Tag Archives: basic research

Werner Heisenberg

photo of Werner Heisenberg

Read a very nice biography from Center for History of Physics of the American Institute of Physics for Werner Heisenberg, the founder of quantum mechanics, and the Heisenberg uncertainty principle:

Heisenberg set himself the task of finding the new quantum mechanics upon returning to GÃ¶ttingen from Copenhagen in April 1925. Inspired by Bohr and his assistant, H.A. Kramers, in Copenhagen, Pauli in Hamburg, and Born in GÃ¶ttingen, Heisenberg’s intensive struggle over the following months to achieve his goal has been well documented by historians. Since the electron orbits in atoms could not be observed, Heisenberg tried to develop a quantum mechanics without them.

He relied instead on what can be observed, namely the light emitted and absorbed by the atoms. By July 1925 Heisenberg had an answer, but the mathematics was so unfamiliar that he was not sure if it made any sense. Heisenberg handed a paper on the derivation to his mentor, Max Born, before leaving on a month-long lecture trip to Holland and England and a camping trip to Scandinavia with his youth-movement group. After puzzling over the derivation, Born finally recognized that the unfamiliar mathematics was related to the mathematics of arrays of numbers known as “matrices.” Born sent Heisenberg’s paper off for publication. It was the breakthrough to quantum mechanics.

Microbes Beneath the Sea Floor

This stuff is cool. Here is the full press release from Penn State, Microbes beneath sea floor genetically distinct

Tiny microbes beneath the sea floor, distinct from life on the Earth’s surface, may account for one-tenth of the Earth’s living biomass, according to an interdisciplinary team of researchers, but many of these minute creatures are living on a geologic timescale.

“Our first study, back in 2006, made some estimates that the cells could double every 100 to 2,000 years,” says Jennifer F. Biddle, PhD. recipient in biochemistry and former postdoctoral fellow in geosciences, Penn State. Biddle is now a postdoctoral associate at the University of North Carolina, Chapel Hill.

The researchers looked at sediment samples from a variety of depths taken off the coast of Peru at Ocean Drilling Site 1229. They report their findings in today’s (July 22) online issue of the Proceedings of the National Academy of Sciences.

“The Peruvian Margin is one of the most active surface waters in the world and lots of organic matter is continuously being deposited there,” says Christopher H. House, associate professor of geoscience. “We are interested in how the microbial world differs in the subsea floor from that in the surface waters.”

The researchers used a metagenomic approach to determine the types of microbes residing in the sediment 3 feet, 53 feet, 105 feet and 164 feet beneath the ocean floor. The use of the metagenomics, where bulk samples of sediment are sequences without separation, allows recognition of unknown organism and determination of the composition of the ecosystem.

“The results show that this subsurface environment is the most unique environment yet studied metagenomic approach known today,” says House. “The world does look very different below the sediment surface.” He notes that a small number of buried genetic fragments exist from the water above, but that a large portion of the microbes found are distinct and adapted to their dark and quiet world.

The researchers, who included Biddle; House; Stephan C. Schuster, associate professor; and Jean E. Brenchley, professor, biochemistry and molecular biology, Penn State; and Sorel Fitz-Gibbon, assistant research molecular biologist at the Center for Astrobiology, UCLA, found that a large percentage of the microbes were Archaea, single-celled organisms that look like Bacteria but are different on the metabolic and genetic levels. The percentage of Archaea increases with depth so that at 164 feet below the sea floor, perhaps 90 percent of the microbes are Archaea. The total number of organisms decreases with depth, but there are lots of cells, perhaps as many as 1,600 million cells in each cubic inch.
Continue reading →

Pseudogap and Superconductivity

MIT physicists shed light on key superconductivity riddle

Hudson’s team is focusing on the state of matter that exists at temperatures just above the temperature at which materials start to superconduct. This state, known as the pseudogap, is poorly understood, but physicists have long believed that characterizing the pseudogap is important to understanding superconductivity.

In their latest work, published online on July 6 in Nature Physics, they suggest that the pseudogap is not a precursor to superconductivity, as has been theorized, but a competing state. If that is true, it could completely change the way physicists look at superconductivity, said Hudson.

“Now, if you want to explain high-temperature superconductivity and you believe the pseudogap is a precursor, you need to explain both. If it turns out that it is a competing state, you can instead focus more on superconductivity,” he said.

Measuring Protein Bond Strength with Optical Tweezers

Using a light touch to measure protein bonds

MIT researchers have developed a novel technique to measure the strength of the bonds between two protein molecules important in cell machinery: Gently tugging them apart with light beams. “It’s really giving us a molecular-level picture of what’s going on,” said Matthew Lang, an assistant professor of biological and mechanical engineering
…
The researchers studied the interactions between the proteins by pinning one actin filament to a surface and controlling the motion of the second one with a beam of light. As the researchers tug on a bead attached to the second filament, the bond mediated by the actin-binding protein eventually breaks.

With this technique, the researchers can get a precise measurement of the force holding the proteins together, which is on the order of piconewtons (10^-12 newtons).

Exploring the Signaling Pathways of Cells

New probe may help untangle cells’ signaling pathways

MIT researchers have designed a new type of probe that can image thousands of interactions between proteins inside a living cell, giving them a tool to untangle the web of signaling pathways that control most of a cell’s activities.

“We can use this to identify new protein partners or to characterize existing interactions. We can identify what signaling pathway the proteins are involved in and during which phase of the cell cycle the interaction occurs,” said Alice Ting, the Pfizer-Laubach Career Development Assistant Professor of Chemistry and senior author of a paper describing the probe published online June 27 by the Journal of the American Chemical Society.

The new technique allows researchers to tag proteins with probes that link together like puzzle pieces if the proteins interact inside a cell. The probes are derived from an enzyme and its peptide substrate. If the probe-linked proteins interact, the enzyme and substrate also interact, which can be easily detected.

To create the probes, the researchers used the enzyme biotin ligase and its target, a 12-amino-acid peptide.

Lancelet Genome Provides Answers on Evolution

Lancelet genome shows how genes quadrupled during vertebrate evolution by Robert Sanders

“If you compare the 23 chromosomes of humans with the 19 chromosomes of amphioxus, you find that both genomes can be expressed in terms of 17 ancestral pieces. So, we can say with some confidence that 550 million years ago, the common ancestor of amphioxus and humans had 17 chromosomal elements.”
…
Each of those 17 ancestral segments was duplicated twice in the evolution of vertebrates, after which most of the routine “housekeeping” genes lost the extra copies. Those left, totaling a couple thousand genes, found new functions that, Putnam said, make us different from all other creatures.

“These few thousand genes have been retooled to make humans more elaborate than their simpler ancestors. They are involved in setting up the body plan of an animal and differentiating different parts of the animal,” he said. “The hypothesis, pretty strongly supported by this data, is that the multiplication of this particular kind of gene and differentiation into different functions was important in the formation of vertebrates as we know them.”

“The most exciting thing that the amphioxus genome does is provide excellent evidence for the idea that Ono proposed in 1970, that the human genome had undergone two rounds of whole-genome duplication with subsequent losses,”

A great example of the scientific method in action. It often isn’t a matter of developing a theory one day, testing it the next and learning the outcome the next. The process can take decades for complex matters.

Bacteria Evolutionary Shift Seen in the Lab

Bacteria make major evolutionary shift in the lab

A major evolutionary innovation has unfurled right in front of researchers’ eyes. It’s the first time evolution has been caught in the act of making such a rare and complex new trait. And because the species in question is a bacterium, scientists have been able to replay history to show how this evolutionary novelty grew from the accumulation of unpredictable, chance events.
…
sometime around the 31,500th generation, something dramatic happened in just one of the populations – the bacteria suddenly acquired the ability to metabolise citrate, a second nutrient in their culture medium that E. coli normally cannot use. Indeed, the inability to use citrate is one of the traits by which bacteriologists distinguish E. coli from other species.
…
The replays showed that even when he looked at trillions of cells, only the original population re-evolved Cit+ – and only when he started the replay from generation 20,000 or greater. Something, he concluded, must have happened around generation 20,000 that laid the groundwork for Cit+ to later evolve.

Lenski and his colleagues are now working to identify just what that earlier change was, and how it made the Cit+ mutation possible more than 10,000 generations later.

Materials Engineers Create Perfect Light “sponge”

Materials engineers create perfect light “sponge”

The team designed and engineered a metamaterial that uses tiny geometric surface features to successfully capture the electric and magnetic properties of a microwave to the point of total absorption.

“Three things can happen to light when it hits a material,” says Boston College Physicist Willie J. Padilla. “It can be reflected, as in a mirror. It can be transmitted, as with window glass. Or it can be absorbed and turned into heat. This metamaterial has been engineered to ensure that all light is neither reflected nor transmitted, but is turned completely into heat and absorbed. It shows we can design a metamaterial so that at a specific frequency it can absorb all of the photons that fall onto its surface.”
…
The metamaterial is the first to demonstrate perfect absorption and unlike conventional absorbers it is constructed solely out of metallic elements, giving the material greater flexibility for applications related to the collection and detection of light, such as imaging, says Padilla, an assistant professor of physics.

At the Heart of All Matter

The hunt for the God particle by Joel Achenbach

Physics underwent one revolution after another. Einstein’s special theory of relativity (1905) begat the general theory of relativity (1915), and suddenly even such reliable concepts as absolute space and absolute time had been discarded in favor of a mind-boggling space-time fabric in which two events can never be said to be simultaneous. Matter bends space; space directs how matter moves. Light is both a particle and a wave. Energy and mass are inter- changeable. Reality is probabilistic and not deterministic: Einstein didn’t believe that God plays dice with the universe, but that became the scientific orthodoxy.
…
Most physicists believe that there must be a Higgs field that pervades all space; the Higgs particle would be the carrier of the field and would interact with other particles, sort of the way a Jedi knight in Star Wars is the carrier of the “force.” The Higgs is a crucial part of the standard model of particle physics—but no one’s ever found it.
…
The Higgs boson is presumed to be massive compared with most subatomic particles. It might have 100 to 200 times the mass of a proton. That’s why you need a huge collider to produce a Higgs—the more energy in the collision, the more massive the particles in the debris. But a jumbo particle like the Higgs would also be, like all oversize particles, unstable. It’s not the kind of particle that sticks around in a manner that we can detect—in a fraction of a fraction of a fraction of a second it will decay into other particles. What the LHC can do is create a tiny, compact wad of energy from which a Higgs might spark into existence long enough and vivaciously enough to be recognized.

Previous posts on CERN and the Higgs boson: The god of small things – CERN Prepares for LHC Operations – CERN Pressure Test Failure – The New Yorker on CERN’s Large Hadron Collider

Electron Filmed for the First Time

Now it is possible to see a movie of an electron. The movie shows how an electron rides on a light wave after just having been pulled away from an atom. This is the first time an electron has ever been filmed. Previously it has been impossible to photograph electrons since their extremely high velocities have produced blurry pictures. In order to capture these rapid events, extremely short flashes of light are necessary, but such flashes were not previously available.

With the use of a newly developed technology for generating short pulses from intense laser light, so-called attosecond pulses, scientists at the Lund University Faculty of Engineering in Sweden have managed to capture the electron motion for the first time. “It takes about 150 attoseconds for an electron to circle the nucleus of an atom. An attosecond is 10-18 seconds long, or, expressed in another way: an attosecond is related to a second as a second is related to the age of the universe,” says Johan Mauritsson, an assistant professor in atomic physics at the Faculty of Engineering, Lund University.

Scientists also hope to find out more about what happens with the rest of the atom when an inner electron leaves it, for instance how and when the other electrons fill in the gap that is created. “What we are doing is pure basic research. If there happen to be future applications, they will have to be seen as a bonus,” adds Johan Mauritsson. The length of the film corresponds to a single oscillation of the light, but the speed has then been ratcheted down considerably so that we can watch it. The filmed sequence shows the energy distribution of the electron and is therefore not a film in the usual sense.

Photo: Experimental results obtained in helium at an intensity of 1:2 x 1013 W=c/m2 are shown. The results are
distinctively different from those taken in argon (Fig. 1).With this higher intensity, more momentum is transferred to the electrons, and in combination with the lower initial energy, some electrons return to the atomic potential for further interaction. In the first panel, we compare the experimental results (right) with theoretical calculations (left) obtained for the same conditions.
Continue reading →