fredag 8 juni 2012

Artificial atoms, mechanized molecules and synthetic chrystals.

Artificial atoms or Quantum dots.
Artificial atom is an object that has bound, discrete electronic states, as is the case with naturally occurring atoms. Semiconductor quantum dots are the most common example of artificial atoms, and are analogies for real atoms. Artificial atoms are made up of more than one atom, but are like single atoms in one important way: when you provide the right amount (or quanta) of energy, they will give off coloured light.

Programmable matter refers to matter which has the ability to change its physical properties (shape, density, moduli, optical properties, etc.) in a programmable fashion, based upon user input or autonomous sensing. Programmable matter is thus linked to the concept of a material which inherently has the ability to perform information processing. .
Programmable matter is a term originally coined in 1991 by Toffoli and Margolus to refer to an ensemble of fine-grained computing elements arranged in space. Their paper describes a computing substrate that is composed of fine-grained compute nodes distributed throughout space which communicate using only nearest neighbor interactions. In this context, programmable matter refers to compute models similar to cellular automata and Lattice Gas Automata. The CAM-8 architecture is an example hardware realization of this model. This function is also known as "digital referenced areas" (DRA) in some forms of self-replicating machine science.
1. The programming could be external to the material and might be achieved by the "application of light, voltage, electric or magnetic fields, etc.". For example, in this school of thought, a liquid crystal display is a form of programmable matter.
2. The individual units of the ensemble can compute and the result of their computation is a change in the ensemble's physical properties.
3.  Scale is one key differentiator between different forms of programmable matter. Nano - cm, and even bigger. At the nanoscale end of the spectrum there are a tremendous number of different bases for programmable matter, ranging from shape changing molecules to quantum dots or artificial atoms. In the micrometer to sub-millimeter range examples include claytronics, MEMS-based units, cells created using synthetic biology, and the utility fog concept.
"Simple" programmable matter see also Smart material.
 Materials that can change their properties based on some input, but do not have the ability to do complex computation by themselves.
1. The physical properties of several complex fluids can be modified by applying a current or voltage, as is the case with liquid crystals.
2.  Metamaterials are artificial composites that can be controlled to react in ways that do not occur in nature. One example developed by David Smith and then by John Pendry and David Schuri is of a material that can have its index of refraction tuned so that it can have a different index of refraction at different points in the material.
3.  Molecules that can change (mechanostereochemistry) their shape, as well as other properties, in response to external stimuli. Can be used individually or en masse, ex, molecules that can change their electrical properties as mechanized molecules,  mechanically-interlocked molecular architectures such as molecular Borromean rings, catenanes and rotaxanes utilizing molecular recognition and molecular self-assembly processes. These topologies can be employed as molecular switches and as motor-molecules, and even applied these structures in the fabrication of nanoelectronic devices and nanoelectromechanical systems (NEMS).
π–stack charachters have been applied to the DNA structure  too, as reductive  electron-transport system, and its oxidative hairpins for hole transfer through DNA. These interactions are important in base stacking of DNA nucleotides, protein folding and protein chrystal formation, template-directed synthesis, materials science, and molecular recognition, Despite intense experimental and theoretical interest, there is no unified description of the factors that contribute to pi stacking interactions. There are compelling computational evidence for the importance of direct interaction in pi stacking. It  seems that the relative contributions of electrostatics, dispersion, and direct interactions to the substituent effects seen in pi stacking interactions are highly dependent on geometry and experimental design. The chromophore has also a special role, and it has been linked to quantum biology. see Mechanisms for DNA charge transport..

Self-Reconfiguring Modular Robotics is a field of robotics in which a group of basic robot modules work together to dynamically form shapes and create behaviours suitable for many tasks. Like Programmable matter SRCMR aims to offer significant improvement to any kind of objects or system by introducing many new possibilities for example:
1. Most important is the incredible flexibility that comes from the ability to change the physical structure and behavior of a solution by changing the software that controls modules.
2. The ability to self-repair by automatically replacing a broken module will make SRCMR solution incredibly resilient.
3. Reducing the environmental foot print by reusing the same modules in many different solutions.

Claytronics,  nanoscale robots ('claytronic atoms', or catoms) designed to form much larger scale machines or mechanisms. The catoms will be sub-millimeter computers that will eventually have the ability to move around, communicate with other computers, change color, and electrostatically connect to other catoms to form different shapes.

Quantum wells, a potential well with only discrete energy values, can hold one or more electrons. Those electrons behave like artificial atoms which, like real atoms, can form covalent bonds, but these are extremely weak. Because of their larger sizes, other properties are also widely different. One way to create quantization is to confine particles, which were originally free to move in three dimensions, to two dimensions, forcing them to occupy a planar region. The effects of quantum confinement take place when the quantum well thickness becomes comparable to the de Broglie wavelength of the carriers (generally electrons and holes), leading to energy levels called "energy subbands", i.e., the carriers can only have discrete energy values. Quantum wells are formed in semiconductors by having a material, like gallium arsenide sandwiched between two layers of a material with a wider bandgap, like aluminium arsenide. These structures can be grown by molecular beam epitaxy or chemical vapor deposition with control of the layer thickness down to monolayers. Thin metal films can also support quantum well states, in particular, metallic thin overlayers grown in metal and semiconductor surfaces. The electron (or hole) is confined by the vacuum-metal interface in one side, and in general, by an absolute gap with semiconductor substrates, or by a projected band gap with metal substrates.

Synthetic biology aims to engineer cells with "novel biological functions." Such cells are usually used to create larger systems (e.g., biofilms) which can be "programmed" utilizing synthetic gene networks such as genetic toggle switches, to change their color, shape, etc. Protocells and other minimal solutions.
Construction of a chemical system capable of replication and evolution, fed only by small molecule nutrients, is now conceivable. This could be achieved by stepwise integration of decades of work on the reconstitution of DNA, RNA and protein syntheses from pure components. Such a minimal cell project would initially define the components sufficient for each subsystem, allow detailed kinetic analyses and lead to improved in vitro methods for synthesis of biopolymers, therapeutics and biosensors. Completion would yield a functionally and structurally understood self-replicating biosystem. Safety concerns for synthetic life will be alleviated by extreme dependence on elaborate laboratory reagents and conditions for viability. Our proposed minimal genome is 113 kbp long and contains 151 genes. We detail building blocks already in place and major hurdles to overcome for completion.
 An external file that holds a picture, illustration, etc.
Object name is msb4100090-f1.jpg Object name is msb4100090-f1.jpg A minimal cell containing biological macromolecules and pathways proposed to be necessary and sufficient for replication from small molecule nutrients. 

See also

Quantum dots are like man-made, detected 1980,  artificial atoms that are described by discrete states.
It is a portion of matter (e.g., semiconductor) whose excitons are confined in all three spatial dimensions. Consequently, such materials have electronic properties intermediate between those of bulk semiconductors and those of discrete molecules. They could only be used in low temperature settings earlie, but this new technology described in Science Daily does not. Quantum dots have previously ranged in size from 2-10 nanometers in diameter.  While typically composed of several thousand atoms, all the atoms pool their electrons to “sing with one voice”, that is, the electrons are shared and coordinated as if there is only one atomic nucleus at the centre.

As with any crystalline semiconductor, a quantum dot's electronic wave functions extend over the crystal lattice. Similar to a molecule, a quantum dot has both a quantized energy spectrum and a quantized density of electronic states near the edge of the band gap. The quantum dot absorption features correspond to transitions between discrete,three-dimensional particle in a box states of the electron and the hole, both confined to the same nanometer-size box.These discrete transitions are reminiscent of atomic spectra and have resulted in quantum dots also being called artificial atoms.
Its electronic characteristics are closely related to the size and shape of the individual crystal. Generally, the smaller the size of the crystal, the larger the band gap, the greater the difference in energy between the highest valence band and the lowest conduction band becomes, therefore more energy is needed to excite the dot, and concurrently, more energy is released when the crystal returns to its resting state. A main advantage with quantum dots is that, because of the high level of control possible over the size of the crystals produced, it is possible to have very precise control over the conductive properties of the material. Quantum dots of different sizes can be assembled into a gradient multi-layer nanofilm.

 Quantum Dots
The National Institute of Nanotechnology at the University of Alberta announced that they created the smallest quantum dot, 2009. From What's the spin on quantum dots.

In a semiconductor crystal lattice, the electrons are squeezed together, since no two nearby electrons can share exactly the same energy level according to Pauli exclusion principle, leading to quantum confinement. The energy level can then be modeled using particle in a box, which leads to the conclusion that the energy levels of the quantum dot is dependent on its size. When the size of the quantum dot is smaller than the critical characteristic length called the Exciton Bohr radius, the electrons crowding lead to the splitting of the original energy levels into smaller ones with smaller gaps between each successive level. The Exciton Bohr radius is larger than the Bohr radius due to the effect of dielectric screening and the influence of periodic lattice structure of the crystal. The quantum dots that have radii larger than the Exciton Bohr radius are said to be in the 'weak confinement regime' and the ones that have radii smaller than the Exciton Bohr radius are said to be in the 'strong confinement regime'. Thus, if the size of the quantum dot is small enough that the quantum confinement effects dominate(typically less than 10 nm), the electronic and optical properties change, and the fluorescent wavelength is determined by the size.

3D confined electron wave functions in a quantum dot. Here, rectangular and triangular-shaped quantum dots are shown. Energy states in rectangular dots are more s-type and p-type. However, in a triangular dot the wave functions are mixed due to confinement symmetry.

Besides confinement in all three dimensions (i.e., a quantum dot), other quantum confined semiconductors include:
  • Quantum wires, which confine electrons or holes in two spatial dimensions and allow free propagation in the third.
  • Quantum wells, which confine electrons or holes in one dimension and allow free propagation in two dimensions. Wells can be of many kinds.
Different sized quantum dots emit different color light due to quantum confinement.

The images in this series represent the electron densities in a quantum dot artificial atom.
Quantum Dot Wave Function  (Image 1)

Part of a series of images depicting electron densities in a quantum dot artificial atom

The visuals were generated by the nanoelectronic modeling tool called NENO 3-D, and were visualized on the nanoVIS rendering service at, a rich, Web-based resource for research, education and collaboration in nanotechnology. was created by the National Science Foundation (NSF)-funded Network for Computational Nanotechnology (NCN), a network of universities with a vision to pioneer the development of nanotechnology, from science to manufacturing, through innovative theory, exploratory simulation and novel cyberinfrastructure. NCN students, staff and faculty are developing the NanoHUB science gateway, while making use of it in their own research and education. Collaborators and partners across the world have joined NCN in this effort.

NanoHUB hosts over 790 resources to help users learn about nanotechnology, including online presentations, courses, learning modules, podcasts, animations, teaching materials and more. Most importantly, NanoHUB offers simulation tools that can be accessed from your Web browser, so you can not only learn about, but also simulate nanotechnology devices. NanoHUB also provides collaboration environment via Workspaces, online meetings and user groups.

 (Date of Image: May 2006)  Image 2.
 Part of a series of images depicting electron densities in a quantum dot artificial atom
Part of a series of images depicting electron densities in a quantum dot artificial atom
Image 3
Credit: Wei Qiao, David Ebert, Marek Korkusinski, Gerhard Klimeck; Network for Computational Nanotechnology, Purdue University

Download the high-resolution JPG version of the image. (399 KB
Use your mouse to right-click (Mac users may need to Ctrl-click) the link above and choose the option that will save the file or target to your computer.

Synthetic chrystals.
Element Six, the world leader in synthetic diamond supermaterials, working in partnership with academics in Harvard University, California Institute of Technology and Max-Planck-Institut für Quantenoptik, has used its Element Six single crystal synthetic diamond grown by chemical vapour deposition (CVD) to demonstrate the capability of quantum bit memory to exceed one second at room temperature.

Using synthetic diamond, Element Six and Harvard University have set a new room temperature quantum information storage record of more than one second – a thousand times longer than previously recorded.

It proved the ability of synthetic diamond to provide the read-out of a quantum bit which had preserved its spin polarisation for several minutes and its memory coherence for over a second. This is the first time that such long memory times have been reported for a material at room temperature, giving synthetic diamond a significant advantage over rival materials and technologies that require complex infrastructure which necessitates, for example, cryogenic cooling.

The versatility, robustness, and potential scalability of this synthetic diamond system may allow for new applications in quantum information science and quantum based sensors used, for example, in nano-scale imaging of chemical/biological processes.

Steve Coe, Element Six Group Innovation Director, explained the success of the collaboration:

"The field of synthetic diamond science is moving very quickly and is requiring Element Six to develop synthesis processes with impurity control at the level of parts per trillion – real nano-engineering control of CVD diamond synthesis. We have been working closely with Professor Lukin's team in Harvard for three years - this result published in Science is an example of how successful this collaboration has been."

Professor Mikhail Lukin of Harvard University's Department of Physics described the significance of the research findings:

"Element Six's unique and engineered synthetic diamond material has been at the heart of these important developments. The demonstration of a single qubit quantum memory with seconds of storage time at room temperature is a very exciting development, which combines the four key requirements of initialisation, memory, control and measurement. These findings might one day lead to novel quantum communication and computation technologies, but in the nearer term may enable a range of novel and disruptive quantum sensor technologies, such as those being targeted to image magnetic fields on the nano-scale for use in imaging chemical and biological processes."

The findings represent the latest developments in quantum information processing, which involves manipulating individual atomic sized impurities in synthetic diamond and exploiting the quantum property spin of an individual electron, with superposition so this quantum spin (qubit) can be both 0 and 1 simultaneously. It is this property that provides a framework for quantum computing, but also for more immediate applications such as novel magnetic sensing technologies.

See also  About protons and atoms.

15 kommentarer:

  1. Researchers have discovered hundreds of new knots in hundreds of proteins. What appeared to be evolutionary cruft may prove useful.

    “The knots are conserved across life, from bacteria to humans. They are doing something very important,” said Joanna Sulkowska, a biophysicist at the University of California, San Diego. Sulkowska and UCSD biophysicist Jose Onuchic led a knot discovery project described online this week in Proceedings of the National Academy of Sciences.

    Biologists knew for decades that artificially synthesized protein strands could tie themselves into knots. But because naturally occurring knots proved hard to find in cells — the first wasn’t discovered until 1994 — researchers assumed evolution had weeded them out.

    “They thought the protein would spend too much time folding to do anything useful on molecular scales, that the landscape of a cell is too complicated to use knots,” Sulkowska said.

    The major challenge of working with any protein is verifying its actual structure. Computer models can hint at a functional form, but until a protein is isolated and scanned, it’s educated guesswork.

    A new algorithm snips virtual protein strands into pieces, then compares the parts. Knots appear as colored sections (gray area) and allow researchers to visualize a protein's full, knotted structure. Image: J. Sulkowska et al./PNAS

    Knotted proteins are even more difficult to study, and traditional protein simulations struggle to predict the forms a knot might take.

    Current algorithms used to understand proteins don’t even allow for the existence of knots.

    To attack the modeling problem, Onuchic’s team developed a new algorithm to search for knots in more than 74,200 known protein sequences recorded in a massive database called the Protein Data Bank.

    Their algorithm found 398 proteins with complex knots and 222 proteins with simple knots. What’s more, the knotted structures they discovered appeared in a wide array of life forms, from bacteria and plants to yeast and humans. Each branch of life seems to have found some way to make specific knots.

    “This didn’t happen by accident. There has to be a reason, a function for these knots,” Sulkowska said. “Now we can earnestly begin to ask this question.”

    Early results by other laboratories suggest that, in bacteria living around scalding-hot deep-sea hydrothermal vents, knots keep some proteins literally tied together. Other forms may play a role in afflictions such as Alzheimer’s disease, and perhaps even infectious diseases.

    Sulkowska and colleagues are actively exploring the infectious disease angle now. Whether or not their own investigations pan out, Sulkowska expects knotted proteins to be proven important to life’s designs. “We use knots every day in the macroscopic world,” she said. “The microscopic world should be no different.”


  3. Ulla,

    Interesting articles lately (from radio science friday) on the paradigm of stem cells and the relation to scaring in heart disease and possibly cancer. Also, bits of the child cells found in the mother... these fund around tumors but not clear if they are helping or starting them. Also new test for 20% with floating tumor cells in a recovery person that will become cancer again.

    Yes, the forms of protein a whole new level of gene reading (using the different codes that code for the same protein for the rate)

    Viruses linked intimately to the health of bacteria thus of the host (us).

    Knots and kinks- well, where they are one sided things change to breaking.

    BTW DNA will have a natural state of the reverse of compacting rather than stretched out like a rubber band on certain scales.

    Keep up your study on invisibility- it seems we are all going in more distant explorations.

    The Pe Sla

  4. Biologist Luc Montagnier surrounded two test tubes, one containing the DNA fragment and the other pure water, with a weak electromagnetic field. He later discovered that the DNA could be detected in the water as well as in the original test tube. He compared the results with controls in which the time limit was lowered, no electromagnetic field was present or was present but at a lower frequency, and one in which both tubes contained pure water. In every one of these cases, the results were NOT the same.


    One thing that I have been thinking of is the extremely fast reconstruction of cancers, if the healed person believs s/he has got it again. This happens within days. Today we have no explanation of what can achieve this.

    Also DNA is swimming freely in our organism, and outside our organism. It is not constrained within the cells.

  5. Semiconductor quantum dots and free radical induced DNA nicking
    Mark Green and Emily Howman

    There is a growing interest in the use of semiconductor quantum dots as fluorescent markers in biological applications. However, there are concerns regarding the potential environmental impact and toxic nature of these nanomaterials. In this study, we have investigated the interaction of water-soluble semiconductor quantum dots with supercoiled DNA.


    Biotoxicity? Interaction with biological matter?

    115 articles.

  7. Since the admin of this web page is working, no uncertainty very soon
    it will be renowned, due to its quality contents. you may like the
    .pdf piece written by : Scott Tucker on quantum gravity
    Also visit my web site Scott Tucker

  8. Ulla, my page today has two relavent links I thought you might be interested in. Pallium...

    The PeSla

  9. Ulla,
    I found this interesting on Astronomy Picture of the Day: animation of DNA replication...

  10. Current algorithms used to understand proteins don’t even allow for the existence of knots.

    Their algorithm found 398 proteins with complex knots and 222 proteins with simple knots. What’s more, the knotted structures they discovered appeared in a wide array of life forms, from bacteria and plants to yeast and humans. Each branch of life seems to have found some way to make specific knots.

    The folding/unfolding is not a linear and a symmetric process? Who knows what is the truth? We simply have no tools to reveal this because we use crystals and rigid structure so much? Enzymes does not function by structure alone, there is also the 'spark of light'. 'G-islands' are not the whole truth?

  12. researchers have been frustrated trying to control the light emitted from quantum dots, which brighten or dim with the proximity of other particles.

    by bringing gold nanoparticles close to the dots and using a DNA template to control the distances,

    The researchers looked at two types of nanoparticles, quantum dots, which glow with fluorescent light when illuminated, and gold nanoparticles, which have long been known to enhance the intensity of light around them. The two could work together to make nanoscale sensors built using rectangles of woven DNA strands, formed using a technique called "DNA origami." These DNA rectangles can be engineered to capture different types of nanoparticles at specific locations with a precision of about one nanometer. Tiny changes in the distance between a quantum dot and a gold nanoparticle near one another on the rectangle cause the quantum dot to glow more or less brightly as it moves away from or toward the gold. Because these small movements can be easily detected by tracking the changes in the quantum dot's brightness, they can be used to reveal, for example, the presence of a particular chemical that is selectively attached to the DNA rectangle.

  13. S.H. Ko, K. Du and J.A. Liddle.Quantum-dot fluorescence lifetime engineering with DNA origami constructs. Angewandte Chemie (Int. Ed.), 52: 1193–1197. doi: 10.1002/anie.201206253.


    Quantum dots have attracted a lot of interest for researchers in photovoltaics because of their claimed ability to achieve extraordinary conversion efficiencies.

    Last year researchers at the University of Buffalo said they could reach 45-percent conversion efficiency with solar cells enabled by quantum dots. And for nearly a decade now quantum dots have even been proposed as a way to achieve electron multiplication or to create so-called “hot carrier” cells for reaching higher conversion rates. However, this line of research has earned some skeptics of late who dismiss the possibility that more than one electron-hole pair can be generated from one photon.

    have demonstrated that quantum dots can self assemble onto nanowires in a way that once again promises improved conversion efficiencies for photovoltaics.

    Nature Materials “Self-assembled Quantum Dots in a Nanowire System for Quantum Photonics,” was that the quantum dots self assemble at the apex of the gallium arsenide/aluminum gallium arsenide core/shell nanowire interface. Further the quantum dots can be positioned precisely relative to the center of the nanowire. When this precise positioning is combined with quantum dots’ ability to confine both the electrons and the holes, the possibilities for this approach look encouraging. - Nature reaches far higher efficiency in photosynthesis, 80 - 90%