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June 03, 2006

Follow up: quantum dots and solar cells

more technical information about the quantum dots releasing multiple excitons for possible improved solar cell efficiency

Previous article on quantum dots and solar cells

Synthetic biology, DNA/RNA nanotech compiled

The state of synthetic biology, which might become DNA/RNA nanotech or the protein assembly pathway.
They are applying the programming/engineering paradigm to DNA and RNA and biology.
automating, making parts etc...
this works well with the Ned Seeman work and the DNA origami, virus assembly of batteries and scaffolds, plus the advanced chemistry and the light enabled molecular machines.

There are those within the field looking to massively scale up (billlions of cells, sequence parts from 900BP up to millions. A ribosome has 2.3 million base pairs), speed up and further automate what they are doing and providing the powerful abstraction layers.

Positional molecular assembly using synthetic biology, DNA, RNA, proteins, self-assembly, viruses and bacteria is surveyed up to 2004

Updated costs based on George Church and Harvard lab Polony sequencing reduces costs for sequencing and synthesizing by over 10 times. Sequencing 11 cents for thousand bases and synthesizing 1 cent per base.

Costs in synthetic genetics A new sequencer produced by 454 Life Sciences Corporation can sequence the genome (3.165 billion base pairs) for $2.2M. Making a hypothetical biological Intel 8088 (3500 transistor. A DNA transistor should take up 450 base pairs. 450 base pairs * 3500 transistors = 1.575M base pairs. 1.575M bp * $1.23 per bp = a total cost of ~$1.94M. the parts in the registry of biological parts tend to be 900 base pairs long (as of the end of 2005).
Making biology more like computer systems and networks
Synthetic biology programmable cells
Survey of dna-rna nanotechnology

A computer simulation of the ribosome undertaken at Los Alamos National Lab involving 2.64M atoms was done in 2005. This type of simulation is a very important step towards understanding the ribosome, and then re-engineering it.

Biobricks would use a registry of parts like the one at MIT Physical parts (currently the parts are on average about 900 base pairs, they can perform electronic like functions) in the DNA Repository have been designed to be assembled into systems using normal cloning techniques based on restriction enzymes, purification, ligation, and transformation - with a twist. BioBrick parts are composable. The result of assembling two parts is itself a part that may be used in future assemblies. As of June 1, 2006, the physical Repository currently contains 178 basic parts and 462 composite parts. 43 parts are currently being synthesized or assembled. 1383 parts are specified and may or may not ever become available. The database contains a total of 2351 part entries.

Standard assembly process Two BioBrick parts, one blue and one green can be assembled into a blue-green system by a process called BioBrick Standard Assembly.

Parallel and Rolling Assembly is faster than standard assembly where many parts are put together BioBrick systems may contain many parts. For example, one could spend 6 months to a year building a 50-part system by assembling the first two parts, adding the third part, adding the fourth part, ... . However, because BioBrick assembly is composable, the same assembly can be done much more quickly (in 3 to 6 weeks, using 6 stages of assembly) by performing many pairwise assemblies at the same time.

Cancer treatment progress

OSHU cancer institute study points to future cancer therapies tailored by the nature of the individual patient's tumor Scientists at the Oregon Health & Science University Cancer Institute and elsewhere have discovered that patients responded differently to the targeted therapy Sunitinib (Sutent) depending on the type of genetic abnormality in their cancer. In my predictions of medicine, longevity was that we will have completely personalized medicine with trials and tests of drugs simulated and with real tissue that model your own DNA and cells

Gene therapy suppresses ovarian cancer growth in mice Ovarian cancer effects 25,000 women per year in the USA. 16,000 per year die from it in US alone. Gene therapy also prevents the onset of diabetes in mice

There is also hopeful signs of being able to modify e-coli bacteria to kill cancer cells

Progress with new trials for the australian developed cervical cancer vaccine is also reported The technology used in the world's first cervical cancer vaccine will be tweaked to fight the most common sexually transmitted disease, genital warts. Australian of the Year and University of Queensland (UQ) cervical cancer vaccine creator Professor Ian Frazer launched a therapeutic vaccine trial for genital warts Tuesday, February 7, 2006.

Patients from Brisbane and China will take part in the joint project for UQ's cancer research centre, the Centre for Immunology and Cancer Research (CICR) and the hospital's sexual health service, Princess Alexandra Sexual Health (PASH). Professor Frazer said the vaccine used virus-like particles to deliver an antigen (protein that produces immunity) for genital warts similar to the cervical cancer vaccine.

"It will target the main causes of visible genital warts which are human papillomavirus (HPV6) and (HPV11)," Dr Frazer said

June 02, 2006

Other tech: Encrypted VOIP using Zfone

Voice over IP phone calls can be encrypted to prevent wiretapping Zfone is the software that implements my new encryption protocol, called ZRTP, in a certain way. Zfone is not a VoIP client; it watches for the packets of Internet data going in and out of the machine and looks for ones that are VoIP related. Upon detection of a VoIP call, it intercedes to encrypt the call by setting up a key agreement in the media stream and encrypts the packets of voice data. As time goes on, you'll start to see ZRTP inside VoIP clients.

other tech: Rat brain interfaced to chip with n a semiconductor chip with 16,384 sensory transistors per square millimetre

Recording the activity patterns of the united cell structure of an intact mammalian brain tissue represents a significant technological breakthrough. Employing the new technique, the biophysicists working under the direction of Peter Fromherz were able to visualize the influence of pharmaceutical compounds on the neural network. This makes the "brain-chip" from Martinsried a novel test system for brain and drug research

Methods commonly used in neurophysiology are invasive, restricted to a small number of cells or suffer from low spatial resolution. The scientists in Martinsried developed a revolutionary non-invasive technique that enables them to record neural communication between thousands of nerve cells in the tissue of a brain slice with high spatial resolution. This technique involves culturing razor-thin slices of the hippocampus region on semiconductor chips. These chips were developed in collaboration with Infineon Technologies AG and excel in their density of sensory transistors: 16384 transistors on an area of one square millimeter record the neural activity in the brain.

Nanotechnology in Japan

Bio of Masakazu Aono who first used an STM to pick and place atoms on silicon.

Aono currently is Research Supervisor, "Nanoscale Quantum Conductor Array" Project, International Cooperative Research Project (ICORP), Japan Science and Technology Agency (JST)

Now, he wants to study an unexplored area of biotechnology. Prof. Aono says, "I want to study thoroughly the slick exchange mechanisms of signals among biological materials using a STM with at least 1,000 probe-tips. My ultimate goal is to create a new paradigm in the computation field based on my research in such an area."

Here is a summary of nanotechnology work in Japan (summary written in 2005)

The most relevant part seems to be (a lot of good work there) Ultimate Manipulation of Atoms and Molecules (1992-2001)

* Private sector partner: Angstrom Technology Partnership
* Public sector partner: National Institute for Advanced Interdisciplinary Research(NAIR)

The purpose of R&D is to develop technology for exactly observing and identifying atoms or molecules, and arranging them in a desired layout. In combination with mechanical probe techniques and beam techniques, the new technology allows the identification, observation, measurement and manipulation of atoms and molecules on the surface of various materials, organic molecules such as DNA, and atomic assembly in free space. R&D of simulation technology will also be pursued to exactly predict atomic and molecular processes. In JYF 1994, it was found possible to manipulate structures down to the atomic level by means of magnetic fields. This suggests the possibility of creating new materials through the control of materials' structures at atomic and molecular levels.

This last project is the most "nanotechnological" project at present, although it has been insisted that the main idea is the manipulation of individual atoms with an eye towards creating materials with new properties. The original impetus for the project was a small band of researchers at Tsukuba's Electrotechnical Laboratory (ETL), who approached MITI with the concept which then found interested partners in the private sector. (Supposedly the ETL researchers' ideas were sparked by D r. Aono's Atomcraft project carried out under ERATO.)

Original plans were for this to be one of the "large-scale" projects run under MITI, but with the development of the ISTF program, the decision was made to incorporate it as one of the ISTF projects. MITI seems to be very insistent on attempting to bring together national laboratories, academia, and the private sector. This project has the Angstrom Technology Partnership as the private sector partner, and the National Institute for Advanced Interdisciplinary Research (NAIR) as the public sector partner. Both have come together to form the Joint Research Center for Atom Technology (JRCAT) to carry out the above- mentioned research. Although universities are not officially associated with the project, several of the researchers are graduate students (mainly from Tsukuba University)or professors working half-time at national laboratories. The research groups involved are the same as those in NAIR (See JRCAT research results below for complete list)

A list of targets to achieve by the final date (2001) include (intermediate goals in parentheses):

* (Control of Local Surface Reactions)--> Manipulation of Atoms/Molecules
* (Control of Subnanometer Structures) --> Control of Bulk Properties
* (Observation and Control of Growing Surfaces) --> Formation of Superstructures
* (Control of Reactions in Atom Clusters) --> Formation of Nanometer Structures
* (Observation of Molecules)--> Molecular Fabrication
* (Simulation Based on First Principle Calculations) --> Reaction System Simulation

A list of the individual members of the Angstrom Technology Partnership (private partners) shows all of the larger Japanese semiconductor companies, as well as a few of the US and Korean ones. Perhaps the most interesting partner is Molecular Simulations, Inc. (formerly Biosym), which is a US company known for its simulation software, particularly for biotechnology and pharmaceutical development.

Other surveys of using DNA and RNA for positional molecular assembly

Positional Assembly Using DNA from 1994 until 2004 at the molecular assembler site (part of the Kinematic Self-Replicating Machines book by Robert Freitas and Ralph Merkle

Positional Assembly Using Proteins as of 2004 at the molecular assembler site (part of the Kinematic Self-Replicating Machines book by Robert Freitas and Ralph Merkle

Positional Assembly Using Microbes and Viruses at the molecular assembler site (part of the Kinematic Self-Replicating Machines book by Robert Freitas and Ralph Merkle

Positional Assembly using other biological means at the molecular assembler site (part of the Kinematic Self-Replicating Machines book by Robert Freitas and Ralph Merkle

Artificial Biological Replicators (1965-2004) at the molecular assembler site (part of the Kinematic Self-Replicating Machines book by Robert Freitas and Ralph Merkle largely discusses the synthetic biology work which I have updated in my recent articles.

Ribosomes: Molecular Positional Assembly for Self-Replication at the molecular assembler site (part of the Kinematic Self-Replicating Machines book by Robert Freitas and Ralph Merkle

Molecular Self-Assembly and Autocatalysis at the molecular assembler site (part of the Kinematic Self-Replicating Machines book by Robert Freitas and Ralph Merkle

Costs in synthetic genetics and computer simulation of a ribosome

A new sequencer produced by 454 Life Sciences Corporation can sequence the genome (3.165 billion base pairs) for $2.2M. Making a hypothetical biological Intel 8088 (3500 transistor. A DNA transistor should take up 450 base pairs. 450 base pairs * 3500 transistors = 1.575M base pairs. 1.575M bp * $1.23 per bp = a total cost of ~$1.94M. the parts in the registry of biological parts tend to be 900 base pairs long (as of the end of 2005).

A computer simulation of the ribosome undertaken at Los Alamos National Lab involving 2.64M atoms was done in 2005. This type of simulation is a very important step towards understanding the ribosome, and then re-engineering it.

Making biology more like computer systems

Synthetic biology extends the spirit of genetic engineering to focus on whole systems of genes and gene products. The focus on systems as opposed to individual genes or pathways is shared by the contemporaneous discipline of systems biology, which analyzes biological organisms in their entirety. The goal of synthetic biology is to extend or modify the behavior of organisms and engineer them to perform new tasks. One useful analogy to conceptualize both the goal and methods of synthetic biology is the computer engineering hierarchy

synthetic biology: Programmable Cells: Engineer Turns Bacteria Into Living Computers

04/27/05 -- In a step toward making living cells function as if they were tiny computers, engineers at Princeton have programmed bacteria to communicate with each other and produce color-coded patterns.

The feat, accomplished in a biology lab within the Department of Electrical Engineering, represents an important proof-of-principle in an emerging field known as "synthetic biology," which aims to harness living cells as workhorses that detect hazards, build structures or repair tissues and organs within the body.

"We are really moving beyond the ability to program individual cells to programming a large collection -- millions or billions -- of cells to do interesting things," said Ron Weiss, an assistant professor of electrical engineering and molecular biology.

Abstract on RNA synthetic biology RNA molecules play important and diverse regulatory roles in the cell by virtue of their interaction with other nucleic acids, proteins and small molecules. Inspired by this natural versatility, researchers have engineered RNA molecules with new biological functions. In the last two years efforts in synthetic biology have produced novel, synthetic RNA components capable of regulating gene expression in vivo largely in bacteria and yeast, setting the stage for scalable and programmable cellular behavior. Immediate challenges for this emerging field include determining how computational and directed-evolution techniques can be implemented to increase the complexity of engineered RNA systems, as well as determining how such systems can be broadly extended to mammalian systems. Further challenges include designing RNA molecules to be sensors of intracellular and environmental stimuli, probes to explore the behavior of biological networks and components of engineered cellular control systems.

DNA/RNA nanotechnology: Survey of synthetic biology

Synthetic biology wiki defines Synthetic Biology is
A) the design and construction of new biological parts, devices, and systems, and
B) the re-design of existing, natural biological systems for useful purposes.

are currently working to

* help specify and populate a set of standard parts that have well-defined performance characteristics and can be used (and re-used) to build biological systems,
* develop and incorporate design methods and tools into an integrated engineering environment,
* reverse engineer and re-design pre-existing biological parts and devices in order to expand the set of functions that we can access and program
* reverse engineer and re-design a 'simple' natural bacterium.

The openwetware project wiki is an effort to promote the sharing of information, know-how, and wisdom among researchers and groups who are working in biology & biological engineering.

Article discussing the prospects and impact of a lot more automation in molecular biology (automated DNA synthesis, transformation, selection, PCR, ligations, and imaging)

Wired article on synthetic biology and biobricks

Biobricks would use a registry of parts like the one at MIT Physical parts in the DNA Repository have been designed to be assembled into systems using normal cloning techniques based on restriction enzymes, purification, ligation, and transformation - with a twist. BioBrick parts are composable. The result of assembling two parts is itself a part that may be used in future assemblies. As of June 1, 2006, the physical Repository currently contains 178 basic parts and 462 composite parts. 43 parts are currently being synthesized or assembled. 1383 parts are specified and may or may not ever become available. The database contains a total of 2351 part entries.

Standard assembly process Two BioBrick parts, one blue and one green can be assembled into a blue-green system by a process called BioBrick Standard Assembly.

Parallel and Rolling Assembly is faster than standard assembly where many parts are put together BioBrick systems may contain many parts. For example, one could spend 6 months to a year building a 50-part system by assembling the first two parts, adding the third part, adding the fourth part, ... . However, because BioBrick assembly is composable, the same assembly can be done much more quickly (in 3 to 6 weeks, using 6 stages of assembly) by performing many pairwise assemblies at the same time.

May 2006 article about synthetic biology in Scientific American

June 01, 2006

Nanocrystal displays: Quantum dots to make vibrant, flexible screens.

The best potential advantage of quantum dot LEDs (QD-LEDs) is that they use much less power than LCDs. In LCDs, a backlight illuminates every pixel on the screen. Dark pixels are simply blocking this light, in effect wasting energy. In part because quantum dots emit light rather than filtering it, a QD-LED display could potentially use one-30th the power of an LCD. Coe-Sullivan of QD Vision, says he expects that it will be about four years before the company has its first commercial product -- probably a small display for a cell phone. But he says the colorful images will be worth the wait.

Advancing nanoscale self-assembly: placing and anchoring many molecules capable of mechanical work onto a surface

Researchers from the University of Bologna, Italy, University of Birmingham, UK, Paul Sabatier University in France and University of California, Los Angeles (UCLA), US, have come up with a technique for arranging molecular machines on a solid surface. The team used a cospreading strategy to create layers of chemically switchable rotaxane molecules on indium tin oxide or calcium fluoride substrates.

This work advancing nanoscale self-assembly. They place and anchor many dumbell molecules capable of mechanical work onto a surface. They have created more complex molecules (some powered and triggered with light) which might be similarly anchored in future work.

Other tech: Slightly modified Cell processors 20 times better than AMD Opterons and Intel Itanium2 chips for supercomputers

computer scientists at the U.S. Department of Energy's Lawrence Berkeley National Laboratory evaluated the processor's performance in running several scientific application kernels, then compared this performance against other processor architectures. The paper, "The Potential of the Cell Processor for Scientific Computing," was written by Samuel Williams, Leonid Oliker, Parry Husbands, Shoaib Kamil and Katherine Yelick, of Berkeley Lab's Future Technologies Group and by John Shalf from NERSC. On average, Cell is eight times faster and at least eight times more power efficient than current Opteron and Itanium processors, despite the fact that Cell's peak double precision performance is fourteen times slower than its peak single precision performance. If Cell were to include at least one fully utilizable pipelined double precision floating point unit, as proposed in their Cell+ implementation, these speedups would easily double. Details on the cell processor are at wikipedia. It includes descriptions of moving from the current 90nm process to 65nm and below. A 65nm cell chip would be two or more times as fast as a 90nm. A 45 nm cell chip would be two or more times faster than a 65nm version.

If the equivalent of a Blue Gene/L computer were made with Cell+ chips would have over 7 petaflop performance. A Cell+ 45nm version of a Blue Gene/L would be 28 petaflops. Cell processors will be made in volume for the Playstation 3, so the costs of the chips should be very competitive.

May 31, 2006

Hamburger economics and China's economy

The Economist magazine uses the McDonald's Big Mac as a simple proxy for the purchasing power parity exchange rate. If this accurately reflects what the long term exchange rate should be in 10-20 years, then Chinese Yuan should eventually convert at 3.39 yuan to the US dollar instead of 8.0 where it currently is. Applying the implied conversion rate to the expected 2006 GDP of China (2.53 trillion for 2006) then China would have a PPP GDP of 5.97 trillion. In 11 years if that was the exchange rate and assuming 8% annual growth, China would catch up to the size of todays US economy. It would take China about 17 years to pass the US economy if its growth was 5% per year greater. (say 8% versus 3%) Assuming that China's growth advantage remains at 4-6% per year and the long term shift in exchange rates then the Chinese economy would pass the US between 2021 and 2027.

May 30, 2006

Quantum dots could create 65% efficient solar cells

Advancing control and improving processes for the creation of quantum dots could enable vastly superior solar cells.

In a paper published in a May, 2005 issue of the American Chemical Society's Nano Letters journal, an NREL team found that tiny "nanocrystals," also known as "quantum dots," produce as many as three electrons from one high-energy photon of sunlight. When today's photovoltaic solar cells absorb a photon of sunlight, the energy gets converted to at most one electron and the rest is lost as heat. "We have shown that solar cells based on quantum dots theoretically could convert more than 65% of the sun's energy into electricity, approximately doubling the efficiency of solar cells," Nozik said. The best cells today convert about 33% of the sun's energy into electricity. In 2004, Richard Schaller and Victor Klimov of Los Alamos National Laboratory in New Mexico were the first to demonstrate the electron multiplication phenomenon predicted by Nozik, using quantum dots made from lead selenide.

Here is a somewhat technical summary of quantum dots and photovoltaics in general.

Quantum dots, that are irradiated with energy that is to 2 - 4 times their band gap energy, produce excitons that correspond to the second, third or forth excited states depending on the energy of the incident photon. The absorbed energy from this single photon produces two or more excitons in the quantum dot, which means that quantum yields, e.g., the percent of excitons produced/photons absorbed, up to 300% have been achieved.3 This phenomenon is referred to as multiple exciton generation (MEG). In 2004, researchers at Los Alamos were the first to demonstrate that if the photon energy is more than three times the band gap of PbSe quantum dots, two or more excitons can be produced with up to 100% efficiency. Since that time, researchers at the National Renewable Energy Laboratory (NREL), University of Colorado and Naval Research Laboratory (NRL) collaboratively demonstrated ultra-efficient MEG in colloidal PbSe and PbS quantum dots, producing three excitons per photon at photon energies at four times the quantum dots band gap.

One high efficiency solar energy device has not been created. The charges need to be taken from the quantum dots to the electrode efficiently. Then the process needs to be scaled up and the costs lowered to be competitive with other methods