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September 22, 2006

More about Observing Molecules

A longer article that reviews the current state and development history of observing single molecules

In 1993, Block and his colleagues were the first to observe the movement of an individual molecule of kinesin, a tiny protein that carries chromosomes, neurotransmitters and other vital cargo along minute tracks called microtubules in living cells. Using a sensitive microscope-based instrument known as an optical trap, the Block team observed that kinesin moves along microtubules in discrete steps that are a mere 8 nanometers long. "Kinesin and other motor molecules are really nature's nanotechnology," he said.

By 2005, he and his colleagues had made dramatic improvements in the optical trap that enabled them to measure a single enzyme moving along a strand of DNA to within a distance of one-tenth of a nanometer, which is equivalent to the diameter of a single hydrogen atom.

"Between 1993 and 2005, the resolution improved from 8 nanometers to 3.4 angstroms," Block said. "That means we were able to make observations that are 25 times smaller in a period of about 10 years.


Block's team has a new DNA sequencing method. They measure how long a single enzyme, called RNA polymerase, pauses at each base's location.

Multiphoton fluorescence microscopy watch chromosomes in action

Using multiphoton fluorescence microscopy, a technique pioneered at Cornell by physicist Watt W. Webb, researchers have for the first time been able to watch chromosomes change their form in order to activate their genes to synthesize key proteins in fruit fly cells. The advance could be a significant step toward understanding the basic processes that underlie gene expression.

Yao used multiphoton microscopy (MPM) to image living salivary gland tissue of Drosophila (fruit flies). Unlike other methods, which lack penetrating power and can damage the specimen, MPM delivers crisp, clear images, even in thicker tissue samples like Drosophila salivary glands.


The research was ultimately possible thanks to the unique composition of the fruit flies' polytene cells -- giant, multistranded chromosomes with hundreds of sets of the genome instead of the usual two sets in conventional cells. This enlarges the usual nuclear dimensions by about 10 times, making them large enough to image the detail.

"This is the first time ever that anyone has been able to see in detail, at native genes in vivo, how a transcription factor is turned on, and how it then is activated," said Webb.


Using another method that Webb engineered at Cornell, called fluorescence recovery after photobleaching, the researchers also discovered that HSF activators bind to hsp70 genes much longer than previously thought before being replaced with new HSFs, which raises new questions about the mechanisms of gene transcription.

September 21, 2006

Superbus - new public transit idea

Dutch working on superbus - aerodynamic bus that can also be a high speed train It is an electric bus designed to be able to switch seamlessly between ordinary roads and dedicated “supertracks”, on which it can reach speeds of 250kph (155mph). It could thus present an alternative to much more expensive magnetic-levitation trains. It is as wide and long as a standard city bus, the Superbus is only 1.7 metres high, or roughly the same height as a sports-utility vehicle. There is no middle aisle. The low-riding Superbus, in contrast, has a separate door for each of its 30-odd seats. The individual doors also allow for rapid loading and unloading of passengers.


The low ceiling and the use of lightweight materials make for a far more streamlined vehicle, which in turn requires only a modest electric motor: though engineers have not yet decided whether the Superbus will be powered by fuel cells or batteries, they estimate that it will be able to accelerate from rest to 100kph in a leisurely 36 seconds.

The future of the project is uncertain. Its intended route, a new transport link connecting Amsterdam with the northern city of Groningen, was recently scrapped by the Dutch government (although the Superbus was deemed the most feasible of all the options considered, which also included a maglev train). In spite of the setback, the project has since received an extra €7m ($9m) in government funding, plus €1m from Connexxion, a local bus company. The Superbus team's latest plan is to unveil a fully functional prototype at the Beijing Olympics in 2008.

Here is the Tuft university website on the superbus

The shift to LEDs and OLEDs for lighting is starting

The Economist magazine looks at LED lights. Incandescents only output 5% of energy input as light. LED and florescents output 20%. LED can be further improved. 20% of the worlds electricity is used for lighting. LEDs could cut that in to 10%.

So far, only a handful of firms are specialising in this market. To compete with the light output of a single 60-watt incandescent bulb that emits about 800 lumens (a measure of light power as perceived by the human eye), companies such as LED Lighting Fixtures and Permlight of Southern California are designing lamps based on clusters of white LEDs that achieve a similar lumen output, but consume a fraction of the power. Initial costs are still higher for such fixtures than for traditional bulbs, but lower electricity bills could make up the difference within a year or two, says Dr Hunter.

The size of LEDs allows for far greater choice in fixture design. LED fixtures resembling large tiles that can be mounted on walls to create checkerboard-like effects or morphing colours. LEDs made of organic materials, called OLEDs, promise even more revolutionary design possibilities. Since they were first commercialised a few years ago, they have mostly appeared in small portable devices, such as mobile phones and digital music-players. Based on ultra-thin, lightweight plastic sheets, OLEDs emit a softer, more distributed light than conventional LEDs and might eventually be turned into softly glowing wallpaper or curtains.

Nanotube Scaffolds for Neural Implants

Nanotube scaffolds are helping stem cells to grow in stroke-damaged brains. Thomas Webster and his collaborators in South Korea found a possible anchor in carbon nanotubes: tiny, highly conductive carbon fibers that not only act as scaffolds, helping stem cells stay rooted to diseased areas, but also seem to play an active role in turning stem cells into neurons. Rats given both nanotubes and cells showed new neural growth in stroke-damaged brain regions in as little as a week.

Particle Acceleration by Stimulated Emission of Radiation -- PASER

Particle Acceleration by Stimulated Emission of Radiation (PASER for Short), a sort of particle analog of the laser process, has been demonstrated, for the first time, by a team of physicists from the Technion-Israel Institute of Technology using the accelerator facilities at the Brookhaven National Lab. In the new proof-of-principle PASER experiment, the active medium consists of a CO2 vapor, and instead of surrendering their energy in the form of stimulated photons, the atoms transfer their energy to a beam of electrons.

Being able to accelerate electrons with energy stored in individual atoms/molecules, a concept now demonstrated with the PASER, provides new opportunities since the accelerated electrons may prove to be significantly "cooler" (they are more collimated in velocity) than in some other prospective acceleration schemes, enabling in turn the secondary generation of high-quality X-rays, which are an essential tool in nano-science.

Branson pledges $3 billion to fight global warming

Branson pledges $3 billion over the next 10 years to fight global warming

According to the government's formula, each kilometre travelled by an airline passenger on a long-haul flight accounts for 0.11kg of carbon dioxide. The Guardian calculated that offsetting Virgin Atlantic's entire annual flight operation would involve planting 59m trees.

The commitment follows last week's announcement by Sir Richard of a new Virgin Fuels business which will invest up to $400m in renewable energy initiatives over the next three years.

The first deal will see Sir Richard backing California-based Cilion which was formed in June to make bioethanol from corn. Virgin's Gaia Capitalism project already stretches across the firm, ranging from biodiesel for its trains to experiments with environmentally friendly fuels for its putative space programme, Virgin Galactic.


Further reading;
Biofuels from switchgrass. The net energy output of switchgrass is about 20 times better than corn's. About 1150 gallons of ethanol could be made on every acre using switchgrass.

Molecular manufacturing video

Molecular manufacturing video from the society of manufacturing engineers

The script of the video is here

They talk with Mark Sims of Nanorex.

Mark says:
Where the real innovation and excitement is from a nanomanufacturing perspective is in the bottom up category. Here we’re dealing with synthesizing molecules or components which are made out of atoms, in a variety of techniques—traditional chemical synthesis, more advanced new methods of creating molecules like carbon nanotubes, dendrites, and other structures that have thousands or millions of atoms in them, into these atomically precise products.

Nanoink makes dip pen nanolithography (DPN) tools. They said:
DPN can directly write materials using different molecular inks that directly transfer from a tip to a substrate. In another instance, those inks could be resists, so the dip pen could be used in a way similar to photolithography to pattern a resist on a substrate, and then to etch three-dimensional structures. Probably one of the most interesting and powerful ways that you can use dip pen nanolithography is to use it as a templating tool, to put down a substance that can act as a pattern for directed self assembly. This is the approach that’s used to fabricate structures in a controllable manner with nanotubes, nanoparticles, and other even biomolecules to produce nanoscale structures.

[Near term commercialization] NanoInk is helping the pharmaceutical industry prevent counterfeiting and diversion of drugs by fabricating nanoscale structures on individual doses of pharmaceutical products. This technology is now being developed with two of the largest pharmaceutical companies in the world. In addition to nano encryption we are also exploring additive repair for photo masks and thin film transistors on LCD panels.


Zyvex's Von Ehr said:
The key differentiator at Zyvex is the precision and the hierarchical scale. We want to make atomically precise materials at the very smallest scale, the nanoscale, put those together into larger subassemblies, and build up to the microscale, then put those together in larger assemblies in what we’re calling the meso or the millimeter scale, and build larger and larger assemblies, but have atomic precision all the way down to the atoms, and all the way up to large things, things potentially as large as a car or even a house someday. We probably won’t design that with atomic precision, but the parts that go in it will be manufactured in high volume and then put together in assemblies.

Tihamer T. Toth-Fejel talks about scaling from one nanomachine:
Take one relatively simple nanomachine that can make a less complicated version of itself. It’s not quite self replication, but basically it takes an input stream... it’s like a machine shop. Using a machine shop you can make an assembly line, so you make an assembly line. What kind of machines do you have there? You have an assembly line of primitive, single use machines that all they can do is make one other different kind of machine shop, like a lathe, a drill and a saw, for example. So you have an entire line of them. Then you take this line, and normally when we think of an assembly line we think of putting pieces on the front end and it gets assembled down the line. What we want is an assembly line that builds things in two dimensions, that builds a plane of devices. That’s how we get to a billion devices. You start with one nanomachine; call it a master maker that builds a nanoline. The nanoline builds a membrane. What the membrane does is, it accepts molecular parts that are made using synthetic chemistry, which we can do today, and assembles them into whatever product you want.

State of dip pen nanolithography

Here is a pdf that describes the technology of dip pen nanolithography. Nanoink is the main company with this technology. They have arrays of 55,000 dip pens and have plans for megadpn arrays with millions of dip pens.

They can deposit various kinds of material onto various substrates. Some deposits are in the 13-25 nanometer size. They are using arrays of scanning probe tips so as the scanning probe accuracy and repeatability is improved the arrays could become molecularly precise.

September 20, 2006

Nissan testing sensors for driver early warning

Japan has infrared sensors hanging from street poles relaying information to car navigation equipment so drivers can map out the quickest routes. Nissan is testing the use of those sensors to provide accident danger alerts to drivers

Nissan plans to gather data to see whether the technology would contribute to reducing accidents and change driver behavior. The Tokyo-based automaker said it hopes to offer its vehicle-alert system commercially by 2010.

Advanced computer storage research from IBM and others

From Computerworld, IBM is working on three advanced memory storage technologies


Carbon annotates, which are molecule-size objects composed entirely of carbon in a cylindrical structure, giving them unique properties.

Nantero Inc. in Woburn, Mass., has built prototypes of a chip called NRAM (for nanotube-based/nonvolatile RAM) that is faster than DRAM, as portable as flash memory, and able to provide permanent storage because the wafer uses nonvolatile storage as its basis

Colossal Storage Corp. in Pokomoke City, Md., is developing a rewritable 3-D volume holographic removable disk media. The nanotechnology under development at Colossal is a possible replacement for today's magnetic disk drives and memory chips. Unlike magnetic media, which only stores data on the surface of the disk drive, holographic optical disk drives use two or more laser beams that work with one another to read and write data throughout the disk media.

Michael Thomas, CEO of Colossal, says holographic optical media drives are superior to other storage nanotechnologies because of their 100+TB capacities, near zero read and write response times and 100-plus year lifespan.

The first generation of holographic optical disk media and disk drives is scheduled to hit the market this year when InPhase Technologies Inc. in Longmont, Colo., releases a 300GB holographic disk and drive. About the same size as today's DVDs, they will hold the equivalent of 64 full-length movies. While they initially will be available in a write-once format, a rewritable disk is on InPhase's product road map.

Seagate Technologies's new HAMR (heat-assisted magnetic recording) technology addresses current concerns about today's perpendicular recording methods for magnetic disk media. HAMR, combined with self-ordered magnetic arrays of iron-platinum particles, is expected to break through the so-called superparamagnetic limit of magnetic recording by more than a factor of 100 to ultimately deliver storage densities as great as 50 terabits per square inch. It is expected after 2010 in commercial drives.

EMdrive issues and discussion

Wikipedia article indicates potential problems with the EM Drive the EM drive is based on microwave radiation pressure in a waveguide chamber. This link is to a pdf by the developer Roger Shawyer.

Some possible flaws in the details of Shawyer's calculations that have been suggested include:

The analysis of the effect of the wave reflecting off of the two ends of the waveguide may be incomplete due to failing to consider the forces caused by the wave impinging upon the conical side of the waveguide; if the large end of the waveguide and the combined system of the small end and the conical sides are considered separately, they both have the same cross-sectional area so one would expect that the radiation pressure upon them would be equal in magnitude yet opposite in direction, thus producing zero net force

The New Scientist article also mentions that as the EMDrive begins to move, the microwave energy resonating in the chamber is drained very quickly - quicker than it can be replenished. This implies that the system is suitable for producing a static force, but not acceleration. This means the EMDrive, if developed further, could be suitable for hovering vehicles and objects, but not for flying around as people would like to imagine. Think of it as a frictionless replacement for wheels. With this consideration, the EMDrive no more violates conservation of momentum and energy than, say, a magnetically levitating train. Instead, it violates the general principle of relativity since it would be possible to distinguish when the device is in freefall (device works) and in free space (device does not work, runs out of energy). This is based on the New Scientist article. However it is possible it will run fine, in pulses, in both zero-gravity and freefall.

The consideration of different frames of inertial reference may be invalid. In other words, the operation of the device may boil down to construction of a ship with a large sail at one end and a small sail at the other end, then standing in the middle and blowing uniformly in all directions; this would only create forces within the boat rather than a force capable of propelling the boat away from any fixed body.

My opinion: It seems others have been willing to give him some more money to build something which he claims will provide a lot of force. The experimental effort looks like it will clearly settle the issue of whether it works. Plus the previous prototype work could be replicated and the existing prototypes analyzed.

There is more discussion at the wikipedia discussion area

September 18, 2006

Condensed multi-wall carbon nanotubes could lead to superstrong fibers

(PDF) A paper on condensed multi-wall carbon nanotubes suggests that they could be an approach to making superstrong fibers suitable for space elevators Target of achieving 48.5+ GPa of tensile strength, good sheer strength and temperature resistance. Zhiping Xu, Lifeng Wang, and Quanshui Zheng of Tsinghua University, Beijing, China wrote the paper.

Record magnetic recording density 421 gbit/inch**2

Seagate expects drive capacity to increase to 275 Gbytes for 1- and 1.8-inch consumer drives, 500 Gbytes for 2.5-inch notebook drives and nearly 2.5 Tbytes for 3.5-inch desktop drives based on the new higher density capability.

Kryder said heat-assisted magnetic recording (HAMR) and bit-patterned media techniques can boost storage capacities to reach or exceed 50 terabits/ inch**2. Drives with those capacities would be have over 200 Tbytes of storage for a 3.5 inch drive.

Intel, UCSB make hybrid Si-laser chip advance


the breakthrough device

By 2010, there should be multi-terabit communication speed inside chips. Computers of all kinds will be far more powerful and it will be far easier, cheaper and faster to integrate multiple chips, cores and computer systems for more effective massively parallel processing.

Researchers at Intel and the University of California, Santa Barbara have made what they say is a major breakthrough in making hybrid silicon lasers that they suggest could have a huge impact on chip-to chip communication and on optical communications networks. The researchers caution that commercializing the laser chip could take till the end of the decade.



Concept of a future integrated terabit silicon optical transmitter containing 25 hybrid silicon lasers, each emitting at a different wavelength, coupled into 25 silicon modulators, all multiplexed together into one output fiber.

The teams indicate bonding the silicon and InP-based laser chips can be achieved at relatively low temperatures and with acceptable and cost effective manufacturing techniques. They suggest the device could handle data rates of between 20Gbit/s to 40Gbit/s, up from today's 10Gbit/s. John Bowers, director of the multidisciplinary optical switching technology center at UC-Santa Barbara, who is involved in the research, says dozens or hundreds of lasers could be integrated on to a single chip.

For a few dollars apiece, such chips could transmit data at 100 times the speed of laser-based communications equipment, called optical transceivers, that typically cost several thousand dollars. The Intel-Santa Barbara work proves that it is possible to make complete photonic devices using standard chip-making machinery, although not entirely out of silicon. "There has always been this final hurdle," said Mario Paniccia, director of the Photonics Technology Lab at Intel. "We have now come up with a solution that optimizes both sides."

In the past it has proved impossible to couple standard silicon with the exotic materials that emit light when electrically charged. But the university team supplied a low-temperature bonding technique that does not melt the silicon circuitry. The approach uses an electrically charged oxygen gas to create a layer of oxide just 25 atoms thick on each material. When heated and pressed together, the oxide layer fuses the two materials into a single chip that conducts information both through wires and on beams of reflected light.

more reading:
More info here at photonics.com

Here is the intel research description

Intel pdf whitepaper on the hybrid silicon laser advance

Intels terascale research project page

Intels computing vision for 2015