in an early-stage research towards the development of a radically new technology.

The experimental implementation of phonons as information carriers in a chip is completely novel and of a clear foundational character. It deals with interaction and manipulation of fundamental particles and their intrinsic dual wave-particle character. Thus, it can only be possible with the participation of an interdisciplinary consortium which will create knowledge in a synergetic fashion and add value in the form of new theoretical tools,  develop novel methods to manipulate coherent phonons with light and build all-optical phononic circuits enabled by optomechanics.

The H2020 FET-Open call “Novel ideas for radically new technologies” aims to support the early stages of joint science and technology research for radically new future technological possibilities. The call is entirely non-prescriptive with regards to the nature or purpose of the technologies that are envisaged and thus targets mainly the unexpected. PHENOMEN is one of the 13 funded Research & Innovation Actions and went through a selection process with a success rate (1.4%) ten times smaller than that for an ERC grant. The retained proposals are expected to foster international collaboration in a multitude of disciplines such as robotics, nanotechnology, neuroscience, information science, biology, artificial intelligence or chemistry.

The Consortium

The PHENOMEN Consortium is made up by:

  • 3 leading research institutes:
  • 3 universities with an internationally recognised track-record in their respective areas of expertise:
  • 1 industrial partner:

2016 Nobel Chemistry Prize for molecular machines

Wednesday, Oct. 5, 2016 was the day three scientists received the Nobel Prize in Chemistry for their work on molecular machines, according to an Oct. 5, 2016 news item on phys.org,

Three scientists won the Nobel Prize in chemistry on Wednesday [Oct. 5, 2016] for developing the world’s smallest machines, 1,000 times thinner than a human hair but with the potential to revolutionize computer and energy systems.

Frenchman Jean-Pierre Sauvage, Scottish-born Fraser Stoddart and Dutch scientist Bernard “Ben” Feringa share the 8 million kronor ($930,000) prize for the “design and synthesis of molecular machines,” the Royal Swedish Academy of Sciences said.

Machines at the molecular level have taken chemistry to a new dimension and “will most likely be used in the development of things such as new materials, sensors and energy storage systems,” the academy said.

Practical applications are still far away—the academy said molecular motors are at the same stage that electrical motors were in the first half of the 19th century—but the potential is huge.

Dexter Johnson in an Oct. 5, 2016 posting on his Nanoclast blog (on the IEEE [Institute of Electrical and Electronics Engineers] website) provides some insight into the matter (Note: A link has been removed),

In what seems to have come both as a shock to some of the recipients and a confirmation to all those who envision molecular nanotechnology as the true future of nanotechnology, Bernard Feringa, Jean-Pierre Sauvage, and Sir J. Fraser Stoddart have been awarded the 2016 Nobel Prize in Chemistry for their development of molecular machines.

The Nobel Prize was awarded to all three of the scientists based on their complementary work over nearly three decades. First, in 1983, Sauvage (currently at Strasbourg University in France) was able to link two ring-shaped molecules to form a chain. Then, eight years later, Stoddart, a professor at Northwestern University in Evanston, Ill., demonstrated that a molecular ring could turn on a thin molecular axle. Then, eight years after that, Feringa, a professor at the University of Groningen, in the Netherlands, built on Stoddardt’s work and fabricated a molecular rotor blade that could spin continually in the same direction.

Speaking of the Nobel committee’s selection, Donna Nelson, a chemist and president of the American Chemical Society told Scientific American: “I think this topic is going to be fabulous for science. When the Nobel Prize is given, it inspires a lot of interest in the topic by other researchers. It will also increase funding.” Nelson added that this line of research will be fascinating for kids. “They can visualize it, and imagine a nanocar. This comes at a great time, when we need to inspire the next generation of scientists.”

The Economist, which appears to be previewing an article about the 2016 Nobel prizes ahead of the print version, has this to say in its Oct. 8, 2016 article,

BIGGER is not always better. Anyone who doubts that has only to look at the explosion of computing power which has marked the past half-century. This was made possible by continual shrinkage of the components computers are made from. That success has, in turn, inspired a search for other areas where shrinkage might also yield dividends.

One such, which has been poised delicately between hype and hope since the 1990s, is nanotechnology. What people mean by this term has varied over the years—to the extent that cynics might be forgiven for wondering if it is more than just a fancy rebranding of the word “chemistry”—but nanotechnology did originally have a fairly clear definition. It was the idea that machines with moving parts could be made on a molecular scale. And in recognition of this goal Sweden’s Royal Academy of Science this week decided to award this year’s Nobel prize for chemistry to three researchers, Jean-Pierre Sauvage, Sir Fraser Stoddart and Bernard Feringa, who have never lost sight of nanotechnology’s original objective.

Optimists talk of manufacturing molecule-sized machines ranging from drug-delivery devices to miniature computers. Pessimists recall that nanotechnology is a field that has been puffed up repeatedly by both researchers and investors, only to deflate in the face of practical difficulties.

There is, though, reason to hope it will work in the end. This is because, as is often the case with human inventions, Mother Nature has got there first. One way to think of living cells is as assemblies of nanotechnological machines. For example, the enzyme that produces adenosine triphosphate (ATP)—a molecule used in almost all living cells to fuel biochemical reactions—includes a spinning molecular machine rather like Dr Feringa’s invention. This works well. The ATP generators in a human body turn out so much of the stuff that over the course of a day they create almost a body-weight’s-worth of it. Do something equivalent commercially, and the hype around nanotechnology might prove itself justified.

Congratulations to the three winners!

Graphene Canada and its second annual conference

An Aug. 31, 2016 news item on Nanotechnology Now announces Canada’s second graphene-themed conference,

The 2nd edition of Graphene & 2D Materials Canada 2016 International Conference & Exhibition (www.graphenecanadaconf.com) will take place in Montreal (Canada): 18-20 October, 2016.

– An industrial forum with focus on Graphene Commercialization (Abalonyx, Alcereco Inc, AMO GmbH, Avanzare, AzTrong Inc, Bosch GmbH, China Innovation Alliance of the Graphene Industry (CGIA), Durham University & Applied Graphene Materials, Fujitsu Laboratories Ltd., Hanwha Techwin, Haydale, IDTechEx, North Carolina Central University & Chaowei Power Ltd, NTNU&CrayoNano, Phantoms Foundation, Southeast University, The Graphene Council, University of Siegen, University of Sunderland and University of Waterloo)
– Extensive thematic workshops in parallel (Materials & Devices Characterization, Chemistry, Biosensors & Energy and Electronic Devices)
– A significant exhibition (Abalonyx, Go Foundation, Grafoid, Group NanoXplore Inc., Raymor | Nanointegris and Suragus GmbH)

As I noted in my 2015 post about Graphene Canada and its conference, the group is organized in a rather interesting fashion and I see the tradition continues, i.e., the lead organizers seem to be situated in countries other than Canada. From the Aug. 31, 2016 news item on Nanotechnology Now,

Organisers: Phantoms Foundation [located in Spain] www.phantomsnet.net
Catalan Institute of Nanoscience and Nanotechnology – ICN2 (Spain) | CEMES/CNRS (France) | GO Foundation (Canada) | Grafoid Inc (Canada) | Graphene Labs – IIT (Italy) | McGill University (Canada) | Texas Instruments (USA) | Université Catholique de Louvain (Belgium) | Université de Montreal (Canada)

You can find the conference website here.

Improving the quality of sight in artificial retinas

Researchers at France’s Centre national de la recherche scientifique (CNRS) and elsewhere have taken a step forward to improving sight derived from artificial retinas according to an Aug. 25, 2016 news item on Nanowerk (Note: A link has been removed),

A major therapeutic challenge, the retinal prostheses that have been under development during the past ten years can enable some blind subjects to perceive light signals, but the image thus restored is still far from being clear. By comparing in rodents the activity of the visual cortex generated artificially by implants against that produced by “natural sight”, scientists from CNRS, CEA [Commissariat à l’énergie atomique et aux énergies alternatives is the French Alternative Energies and Atomic Energy Commission], INSERM [Institut national de la santé et de la recherche médicale is the French National Institute of Health and Medical Research], AP-HM [Assistance Publique – Hôpitaux de Marseille] and Aix-Marseille Université identified two factors that limit the resolution of prostheses.

Based on these findings, they were able to improve the precision of prosthetic activation. These multidisciplinary efforts, published on 23 August 2016 in eLife (“Probing the functional impact of sub-retinal prosthesis”), thus open the way towards further advances in retinal prostheses that will enhance the quality of life of implanted patients.

An Aug. 24, 2015 CNRS press release, which originated the news item, expands on the theme,

A retinal prosthesis comprises three elements: a camera (inserted in the patient’s spectacles), an electronic microcircuit (which transforms data from the camera into an electrical signal) and a matrix of microscopic electrodes (implanted in the eye in contact with the retina). This prosthesis replaces the photoreceptor cells of the retina: like them, it converts visual information into electrical signals which are then transmitted to the brain via the optic nerve. It can treat blindness caused by a degeneration of retinal photoreceptors, on condition that the optical nerve has remained functional1. Equipped with these implants, patients who were totally blind can recover visual perceptions in the form of light spots, or phosphenes.  Unfortunately, at present, the light signals perceived are not clear enough to recognize faces, read or move about independently.

To understand the resolution limits of the image generated by the prosthesis, and to find ways of optimizing the system, the scientists carried out a large-scale experiment on rodents.  By combining their skills in ophthalmology and the physiology of vision, they compared the response of the visual system of rodents to both natural visual stimuli and those generated by the prosthesis.

Their work showed that the prosthesis activated the visual cortex of the rodent in the correct position and at ranges comparable to those obtained under natural conditions.  However, the extent of the activation was much too great, and its shape was much too elongated.  This deformation was due to two separate phenomena observed at the level of the electrode matrix. Firstly, the scientists observed excessive electrical diffusion: the thin layer of liquid situated between the electrode and the retina passively diffused the electrical stimulus to neighboring nerve cells. And secondly, they detected the unwanted activation of retinal fibers situated close to the cells targeted for stimulation.

Armed with these findings, the scientists were able to improve the properties of the interface between the prosthesis and retina, with the help of specialists in interface physics.  Together, they were able to generate less diffuse currents and significantly improve artificial activation, and hence the performance of the prosthesis.

This lengthy study, because of the range of parameters covered (to study the different positions, types and intensities of signals) and the surgical problems encountered (in inserting the implant and recording the images generated in the animal’s brain) has nevertheless opened the way towards making promising improvements to retinal prostheses for humans.

This work was carried out by scientists from the Institut de Neurosciences de la Timone (CNRS/AMU) and AP-HM, in collaboration with CEA-Leti and the Institut de la Vision (CNRS/Inserm/UPMC).

Artificial retinas


© F. Chavane & S. Roux.

Activation (colored circles at the level of the visual cortex) of the visual system by prosthetic stimulation (in the middle, in red, the insert shows an image of an implanted prosthesis) is greater and more elongated than the activation achieved under natural stimulation (on the left, in yellow). Using a protocol to adapt stimulation (on the right, in green), the size and shape of the activation can be controlled and are more similar to natural visual activation (yellow).


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

Probing the functional impact of sub-retinal prosthesis by Sébastien Roux, Frédéric Matonti, Florent Dupont, Louis Hoffart, Sylvain Takerkart, Serge Picaud, Pascale Pham, and Frédéric Chavane. eLife 2016;5:e12687 DOI: http://dx.doi.org/10.7554/eLife.12687 Published August 23, 2016

This paper appears to be open access.