Tag Archives: neurons

Brain-on-a-chip 2014 survey/overview

Michael Berger has written another of his Nanowerk Spotlight articles focussing on neuromorphic engineering and the concept of a brain-on-a-chip bringing it up-to-date April 2014 style.

It’s a topic he and I have been following (separately) for years. Berger’s April 4, 2014 Brain-on-a-chip Spotlight article provides a very welcome overview of the international neuromorphic engineering effort (Note: Links have been removed),

Constructing realistic simulations of the human brain is a key goal of the Human Brain Project, a massive European-led research project that commenced in 2013.

The Human Brain Project is a large-scale, scientific collaborative project, which aims to gather all existing knowledge about the human brain, build multi-scale models of the brain that integrate this knowledge and use these models to simulate the brain on supercomputers. The resulting “virtual brain” offers the prospect of a fundamentally new and improved understanding of the human brain, opening the way for better treatments for brain diseases and for novel, brain-like computing technologies.

Several years ago, another European project named FACETS (Fast Analog Computing with Emergent Transient States) completed an exhaustive study of neurons to find out exactly how they work, how they connect to each other and how the network can ‘learn’ to do new things. One of the outcomes of the project was PyNN, a simulator-independent language for building neuronal network models.

Scientists have great expectations that nanotechnologies will bring them closer to the goal of creating computer systems that can simulate and emulate the brain’s abilities for sensation, perception, action, interaction and cognition while rivaling its low power consumption and compact size – basically a brain-on-a-chip. Already, scientists are working hard on laying the foundations for what is called neuromorphic engineering – a new interdisciplinary discipline that includes nanotechnologies and whose goal is to design artificial neural systems with physical architectures similar to biological nervous systems.

Several research projects funded with millions of dollars are at work with the goal of developing brain-inspired computer architectures or virtual brains: DARPA’s SyNAPSE, the EU’s BrainScaleS (a successor to FACETS), or the Blue Brain project (one of the predecessors of the Human Brain Project) at Switzerland’s EPFL [École Polytechnique Fédérale de Lausanne].

Berger goes on to describe the raison d’être for neuromorphic engineering (attempts to mimic biological brains),

Programmable machines are limited not only by their computational capacity, but also by an architecture requiring (human-derived) algorithms to both describe and process information from their environment. In contrast, biological neural systems (e.g., brains) autonomously process information in complex environments by automatically learning relevant and probabilistically stable features and associations. Since real world systems are always many body problems with infinite combinatorial complexity, neuromorphic electronic machines would be preferable in a host of applications – but useful and practical implementations do not yet exist.

Researchers are mostly interested in emulating neural plasticity (aka synaptic plasticity), from Berger’s April 4, 2014 article,

Independent from military-inspired research like DARPA’s, nanotechnology researchers in France have developed a hybrid nanoparticle-organic transistor that can mimic the main functionalities of a synapse. This organic transistor, based on pentacene and gold nanoparticles and termed NOMFET (Nanoparticle Organic Memory Field-Effect Transistor), has opened the way to new generations of neuro-inspired computers, capable of responding in a manner similar to the nervous system  (read more: “Scientists use nanotechnology to try building computers modeled after the brain”).

One of the key components of any neuromorphic effort, and its starting point, is the design of artificial synapses. Synapses dominate the architecture of the brain and are responsible for massive parallelism, structural plasticity, and robustness of the brain. They are also crucial to biological computations that underlie perception and learning. Therefore, a compact nanoelectronic device emulating the functions and plasticity of biological synapses will be the most important building block of brain-inspired computational systems.

In 2011, a team at Stanford University demonstrates a new single element nanoscale device, based on the successfully commercialized phase change material technology, emulating the functionality and the plasticity of biological synapses. In their work, the Stanford team demonstrated a single element electronic synapse with the capability of both the modulation of the time constant and the realization of the different synaptic plasticity forms while consuming picojoule level energy for its operation (read more: “Brain-inspired computing with nanoelectronic programmable synapses”).

Berger does mention memristors but not in any great detail in this article,

Researchers have also suggested that memristor devices are capable of emulating the biological synapses with properly designed CMOS neuron components. A memristor is a two-terminal electronic device whose conductance can be precisely modulated by charge or flux through it. It has the special property that its resistance can be programmed (resistor) and subsequently remains stored (memory).

One research project already demonstrated that a memristor can connect conventional circuits and support a process that is the basis for memory and learning in biological systems (read more: “Nanotechnology’s road to artificial brains”).

You can find a number of memristor articles here including these: Memristors have always been with us from June 14, 2013; How to use a memristor to create an artificial brain from Feb. 26, 2013; Electrochemistry of memristors in a critique of the 2008 discovery from Sept. 6, 2012; and many more (type ‘memristor’ into the blog search box and you should receive many postings or alternatively, you can try ‘artificial brains’ if you want everything I have on artificial brains).

Getting back to Berger’s April 4, 2014 article, he mentions one more approach and this one stands out,

A completely different – and revolutionary – human brain model has been designed by researchers in Japan who introduced the concept of a new class of computer which does not use any circuit or logic gate. This artificial brain-building project differs from all others in the world. It does not use logic-gate based computing within the framework of Turing. The decision-making protocol is not a logical reduction of decision rather projection of frequency fractal operations in a real space, it is an engineering perspective of Gödel’s incompleteness theorem.

Berger wrote about this work in much more detail in a Feb. 10, 2014 Nanowerk Spotlight article titled: Brain jelly – design and construction of an organic, brain-like computer, (Note: Links have been removed),

In a previous Nanowerk Spotlight we reported on the concept of a full-fledged massively parallel organic computer at the nanoscale that uses extremely low power (“Will brain-like evolutionary circuit lead to intelligent computers?”). In this work, the researchers created a process of circuit evolution similar to the human brain in an organic molecular layer. This was the first time that such a brain-like ‘evolutionary’ circuit had been realized.

The research team, led by Dr. Anirban Bandyopadhyay, a senior researcher at the Advanced Nano Characterization Center at the National Institute of Materials Science (NIMS) in Tsukuba, Japan, has now finalized their human brain model and introduced the concept of a new class of computer which does not use any circuit or logic gate.

In a new open-access paper published online on January 27, 2014, in Information (“Design and Construction of a Brain-Like Computer: A New Class of Frequency-Fractal Computing Using Wireless Communication in a Supramolecular Organic, Inorganic System”), Bandyopadhyay and his team now describe the fundamental computing principle of a frequency fractal brain like computer.

“Our artificial brain-building project differs from all others in the world for several reasons,” Bandyopadhyay explains to Nanowerk. He lists the four major distinctions:
1) We do not use logic gate based computing within the framework of Turing, our decision-making protocol is not a logical reduction of decision rather projection of frequency fractal operations in a real space, it is an engineering perspective of Gödel’s incompleteness theorem.
2) We do not need to write any software, the argument and basic phase transition for decision-making, ‘if-then’ arguments and the transformation of one set of arguments into another self-assemble and expand spontaneously, the system holds an astronomically large number of ‘if’ arguments and its associative ‘then’ situations.
3) We use ‘spontaneous reply back’, via wireless communication using a unique resonance band coupling mode, not conventional antenna-receiver model, since fractal based non-radiative power management is used, the power expense is negligible.
4) We have carried out our own single DNA, single protein molecule and single brain microtubule neurophysiological study to develop our own Human brain model.

I encourage people to read Berger’s articles on this topic as they provide excellent information and links to much more. Curiously (mind you, it is easy to miss something), he does not mention James Gimzewski’s work at the University of California at Los Angeles (UCLA). Working with colleagues from the National Institute for Materials Science in Japan, Gimzewski published a paper about “two-, three-terminal WO3-x-based nanoionic devices capable of a broad range of neuromorphic and electrical functions”. You can find out more about the paper in my Dec. 24, 2012 posting titled: Synaptic electronics.

As for the ‘brain jelly’ paper, here’s a link to and a citation for it,

Design and Construction of a Brain-Like Computer: A New Class of Frequency-Fractal Computing Using Wireless Communication in a Supramolecular Organic, Inorganic System by Subrata Ghoshemail, Krishna Aswaniemail, Surabhi Singhemail, Satyajit Sahuemail, Daisuke Fujitaemail and Anirban Bandyopadhyay. Information 2014, 5(1), 28-100; doi:10.3390/info5010028

It’s an open access paper.

As for anyone who’s curious about why the US BRAIN initiative ((Brain Research through Advancing Innovative Neurotechnologies, also referred to as the Brain Activity Map Project) is not mentioned, I believe that’s because it’s focussed on biological brains exclusively at this point (you can check its Wikipedia entry to confirm).

Anirban Bandyopadhyay was last mentioned here in a January 16, 2014 posting titled: Controversial theory of consciousness confirmed (maybe) in  the context of a presentation in Amsterdam, Netherlands.

Listening to an individual brain cell using a carbon nanotube ‘harpoon’

Apparently, the prime motivation for listening to individual neurons or brain cells is to “better understand the computational complexity of the brain,” according to a June 20,  2013 news item on Azonano,

The new brain cell spear is a millimeter long, only a few nanometers wide and harnesses the superior electromechanical properties of carbon nanotubes to capture electrical signals from individual neurons.

“To our knowledge, this is the first time scientists have used carbon nanotubes to record signals from individual neurons, what we call intracellular recordings, in brain slices or intact brains of vertebrates,” said Bruce Donald, a professor of computer science and biochemistry at Duke University who helped developed the probe.

The June 19, 2013 Duke University news release by Ashley Yeager, which originated the news item, provides some insight into the current state of the art and how this new technique is an improvement,

Currently, they use two main types of electrodes, metal and glass, to record signals from brain cells. Metal electrodes record spikes from a population of brain cells and work well in live animals. Glass electrodes also measure spikes, as well as the computations individual cells perform, but are delicate and break easily.”The new carbon nanotubes combine the best features of both metal and glass electrodes. They record well both inside and outside brain cells, and they are quite flexible. Because they won’t shatter, scientists could use them to record signals from individual brain cells of live animals,” said Duke neurobiologist Michael Platt, who was not involved in the study.

This is not the first time researchers have tried to use carbon nanotubes for this purpose, from the news release,

In the past, other scientists have experimented with carbon nanotube probes. But the electrodes were thick, causing tissue damage, or they were short, limiting how far they could penetrate into brain tissue. They could not probe inside individual neurons.

To change this, Donald began working on a harpoon-like carbon-nanotube probe with Duke neurobiologist Richard Mooney five years ago. The two met during their first year at Yale in the 1976, kept in touch throughout graduate school and began meeting to talk about their research after they both came to Duke.

Mooney told Donald about his work recording brain signals from live zebra finches and mice. The work was challenging, he said, because the probes and machinery to do the studies were large and bulky on the small head of a mouse or bird.

With Donald’s expertise in nanotechnology and robotics and Mooney’s in neurobiology, the two thought they could work together to shrink the machinery and improve the probes with nano-materials.

To make the probe, graduate student Inho Yoon and Duke physicist Gleb Finkelstein used the tip of an electrochemically sharpened tungsten wire as the base and extended it with self-entangled multi-wall carbon nanotubes to create a millimeter-long rod. The scientists then sharpened the nanotubes into a tiny harpoon using a focused ion beam at North Carolina State University.

Yoon then took the nano-harpoon to Mooney’s lab and jabbed it into slices of mouse brain tissue and then into the brains of anesthetized mice. The results show that the probe transmits brain signals as well as, and sometimes better than, conventional glass electrodes and is less likely to break off in the tissue. The new probe also penetrates individual neurons, recording the signals of a single cell rather than the nearest population of them.

Based on the results, the team has applied for a patent on the nano-harpoon.  Platt said scientists might use the probes in a range of applications, from basic science to human brain-computer interfaces and brain prostheses.

Donald said the new probe makes advances in those directions, but the insulation layers, electrical recording abilities and geometry of the device still need improvement.

The research paper is available in the open access journal PLoS ONE,

Intracellular Neural Recording with Pure Carbon Nanotube Probes by Inho Yoon, Kosuke Hamaguchi, Ivan V. Borzenets, Gleb Finkelstein, Richard Mooney, and Bruce R. Donald. 2013. PLOS ONE. DOI: 10.1371/journal.pone.0065715

As for calling this a ‘harpoon’, these carbon nanotube probes really do resemble harpoons,

This image, taken with a scanning electron microscope, shows a new brain electrode that tapers to a point as thick as a single carbon nanotube. Credit: Inho Yoon and Bruce Donald, Duke.  [downloaded from http://today.duke.edu/2013/06/brainharpoon]

This image, taken with a scanning electron microscope, shows a new brain electrode that tapers to a point as thick as a single carbon nanotube. Credit: Inho Yoon and Bruce Donald, Duke. [downloaded from http://today.duke.edu/2013/06/brainharpoon]

You can compare it to this harpoon from The Specialists Prop House, Traditional harpoon page,

[downloaded from The Specialists Prop House, Traditional harpoon page, http://thespecialistsltd.com/traditional-harpoon]

[downloaded from The Specialists Prop House, Traditional harpoon page, http://thespecialistsltd.com/traditional-harpoon]

I have written about some of the neuroscience work coming out of Duke University in the past, e.g., my March 4, 2013 posting about Miguel Nicolelis’ work on brain-to-brain communication.

Memristors and dogs

They’ve managed to recreate Pavlov’s classic experiment with dogs and feeding bells using an electronic circuit and teaching it to respond to a stimulus just as the dogs learned to respond. From the May 8, 2012 news item on Science Daily,

The bell rings and the dog starts drooling. Such a reaction was part of studies performed by Ivan Pavlov, a famous Russian psychologist and physiologist and winner of the Nobel Prize for Physiology and Medicine in 1904. His experiment, nowadays known as “Pavlov’s Dog,” is ever since considered as a milestone for implicit learning processes. By using specific electronic components scientists form the Technical Faculty and the Memory Research at the Kiel University together with the Forschungszentrum Jülich were now able to mimic the behavior of Pavlov`s dog.

I found this image on the May 8, 2012 news release webpage at the University of Kiel (Germany) website,

The experiment called “Pavlov’s Dog” shows that acoustic stimulations can cause physical reactions. Scientists of Kiel University redesigned this mental learning process. Source: Kohlstedt

Also from the May 8, 2012 news release on the University of Kiel website,

“We used memristive devices in order to mimic the associative behaviour of Pavlov’s dog in form of an electronic circuit”, explains Professor Hermann Kohlstedt, head of the working group Nanoelectronics at the University of Kiel.

Memristors are a class of electronic circuit elements which have only been available to scientists in an adequate quality for a few years. They exhibit a memory characteristic in form of hysteretic current-voltage curves consisting of high and low resistance branches. In dependence on the prior charge flow through the device these resistances can vary. Scientists try to use this memory effect in order to create networks that are similar to neuronal connections between synapses. “In the long term, our goal is to copy the synaptic plasticity onto electronic circuits. We might even be able to recreate cognitive skills electronically”, says Kohlstedt. The collaborating scientific working groups in Kiel and Jülich have taken a small step toward this goal.

The project set-up consisted of the following: two electrical impulses were linked via a memristive device to a comparator. The two pulses represent the food and the bell in Pavlov’s experiment. A comparator is a device that compares two voltages or currents and generates an output when a given level has been reached. In this case, it produces the output signal (representing saliva) when the threshold value is reached. In addition, the memristive element also has a threshold voltage that is defined by physical and chemical mechanisms in the nano-electronic device. Below this threshold value the memristive device behaves like any ordinary linear resistor. However, when the threshold value is exceeded, a hysteretic (changed) current-voltage characteristic will appear.

“During the experimental investigation, the food for the dog (electrical impulse 1) resulted in an output signal of the comparator, which could be defined as salivation. Unlike to impulse 1, the ring of the bell (electrical impulse 2) was set in such a way that the compartor’s output stayed unaffected – meaning no salivation”, describes Dr. Martin Ziegler, scientist at the Kiel University and the first-author of the publication. After applying both impulses simultaneously to the memristive device, the threshold value was exceeded. The working group had activated the memristive memory function. Multiple repetitions led to an associative learning process within the circuit – similar to Pavlov’s dogs. “From this moment on, we had only to apply electrical impulse 2 (bell) and the comparator generated an output signal, equivalent to salivation”, says Ziegler and is very pleased with these results. Electrical impulse 1 (feed) triggers the same reaction as it did before the learning. Hence, the electric circuit shows a behaviour that is termed classical conditioning in the field of psychology. Beyond that, the scientists were able to prove that the electrical circuit is able to unlearn a particular behaviour if both impulses were not longer applied simultaneously.

My most recent posting (and I have many) on memristors is from April 19, 2012 where I mentioned an artificial synapse developed with them at the University of Michigan and also noted that HP Labs has claimed it will be releasing ‘memristor-based’ products in2013.

The May 8, 2012 news item on Science Daily includes the full citation for the team’s paper and a link to it (the paper is behind a paywall).

Nanocellulose as scaffolding for nerve cells

Swedish scientists have announced success with growing nerve cells using nanocellulose as the scaffolding. From the March 19, 2012 news item on Naowerk,

Researchers from Chalmers and the University of Gothenburg have shown that nanocellulose stimulates the formation of neural networks. This is the first step toward creating a three-dimensional model of the brain. Such a model could elevate brain research to totally new levels, with regard to Alzheimer’s disease and Parkinson’s disease, for example.

“This has been a great challenge,” says Paul Gatenholm, Professor of Biopolymer Technology at Chalmers.?Until recently the cells were dying after a while, since we weren’t able to get them to adhere to the scaffold. But after many experiments we discovered a method to get them to attach to the scaffold by making it more positively charged. Now we have a stable method for cultivating nerve cells on nanocellulose.”

When the nerve cells finally attached to the scaffold they began to develop and generate contacts with one another, so-called synapses. A neural network of hundreds of cells was produced. The researchers can now use electrical impulses and chemical signal substances to generate nerve impulses, that spread through the network in much the same way as they do in the brain. They can also study how nerve cells react with other molecules, such as pharmaceuticals.

I found the original March 19, 2012 press release  and an image on the University of Chalmers website,

Nerve cells growing on a three-dimensional nanocellulose scaffold. One of the applications the research group would like to study is destruction of synapses between nerve cells, which is one of the earliest signs of Alzheimer’s disease. Synapses are the connections between nerve cells. In the image, the functioning synapses are yellow and the red spots show where synapses have been destroyed. Illustration: Philip Krantz, Chalmers

This latest research from Gatenholm and his team will be presented at the American Chemical Society annual meeting in San Diego, March 25, 2012.

The research team from Chalmers University and its partners are working on other applications for nanocellulose including one for artificial ears. From the Chalmers University Jan. 22, 2012 press release,

As the first group in the world, researchers from Chalmers will build up body parts using nanocellulose and the body’s own cells. Funding will be from the European network for nanomedicine, EuroNanoMed.

Professor Paul Gatenholm at Chalmers is leading and co-ordinating this European research programme, which will construct an outer ear using nanocellulose and a mixture of the patient’s own cartilage cells and stem cells.

Previously, Paul Gatenholm and his colleagues succeeded, in close co-operation with Sahlgrenska University Hospital, in developing artificial blood vessels using nanocellulose, where small bacteria “spin” the cellulose.

In the new programme , the researchers will build up a three-dimensional nanocellulose network that is an exact copy of the patient’s healthy outer ear and construct an exact mirror image of the ear. It will have sufficient mechanical stability for it to be used as a bioreactor, which means that the patient’s own cartilage and stem cells can be cultivated directly inside the body or on the patient, in this case on the head. [Presumably the patient has one ear that is healthy and the researchers are attempting to repair or replace an unhealthy ear on the other side of the head.]

As for the Swedish perspective on nanocellulose (from the 2010 press release),

Cellulose-based material is of strategic significance to Sweden and materials science is one of Chalmers eight areas of advance. Biopolymers are highly interesting as they are renewable and could be of major significance in the development of future materials.

Further research into using the forest as a resource for new materials is continuing at Chalmers within the new research programme that is being built up with different research groups at Chalmers and Swerea – IVF. The programme is part of the Wallenberg Wood Science Center, which is being run jointly by the Royal Institute of Technology in Stockholm and Chalmers under the leadership of Professor Lars Berglund at the Royal Institute of Technology.

The 2012 press release announcing the work on nerve cells had this about nanocellulose,

Nanocellulose is a material that consists of nanosized cellulose fibers. Typical dimensions are widths of 5 to 20 nanometers and lengths of up to 2,000 nanometers. Nanocellulose can be produced by bacteria that spin a close-meshed structure of cellulose fibers. It can also be isolated from wood pulp through processing in a high-pressure homogenizer.

I last wrote about the Swedes and nanocellulose in a Feb. 15, 2012 posting about recovering it (nanocellulose) from wood-based sludge.

As for anyone interested in the Canadian scene, there is an article by David Manly in the Jan.-Feb. 2012 issue of Canadian Biomass Magazine that focuses largely on economic impacts and value-added products as they pertain to nanocellulose manufacturing production in Canada. You can also search this blog as I have covered the nanocellulose story in Canada and elsewhere as extensively as I can.

Carbon nanotubes, neurons, and spinal cords (plus a brief plug for the Isabelle Stengers talk being livestreamed today)

Mention scaffolds, nanotechnology, and cells and I think of tissue engineering. Michael Berger’s March 2, 2012 Spotlight essay, Exploring the complexity of nanomaterial-neural interfaces, on Nanowerk mentions all three. From the essay,

Carbon nanotubes, like the nervous cells of our brain, are excellent electrical signal conductors and can form intimate mechanical contacts with cellular membranes, thereby establishing a functional link to neuronal structures. …

Now, researchers have, for the first time, explored the impact of carbon nanotube scaffolds on multilayered neuronal networks. Up to now, all known effects of carbon nanotubes on neurons – namely their reported ability to potentiate neuronal signaling and synapses – have been described in bi-dimensional cultured networks where nanotube/neuron hybrids were developed on a monolayer of dissociated brain cells.

In their work, a team of scientists in Italy, led by professors Maurizio Prato and Laura Ballerini, used slices from the spinal cords of mice to model multilayer-tissue complexity. They interfaced these spinal segments to multi-walled carbon nanotube (MWCNT) scaffolds for weeks at a time to see whether and how the interactions at the monolayer level are translated to multilayered nerve tissues.

I found this part of the explanation a little easier to understand,

According to the team, interfacing spinal cord explants [cells removed from living tissue and cultivated in artificial media] to purified carbon nanotubes over a longer period (weeks) induces two major effects: First, the number and length of neuronal fibers outgrowing the spinal segment increases, associated with changes in growth cone activity and in fiber elastomechanical properties. And, secondly, the researchers point out that after weeks of MWCNT  interfacing, neurons located at as far as five cell layers from the substrate display an increased efficacy in synaptic responses – which could represent either an improvement or a pathological behavior – presumably mediated by ongoing plasticity driven by the neuron/MWCNT hybrids.

If this increased efficacy in synaptic responses should represent an improvement, it suggests to me that it could be helpful with spinal cord injuries at some point. The researchers themselves are not speculating that far into the future (from the Berger essay),

They [Prato and Ballerini] note that this is important because it exploits the design of artificial micro- and nanoscale devices that cooperate with neuronal network activity, thereby creating hybrid structures able to cross the barriers between artificial devices and neurons.

Taken in conjunction with today’s (March 5, 2012) earlier posting (Carbon and neural implants), it seems that there is a great deal of work being done to integrate ‘machine’ and flesh so we achieve machine/flesh. While I don’t believe that philosopher and chemist Isabelle Stengers will be addressing those specific issues in her  talk, Cosmopolitics, being livestreamed here later today (3:30 pm PST) from Halifax (Nova Scotia), she does touch on this,

Professor Stengers’ keynote address will examine sciences and the consequences of what has been called progress. Is it possible to reclaim modern practices, to have them actively taking into account what they felt entitled to ignore in the name of progress? Or else, can they learn to “think with” instead of define and judge?  [emphasis mine]

I don’t know what she means by ‘think with’ but it strikes me that it represents a significant shift of thought as it implies a relationship that is not separated (or bounded) in the ways we have traditionally observed. Defining and judging are made possible by the notion of separation (boundaries); machine and flesh have been viewed from the perspective of boundaries and separation; machine/flesh seems more like ‘thinking with’.