Biomimicry: Biologically Inspired Engineering

[rwenzori]

World's Smallest Computers Made of DNA and Other Biological Molecules Made to 'Think' Logically

Wow! Jesus can do syllogisms!

 

[Phronesis]

Nanoelectronic Transistor Combined With Biological Machine Could Lead To Better Electronics

ScienceDaily (Aug. 10, 2009) — If artificial devices could be combined with biological machines, laptops and other electronic devices could get a boost in operating efficiency.

An artist's representation of a nanobioelectronic device incorporating alamethycin biological pore. In the core of the device is a silicon nanowire (grey), covered with a lipid bilayer (blue). The bilayer incorporates bundles of alamethicin molecules (purple) that form pore channels in the membrane. Transport of protons though these pore channels changes the current through the nanowire. (Credit: Image by Scott Dougherty, LLNL)​

Lawrence Livermore National Laboratory researchers have devised a versatile hybrid platform that uses lipid-coated nanowires to build prototype bionanoelectronic devices.

Mingling biological components in electronic circuits could enhance biosensing and diagnostic tools, advance neural prosthetics such as cochlear implants, and could even increase the efficiency of future computers.

While modern communication devices rely on electric fields and currents to carry the flow of information, biological systems are much more complex. They use an arsenal of membrane receptors, channels and pumps to control signal transduction that is unmatched by even the most powerful computers. For example, conversion of sound waves into nerve impulses is a very complicated process, yet the human ear has no trouble performing it.

“Electronic circuits that use these complex biological components could become much more efficient,” said Aleksandr Noy, the LLNL lead scientist on the project.

While earlier research has attempted to integrate biological systems with microelectronics, none have gotten to the point of seamless material-level incorporation.

“But with the creation of even smaller nanomaterials that are comparable to the size of biological molecules, we can integrate the systems at an even more localized level,” Noy said.

To create the bionanoelectronic platform the LLNL team turned to lipid membranes, which are ubiquitous in biological cells. These membranes form a stable, self-healing,and virtually impenetrable barrier to ions and small molecules.

“That's not to mention that these lipid membranes also can house an unlimited number of protein machines that perform a large number of critical recognition, transport and signal transduction functions in the cell,” said Nipun Misra, a UC Berkeley graduate student and a co-author on the paper.

Julio Martinez, a UC Davis graduate student and another co-author added: “Besides some preliminary work, using lipid membranes in nanoelectronic devices remains virtually untapped.”

The researchers incorporated lipid bilayer membranes into silicon nanowire transistors by covering the nanowire with a continuous lipid bilayer shell that forms a barrier between the nanowire surface and solution species.

“This 'shielded wire' configuration allows us to use membrane pores as the only pathway for the ions to reach the nanowire,” Noy said. “This is how we can use the nanowire device to monitor specific transport and also to control the membrane protein.”

The team showed that by changing the gate voltage of the device, they can open and close the membrane pore electronically.

 

[Phronesis]

Nice article about the challenges scientists in synthetic (aka design) biology find while designing metalloproteins using unnatural amino acids.

Design of functional metalloproteins
NATURE|Vol 460|13 August 2009|doi:10.1038/nature08304

Metalloproteins catalyse some of the most complex and important processes in nature, such as photosynthesis and water oxidation. An ultimate test of our knowledge of how metalloproteins work is todesign new metalloproteins. Doing so not only can reveal hidden structural features that may be missing from studies of native metalloproteins and their variants, but also can result in new metalloenzymes for biotechnological and pharmaceutical applications. Although it is much more challenging to design metalloproteins than non-metalloproteins, much progress has been made in this area, particularly in functional design, owing to recent advances in areas such as computational and structural biology.

Lessons learned and future challenges

The majority of the successes in the field of metalloprotein design are derived from the construction of a geometrically correct, sterically compatible primary coordination sphere sufficient to reproduce the structure and function of a desired metal centre, such as a bis-histidine haem or His2Cys2 tetrahedral Zn(ii) site. However, many metal-binding sites in proteins, such as the type-1 copper and CuA centres, are not necessarily in their preferred metal-ion geometric states. Therefore, one future challenge is to design metal sites and metal clusters with unique geometric requirements. Other challenges include the design of metal sites at the interface of two or more proteins, which occur often in proteins but have not been designed until recently39,40, and the design of metal-binding sites from membrane proteins, which has also been rarely achieved. A greater challenge is the design of protein metal-binding sites requiring helpers called metallochaperones. Consideration of the interactions between metal ions and protein hosts is not enough to confer function, making their interactions with metallochaperones necessary in the design process. In addition to metal-binding- site design, functional metalloproteins also require the design of a substrate-binding site for catalysis. A higher level of complexity involves coupling the redox reaction of a designed metal-binding site to proton transfer, conformational change or charge separation.

Agents (aka scientists) designing new lifeforms.

 

[Phronesis]

Folded biomimetic oligomers for enantioselective catalysis

Many naturally occurring biopolymers (i.e., proteins, RNA, DNA) owe their unique properties to their well-defined three-dimensional structures. These attributes have inspired the design and synthesis of folded architectures with functions ranging from molecular recognition to asymmetric catalysis. Among these are synthetic oligomeric peptide (“foldamer”) mimics, which can display conformational ordering at short chain lengths. Foldamers, however, have not been explored as platforms for asymmetric catalysis. This report describes a library of synthetic helical “peptoid” oligomers that enable enantioselective transformations at an embedded achiral catalytic center, as illustrated by the oxidative kinetic resolution of 1-phenylethanol. In an investigation aimed at elucidating key structure–function relationships, we have discovered that the enantioselectivity of the catalytic peptoids depends on the handedness of the asymmetric environment derived from the helical scaffold, the position of the catalytic center along the peptoid backbone, and the degree of conformational ordering of the peptoid scaffold. The transfer of chiral information from a folded scaffold can enable the use of a diverse assortment of embedded achiral catalytic centers, promising a generation of synthetic foldamer catalysts for enantioselective transformations that can be performed under a broad range of reaction environments.

 

[Phronesis]

Ancient Diatoms Lead To New Technology For Solar Energy

ScienceDaily (Apr. 9, 2009) — Engineers at Oregon State University have discovered a way to use an ancient life form to create one of the newest technologies for solar energy, in systems that may be surprisingly simple to build compared to existing silicon-based solar cells.

The secret: diatoms.

These tiny, single-celled marine life forms have existed for at least 100 million years and are the basis for much of the life in the oceans, but they also have rigid shells that can be used to create order in a natural way at the extraordinarily small level of nanotechnology.

By using biology instead of conventional semiconductor manufacturing approaches, researchers at OSU and Portland State University have created a new way to make "dye-sensitized" solar cells, in which photons bounce around like they were in a pinball machine, striking these dyes and producing electricity. This technology may be slightly more expensive than some existing approaches to make dye-sensitized solar cells, but can potentially triple the electrical output.

"Most existing solar cell technology is based on silicon and is nearing the limits of what we may be able to accomplish with that," said Greg Rorrer, an OSU professor of chemical engineering. "There's an enormous opportunity to develop different types of solar energy technology, and it's likely that several forms will ultimately all find uses, depending on the situation."

Dye-sensitized technology, for instance, uses environmentally benign materials and works well in lower light conditions. And the new findings offer advances in manufacturing simplicity and efficiency.

"Dye-sensitized solar cells already exist," Rorrer said. "What's different in our approach are the steps we take to make these devices, and the potential improvements they offer."

The new system is based on living diatoms, which are extremely small, single-celled algae, which already have shells with the nanostructure that is needed. They are allowed to settle on a transparent conductive glass surface, and then the living organic material is removed, leaving behind the tiny skeletons of the diatoms to form a template.

A biological agent is then used to precipitate soluble titanium into very tiny "nanoparticles" of titanium dioxide, creating a thin film that acts as the semiconductor for the dye-sensitized solar cell device. Steps that had been difficult to accomplish with conventional methods have been made easy through the use of these natural biological systems, using simple and inexpensive materials.

"Conventional thin-film, photo-synthesizing dyes also take photons from sunlight and transfer it to titanium dioxide, creating electricity," Rorrer said. "But in this system the photons bounce around more inside the pores of the diatom shell, making it more efficient."

The physics of this process, Rorrer said, are not fully understood – but it clearly works. More so than materials in a simple flat layer, the tiny holes in diatom shells appear to increase the interaction between photons and the dye to promote the conversion of light to electricity, and improve energy production in the process.

The insertion of nanoscale tinanium oxide layers into the diatom shell has been reported in ACS Nano, a publication of the American Chemical Society, and the Journal of Materials Research, a publication of the Materials Research Society. The integration of this material into a dye-sensitized solar cell device was also recently described at the fourth annual Greener Nanoscience Conference.

The work is supported by the National Science Foundation and the Safer Nanomaterials and Nanomanufacturing Initiative, a part of the Oregon Nanoscience and Microtechnologies Institute.

Diatoms are ancient, microscopic organisms that are found in the fossil record as far back as the time of the dinosaurs. They are a key part of the marine food chain and help cycle carbon dioxide from the atmosphere.

But in recent years their tiny, silica shells have attracted increasing attention as a way to create structure at the nano level. Nature is the engineer, not high tech tools. This is providing a more efficient, less costly way to produce some of the most advanced materials in the world

.

 

[Balstrome]

Does anyone actually read all this spam ? I don't welcome to my ignore list.

 

[rwenzori]

Does anyone actually read all this spam ?

Not that I know of.

 

[w1z4rd]

Some real biologically inspired human engineering (this time with evolving robots and natural selection!)
http://mybroadband.co.za/vb/showthread.php?t=157742

*Summon*

 

[Phronesis]

Some real biologically inspired human engineering (this time with evolving robots and natural selection!)
http://mybroadband.co.za/vb/showthread.php?t=157742

*Summon*

Nice link . Thanks .


Scientists design...

Researchers have developed an artificial version of the Golgi organelle, shown in this illustration of a cell cross-section. The device could lead to a better method for producing heparin, they say. (Credit: The American Chemical Society)​

'Artificial Golgi' May Provide New Insight Into Key Cell Structure

ScienceDaily (Aug. 3, 2009) — Scientists in New York and North Carolina are reporting assembly of the first functioning prototype of an artificial Golgi organelle. That key structure inside cells helps process and package hormones, enzymes, and other substances that allow the body to function normally. The lab-on-a-chip device could lead to a faster and safer method for producing heparin, the widely used anticoagulant or blood thinner, the researchers note.

The Golgi organelle is named for Camillo Golgi, the Italian scientist and Nobel Prize winner who discovered the structure in 1898. It is composed of a network of sacs, stacked like a deck of playing cards, located inside cells. In the new study, Robert Linhardt and colleagues point out that Golgi bodies are one of the most poorly understood organelles (specialized structures inside cells) in the human body. Scientists already know, however, that the organelles play a key role in producing heparin, a substance that helps prevent clotting.

The researchers describe development of a prototype lab-on-a-chip device that closely mimics the natural Golgi apparatus. They showed in lab tests that the device could quickly and efficiently produce heparin. It did so in an assembly-line fashion using a combination of enzymes, sugars and other raw materials and demonstrated that the substance has a strong clot-fighting potential. In the future, an "artificial Golgi" could lead to a faster and safer method for producing heparin, the scientists suggest.

 

[DJ...]

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[Phronesis]

Buy shoes. Nike, Adidas, Puma best prices in China - http://www.crunchgear.com/wp-content/photos/spam_1.jpg

Another troll from the pointless posse, posting more pointless.... spam. Guess that is what you get for being an expert in derailing and nothing else... Anyway...

 

[Phronesis]

DNA is not only useful for storing information, it makes pretty pictures as well...on a nanoscale.

Nanoscale Origami From DNA

ScienceDaily (Aug. 7, 2009) — Scientists at the Technische Universitaet Muenchen (TUM) and Harvard University have thrown the lid off a new toolbox for building nanoscale structures out of DNA, with complex twisting and curving shapes. In the August 7 issue of the journal Science, they report a series of experiments in which they folded DNA, origami-like, into three dimensional objects including a beachball-shaped wireframe capsule just 50 nanometers in diameter.

Scientists at the Technische Universitaet Muenchen and Harvard University have thrown the lid off a new toolbox for building nanoscale structures out of DNA, with complex twisting and curving shapes. They report a series of experiments in which they folded DNA, origami-like, into 3-D objects including a beach ball-shaped wireframe capsule just 50 nanometers in diameter. (Credit: Used by permission of H. Dietz, TUM Dept. of Physics, all rights reserved.)​

See the triangle? Look at what these guys are doing with it:

Building circuit boards using DNA scaffolding

High concentrations of triangular DNA origami binding to wide lines on a lithographically patterned surface; the inset shows individual origami structures at high resolution​

There have been a few breakthroughs in recent years that hold the promise of sustaining Moore’s Law for some time to come. These include attaching molecules to silicon and replacing copper interconnects with graphene. Now IBM are proposing a new way to pack more power and speed into computer chips by using DNA molecules as scaffolding for transistors fabricated with carbon nanotubes and silicon wires.

The new approach developed by scientists at IBM and the California Institute of Technology uses DNA molecules as scaffolding or miniature circuit boards for the precise assembly of components such as millions of carbon nanotubes, nanowires and nanoparticles, that could be deposited and self-assembled into precise patterns by sticking to the DNA molecules.

The researchers say such a technique may provide a way to reach sub-22 nm lithography on surfaces compatible with today’s semiconductor manufacturing equipment. The technique allows for DNA nanostructures such as squares, triangles and stars to be prepared with dimensions of 100-150 nm on an edge and a thickness of the width of the DNA double helix.

“The cost involved in shrinking features to improve performance is a limiting factor in keeping pace with Moore’s Law and a concern across the semiconductor industry,” said IBM researcher, Spike Narayan. “The combination of this directed self-assembly with today’s fabrication technology eventually could lead to substantial savings in the most expensive and challenging part of the chip-making process.”

The research is detailed in the paper, “Placement and orientation of DNA nanostructures on lithographically patterned surfaces,” will be published in the September issue of Nature Nanotechnology.

More pics:

Directed self-assembly... Seems like a useful design tool to make use of nature and design to get to an optimal solution.

 

[rwenzori]

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Hear hear!

 

[Phronesis]

Invasive Green Mussel May Inspire New Forms Of Wet Adhesion

ScienceDaily (Aug. 27, 2009) — The green mussel is known for being a notoriously invasive fouling species, but scientists have just discovered that it also has a very powerful form of adhesion in its foot, according to a recent article in the Journal of Biological Chemistry. The stickiness of the mussel's foot could possibly be copied to form new man-made adhesives.

The green mussel's sticky adhesiveness has the potential to help form strong bonds in wet surfaces, including teeth and bones. In addition, the adhesive could be used to repair ships that have developed cracks while at sea and must be repaired in a wet environment.

 

[Phronesis]

Interesting:

Borrowing an idea from nature could lead to technology capable of producing full-colour prints in a fraction of a second, according to South Korean engineers.

Biomimicry at its finest.
Magic ink offers full-colour printing in an instant

Many insects and birds owe their bright colours to the interaction of light with finely-patterned surface textures, rather than relying on pigments. The iridescent colours of a peacock's tail are largely a result of the interaction of light with just one biological material – melanin rods.

Engineers have long experimentedMovie Camera with replicating these so-called structural colours in synthetic materials, and now Sunghoon Kwon's team at Seoul National University in South Korea has managed it.

Their M-Ink can be used to produce any colour in the visible spectrum and could lead to a new method of cheap and fast full-colour printing, Kwon says.

 

[Avatar_5]

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I didn't lol.

I rofl'd.

 

[Phronesis]

These guys used biomolecular machines to design their own devices that efficiently sorts and transports individual molecules. The technology can be used to build portable, selective, and sensitive biosensors...

Biomolecular motor-driven molecular sorter

We have developed a novel, microfabricated, stand-alone microfluidic device that can efficiently sort and concentrate (bio-)analyte molecules by using kinesin motors and microtubules as a chemo-mechanical transduction machine. The device removes hundreds of targeted molecules per second from an analyte stream by translocating functionalized microtubules with kinesin across the stream and concentrating them at a horseshoe-shaped collector. Target biomolecule concentrations increase up to three orders of magnitude within one hour of operation.

 

[Phronesis]

Watch out, the engineering marvels in your teeth might be used in aerospace technologies...

Flying By The Skin Of Our Teeth

ScienceDaily (Sep. 6, 2009) — It's been a mystery: how can our teeth withstand such an enormous amount of pressure, over many years, when tooth enamel is only about as strong as glass? A new study by Prof. Herzl Chai of Tel Aviv University's School of Mechanical Engineering and his colleagues at the National Institute of Standards and Technology and George Washington University gives the answer.

The researchers applied varying degrees of mechanical pressure to hundreds of extracted teeth, and studied what occurred on the surface and deep inside them. The study, published in the May 5, 2009, issue of the Proceedings of the National Academy of Science, shows that it is the highly-sophisticated structure of our teeth that keeps them in one piece — and that structure holds promising clues for aerospace engineers as they build the aircraft and space vehicles of the future.

"Teeth are made from an extremely sophisticated composite material which reacts in an extraordinary way under pressure," says Prof. Chai. "Teeth exhibit graded mechanical properties and a cathedral-like geometry, and over time they develop a network of micro-cracks which help diffuse stress. This, and the tooth's built-in ability to heal the micro-cracks over time, prevents it from fracturing into large pieces when we eat hard food, like nuts."

News the aviation industry can bite into

The automotive and aviation industries already use sophisticated materials to prevent break-up on impact. For example, airplane bodies are made from composite materials — layers of glass or carbon fibers — held together by a brittle matrix.

In teeth, though, fibers aren't arranged in a grid, but are "wavy" in structure. There are hierarchies of fibers and matrices arranged in several layers, unlike the single-thickness layers used in aircrafts. Under mechanical pressure, this architecture presents no clear path for the release of stress. Therefore, "tufts" — built-in micro cracks — absorb pressure in unison to prevent splits and major fractures. As Prof. Chai puts it, tooth fractures "have a hard time deciding which way to go," making the tooth more resistant to cracking apart. Harnessing this property could lead to a new generation of much stronger composites for planes.

Prof. Chai, himself an aerospace engineer, suggests that if engineers can incorporate tooth enamel's wavy hierarchy, micro-cracking mechanism, and capacity to heal, lighter and stronger aircraft and space vehicles can be developed. And while creating a self-healing airplane is far in the future, this significant research on the composite structure of teeth can already begin to inspire aerospace engineers — and, of course, dentists.

Creating a super-smile

Dental specialists looking for new ways to engineer that picture-perfect Hollywood smile can use Dr. Chai's basic research to help invent stronger crowns, better able to withstand oral wear-and-tear. "They can create smart materials that mimic the properties found in real teeth," he says.

In natural teeth, there may not be any way to speed up the self-healing ability of tooth enamel, which the Tel Aviv University research found is accomplished by a glue-like substance that fills in micro-cracks over time. But fluoride treatments and healthy brushing habits can help to fill in the tiny cracks and keep teeth strong.

 

[Phronesis]

Hey look at those intelligently designed DNA letters. A technology that can be applied for future technological designs....

BYU Written with DNA

Using a new technology, researchers at Brigham Young University have written BYU with DNA.

The letters are so small that hundreds of thousands would fit inside the period at the end of this sentence.

Adam Woolley and co-authors Elisabeth Pound, Jeff Ashton and Hector Becerril have devised ways to fold DNA into nanoscale structures that have multiple branching points. They also describe procedures to form nanostructures of various different sizes using the method of "DNA origami." This work has potential application in forming nanoelectronic devices.

The "small, thin structures with square junctions have potential applications in nanoelectronics, addressing the need for narrow, branched features for wiring," the researchers said.

Same guys that did these? (See post #32)

 

[Phronesis]

Bio-inspired spam detection.... with the immune system as inspiration...

ALIFE Conference to reveal bio-inspired spam detection

An algorithm for spam recognition inspired by the immune system will be presented at the first European conference on Artificial Life (ALIFE XI) being held in Winchester this week.

Alaa Abi-Haidar and Luis Rocha from the Department of Informatics, Indiana University, Bloomington, USA and the Instituto Gulbenkian de Ciencia, Portugal, will present a paper entitled Adaptive Spam Detection Inspired by the Immune System on Thursday 7 August. They will describe how in the same way as the vertebrate adaptive immune system learns to distinguish harmless from harmful substances, these principles can be applied to spam detection.

In their presentation, the authors will claim that this bio-inspired spam detection algorithm based on the cross-regulation model of T-cell dynamics, is equally as competitive as state-of-the-art spam binary classifiers and provides a deeper understanding of the behaviour of T-cell cross-regulation systems.

The newly-formed Science and Engineering of Natural Systems (SENSe) group within the University of Southampton's School of Electronics and Computer Science (ECS) is to host this year’s conference, which will take place at the University of Winchester West Downs Campus, involving 250 participants and more paper presentations than ever before.

`This is a critical time for Artificial Life,' said Dr Seth Bullock at ECS, the conference chairman. `The field is on the verge of synthesising living cells, a feat that the Artificial Life community could only dream of when it started out in the late 80s.'

Keynote speakers include internationally leading experts such as Professor Stuart Kauffman, author of The Origins of Order, Professor Peter Schuster, editor-in-chief of the journal Complexity, Professor Eva Jablonka, author of Evolution in Four Dimensions (with Marion Lamb), and Professor Andrew Ellington, a leading pioneer in the new science of synthetic biology.

Professor Takashi Ikegami from the University of Tokyo will open the conference, speaking on work spanning self-organisation and autopoiesis in systems of birds, robots, children, flies, cells, and even oil droplets. The conference is unified by a focus on understanding the fundamental behavioural dynamics of embedded, embodied, evolving and adaptive systems.

No wonder scientists are increasingly taking on board computer science talk to describe biological systems.