Number 803, November 29, 2006
by Phil Schewe, Ben Stein, and Davide Castelvecchi
Protein Folding in a Curved Space
Physicists at the Università di
Firenze, in Italy, have put a new slant on the protein folding
problem. Proteins are special polymers made of amino acids. Generic
polymers, when you cool them enough, will collapse in a ball.
Proteins do
something more interesting: they fold up into a particular compact
form. If a protein fails to find this form it won't be able to carry
out its designated function and disease can result. For instance,
some nonfolding proteins will aggregate into long filaments, amyloid
fibrils, and this has proven to be the basis for neurodegenerative
diseases like Alzheimer's.
Finding the precise dynamics behind protein folding would be like
Isaac Newton finding the laws of universal gravitation. We aren't
at that point yet, but there are ways of investigating some of the
steps proteins take to arrive at their proper form. One fruitful
approach is to see the multi-step process as taking place in a
series of energy transactions. At any moment the protein can be
represented as a point moving around in an abstract space whose
coordinates correspond to all possible configurations and the
associated energy needed to have that structure, sort of like a ball
rolling along on the inner surface of a bowl. The bowl might have
some partitions, and the ball might be able to roll up out of one
compartment and into a neighboring one if its energy is sufficient,
or if the wall between compartments is low enough, or if some extra
energy (maybe in the form of heat or a chemical reaction) is added.
Lapo Casetti (casetti@fi.infn.it) and Lorenzo Mazzoni have attempted
to make the "energy landscape" method even more geometrical by
characterizing the folding forces at work as being a form of
curvature in the bowl-like well in which the protein is operating.
This is analogous to what Albert Einstein did in characterizing
gravity as the curvature of spacetime in which planets and stars
move about. Mazzoni and Casetti seek to determine what it is about
the curvature of the energy landscape that encourages proteins to
fold and other polymers not to fold.
Mazzoni and Casetti,
Physical Review Letters, 24 November 2006
Contact Lapo Casetti
Università di Firenze
casetti@fi.infn.it
Warm Detectors Look At Brain Magnetism
The brain and heart both
generate weak magnetic fields which, in ways different from electric
fields, can reveal subtle clues about such maladies as epilepsy and
arrhythmias. Sensitive magnetometers, based on superconducting
quantum interference devices (SQUIDs), have been used to prepare
detailed magnetoencephalograms (MEGs). Unfortunately, these devices
require liquid helium and all its associated cryogenic equipment.
Michael Romalis, a Princeton University physicist, detects the brain's faint
magnetic fields using instead a vessel filled with potassium atoms,
which have been polarized by a laser beam. The brain fields cause
the potassium atoms to precess in a measurable way. Already, Romalis
(romalis@princeton.edu) says, his device has attained a sensitivity
30 times better than previous atomic magnetometers used for
biosensors, and a spatial resolution comparable to that for SQUIDs,
with the prospect of improving by another factor of ten.
In a related
paper, Romalis's group in collaboration with Karen Sauer from George
Mason University used a different kind of potassium magnetometer to detect
radio-frequency signals generated by ammonium nitrate (which is
often
used in explosives) with a sensitivity some 10 times better than
with conventional devices.
A team of Italian and German physicists has
developed a new, flexible fabrication technique for rewritable
photonic crystal devices, which could make it easier to create and
modify circuits in which photons process information in the same way
that electric currents do in electronics.
Photonic crystals are
structures with a periodically varying refractive index that affects
the transmission of light inside the crystal; they behave like a
mirror by blocking light propagation at some wavelengths and behave
like a transparent medium by letting other wavelengths get through.
Defects in the periodic structure, arranged in specific geometries,
can act as resonant cavities, mirrors, waveguides, or the optical
analogue of transistors.
The new technique is based on a two-dimensional lattice of
microscopic pores arranged in a beehive pattern. The researchers can
then insert defects by injecting different materials into the pores,
which are a few hundreds of nanometers wide. In the photonic
crystal, light is mostly confined to the two-dimensional structure,
but small amounts leak outside of the plane and can be read out with
a near-field microscope. Francesca Intonti, of the European
Laboratory for Non-linear Spectroscopy, in Florence, says that the
technique makes it easier and more flexible to experiment with
different materials and configurations, compared with other
fabrication techniques such as lithography; using liquids also
allows for the circuits to be reconfigured at will. Another
possibility, she says, could be to inject liquid crystals, whose
refraction index could then be tuned from the outside, or
light-emitting materials, which could act as local sources of laser
light. So far, the researchers have created photonic components
pixel by pixel, but in principle the process could be automatized,
Intonti says.
Enlarge text
Shrink text
Print
E-mail
Digg this
Del.icio.us
Furl