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Time : The Unresolved Mystery of Physics.

The physics world accepts the idea of spacetime, a combined metrical entity which puts time on the same footing as the visible three spatial dimensions. Further spatial dimensions are added in some theories to help assimilate all physical forces into a unified model of reality. But what about adding an extra dimension of time too? Itzak Bars and Yueh-Cheng Kuo of the University of Southern California do exactly that, and add an extra spatial dimension too.

Bars explains this proposal with a comparison. Just as a projection of a 3D object onto a 2D wall can have many different shapes, and each such shape is incapable of fully conveying all the properties of the 3D object, so the single-time description of dynamics in the standard formulation of physics is insufficient to capture many properties of dynamical systems which have remained mysterious or unnoticed.

The addition of an extra time and an extra space dimension, together with a requirement that all motion in the enlarged space be symmetric under an interchange of position and momentum at any instant, reproduces all possible dynamics in ordinary spacetime, and brings to light many relationships and hidden symmetries that are actually present in our own universe.

The hidden relationships among dynamical systems are akin to relationships that exist between the multiple shadows of a 3D object projected on a 2D wall. In this case the object is in a spacetime of 4 space and 2 time dimensions while the shadows are in 3 space and 1 time dimensions. The motion in 4+2 dimensions is actually much more symmetric and simpler than the complex motions of the shadows in 3+1 dimensions.

Besides the general unification of dynamics described above, what does this addition to one extra time and one extra space dimension (in addition to all those extra space dimensions called for in string theory) accomplish that could not be achieved without it? Bars (bars@usc.edu) says that his theory explains CP conservation in the strong interactions described by QCD without the need for a new particle, the axion, which has not been found in experiments.

It also explains the fact that the elliptical orbit of planets remains fixed (not counting well-known tiny precessions). This “Runge-Lenz” symmetry effect has remained somewhat mysterious in the study of celestial mechanics, but now could be understood as being due to the symmetry of rotations into the fourth space dimension.

A similar symmetry observed in the spectrum of hydrogen would also be accounted for in 2-time physics, and again explained as a symmetry of rotations into the extra space and time dimensions. There are many such examples of hidden symmetries in the macroscopic classical world as well as in the microscopic quantum world, Bars argues, which can be addressed for the first time with the new 2T formulation of physics.

There have been previous attempts to formulate theories with a second time axis, but Bars says that most of these efforts have been compromised by problems with unitarity (the need for the sum of all probabilities of occurrences to be no greater than 1) and causality (maintaining the thermodynamic arrow of time).

The USC theorists have reformulated their model to fit into the ongoing supersymmetry version of the standard model and expect their ideas to be tested in computer simulations and in experiments yet to come. (Physical Review Letters, upcoming article)

First Direct Measurement of DNA Stacking Forces

DNA is one of the most important and studied molecules around, and yet only now has a team of scientists, working at Duke University, succeeded in measuring the force between the nucleotides in a single-stranded DNA (ssDNA) molecule, using an atomic force microscope (AFM).

A double-stranded DNA is characterized by two principal forces---the stacking force between base units along the length of the double helix and the pairing force (Watson-Crick pairing) between the opposing base units forming the rungs of the helix. Measurements of DNA elasticity dating back to the 1990s (http://www.aip.org/pnu/1997/split/pnu312-1.htm) were done with double-stranded DNA, and it is difficult to separate the effects of the pairing and stacking forces.

That's why Piotr E. Marszalek (pemar@duke.edu) and his colleagues (Changhong Ke, Michael Humeniuk, and Hanna S-Gracz) turned to ssDNA. They rigged an artificial ssDNA consisting only of adenine base units attached to a gold substrate, and then pulled it with an AFM tip.

With a force resolution of about 1 pico-Newton, the Duke apparatus detected one plateau in elasticity (of the stacking force) at around 23 pN, which was expected, and then a second plateau around 113 pN. (Ke et al. Physical Review Letters, upcoming article)( a paper measuring forces for a single RNA molecule, finding a single force plateau at 20 pN, appeared in Seol et al., Phys Rev Lett, 13 April 2007)

News inside News-
IMPORTANT PROCESSES IN SINGLE DNA MOLECULES -
IMPORTANT PROCESSES IN SINGLE DNA MOLECULES have been observed for the first time by using the atomic force microscope (AFM), in which the deflections of a tiny stylus over the contours of a surface can be turned into molecular-scale images. At the APS Meeting this week in Kansas City, Carlos Bustamante of the University of Oregon (541-346-1537) and his colleagues presented movies showing the first stages of DNA replication, in which a protein is seen to slide on DNA like a bead on a string to find the exact site where it could attach and start the replication process. Binding DNA and RNA polymerase (the protein that mediates the transcription of DNA into RNA) to a mica surface, Neil Thomson of UC-Santa Barbara (805-893-4544) and his colleagues produced 5-nm-resolution movies of the transcription process, in which RNA polymerase pins down the middle of a single DNA strand and then pulls the strand through as it starts transcribing the DNA into RNA using RNA-building-blocks called NTPs (Biochemistry, 21 Jan. 1997). Using an AFM, Gil Lee of the Naval Research Laboratory (202- 763-5383) found that a force of about 600 piconewtons was required to tear apart two complementary strands of DNA, namely a 20-base-pair-long strand of polycytosine (a form of single-strand DNA) from single strands of polyinosine averaging 160 base-pairs long.

Duke Engineers Building 'Erasible' Detectors, 'Nanobrushes' and DNA 'Highrises'-
A Duke University engineering group is doing pioneering work at very diminutive dimensions. Their basic studies could lead to genetically engineered proteins that can form erasable chemical detectors; self-grown forests of molecular "bottlebrushes" that keep themselves contamination-free; and auto-assembled DNA "towers" that could become anchors for the tiniest of devices.

Professor of biomedical engineering Ashutosh Chilkoti of Duke's Pratt School of Engineering will describe such advances in designing bio-detectors and structures scaled in the millionths and billionths of a meter in a Wednesday, March 29, 2006, talk at the American Chemical Society's 231st national meeting in Atlanta.

He will speak at a session beginning at 8:30 a.m. in the Juniper Room in Atlanta's OMNI at CNN Center. His group's work is supported by the National Science Foundation, the National Institutes of Health and Duke's Center for Biologically Inspired Materials and Materials Systems.

The proposed erasable detectors are made of artificial elastin-like polypeptides (ELPs), which are short segments of proteins normally soluble in water. Crafted through genetic engineering with the aid of bacteria, such ELPs have the useful property of coming out of a solution to form a solid whenever a slight temperature increase or other alterations to the water induces a phase change.

Chilkoti's group reported in the November 1999 issue of the journal Nature Biotechnology that an ELP could also be chemically linked with another protein so that both "fusion proteins" leave solution together after such phase changes.

Following that discovery, for which Duke has applied for a patent, Chilkoti's team reported in the February 2003 issue of Analytical Chemistry that this method could be used to create a "reversible" protein sensor on a glass slide.

After dotting such a slide with microscopic amounts of surface-bound ELPs, the researchers discovered that dissolved fusion proteins would selectively attach to those microdots upon leaving the solution.

They also found the "captured" fusion proteins could pull other select proteins from solution so those could be chemically identified. Finally, they confirmed that microdot array could then be wiped clean of all attached proteins simply by "reversing the phase transition," Chilkoti said in an interview.

In this case, the researchers added salt to the solution to induce the same kind of phase changes as does raising the water temperature.

"It's a way of creating what I would call a cleanable surface for sensing," Chilkoti said. "We can create a surface for a sensor, do a binding reaction, detect a signal, then release everything. Then we could repeat the same process with the same fusion protein, or a different one."

But the dots used in that experiment were "microns" wide -- at the millionths of a meter scale. Chilkoti's team wondered if the process would also work at the thousand-times-smaller "nanometer" scale (billionths of a meter) to capture a few hundred individual molecules.

So they collaborated with Stefan Zauscher, a Duke assistant professor of mechanical engineering and materials science whose group has an Atomic Force Microscope that can deposit nanoscale amounts of material through a process called "dip pen nanolithography" (DPN).

Instead of using a glass slide, that collaboration fabricated a gold surface on which to bind ELP nanodots because "DPN really works well on gold," Chilkoti said. Repeating the reversible phase change experiments to draw proteins from solution for detection, "we found it worked even better at the nanoscale," he added.

A major reason for their improved success is that the gold surface was specially modified to prevent stray proteins from attaching to the experimental array, he said. "There was nothing binding in the background, so we could get extraordinary reversibility. We would have a clean surface, and we could do it over and over."

The goal of keeping away stray proteins also motivated Chilkoti's group to grow forests of special 15-nanometer-high polymer brushes with fuzzy branches that could act as raised platforms on which to locate ELP protein sensors or other molecular sized devices.

In a paper in the February 2004 issue of the journal Advanced Materials, Chilkoti and colleagues described building such a "non-fouling" platform by inducing methyl methacrylate molecules to grow into tall stalks from a gold surface through a self-assembly process known as "atom transfer radical polymerization."

In the same process, molecules of polyethylene glycol (PEG) were also induced to form fuzzy branches extending from those stalks, creating the overall look of bottle brushes.

In this case, the PEG branches formed a protective barrier that kept unwanted proteins from coming out of solution and sticking to the platform. "PEG is the gold standard for making a film or coating that is protein resistant," Chilkoti said. "But it has been difficult to get it to work on a range of materials."

In an attempt to use nature's method to grow chain-like polymers, Chilkoti's and Zauscher's laboratories are now exploring a method to build nanotowers of DNA -- the master molecule that makes up genes -- block by block from the surface.

In a paper published online on Sept. 27, 2005, in the Journal of the American Chemical Society, the Duke researchers described how the enzyme terminal deoxynucleotidyl transferase (TdTase) could be used to induce short DNA strands to form extensive chains. Those "polymerizing" chains, growing vertically from nanodots of gold patterned onto silicon, assembled into tower-like structures .

The process worked in a solution of enzyme and DNA building blocks -- called nucleotides -- with the TdTase grabbing floating nucleotides and pulling those into the extending structure.

"We believe that TdTase-catalyzed surface-initiated polymerization of DNA will be a useful tool for the fabrication of complex biomolecular structures with nanoscale resolution," the researchers wrote.

Release link: http://www.aip.org