An accurate calculation of atomistic dynamics requires extensive
computer power. To produce a millisecond movie of moving molecules
literally takes ages even by the fastest supercomputer. Chemical
reactions require even longer timescales as they involve rare
collisions between molecules with a very specific orientation and
momentum. Luckily, intelligent algorithms prevent us for having to
wait that long. The recently developed path sampling methods can be
best described as a kind of "Improbability Drive" from the
"Hitchhiker's Guide to the Galaxy"[1]. Instead of performing a single
calculation, a series of simulations is released. The probability of
being reactive is artificially enhanced at each step. Still, reaction
rate evaluations can last for several months. One of the problems is
that present methods have much difficulty to find competing mechanisms
once it is trapped in a specific reaction channel. This letter [2]
shows how the efficiency can be improved considerably when the
separate simulations are allowed to exchange information during the
run. A test on the opening transition of DNA showed that the
efficiency increased by a factor 20. This opens up the possibility to
study many interesting problems which were hitherto impossible.
[1] Douglas Adams, "The Hitchhiker's Guide to the Galaxy", 1979
[2] Titus S. van Erp, "Reaction rate calculation by parallel path
swapping", Phys. Rev. Lett. accepted for publication (Article is
expected to be published in the July 6, 2007 issue).
***
Atomic Force Spectroscopy Captures the Fundamental Forces Stabilizing DNA Structure
Piotr Marszalek and colleagues at Duke University's Pratt School of Engineering have reported the first direct measurements of the forces that contribute to the stability of DNA structure. DNA molecules consist of two intertwined chains, and it is the precise sequence of stacked nucleotides-the four different varieties of 'links' in each chain--that encodes the genetic blueprint of all living organisms. The DNA structure is primarily stabilized by two types of interactions: hydrogen-bonding between complementary nucleotide bases in opposite chains (Watson-Crick pairing) and base stacking between nucleotides that are positioned on top of each other along the DNA axis. The respective contribution of these interactions to DNA's integrity has been difficult to establish because these interactions cannot be isolated in the complete double helix. Now, the research team has captured the "mechanical fingerprint" of a single-stranded DNA (ssDNA) chain by atomic force microscopy, a method that allows force measurements at the level of individual molecules. They attached ssDNA molecules consisting solely of adenines (one of the four nucleotide bases) to a gold substrate and grabbed the end of individual molecules with the microscope's cantilever tip. They then repeatedly stretched and relaxed the DNA and measured its elasticity profiles. Unexpectedly, they found two pronounced plateau features in the force-extension relationships (at ~23 pN and ~113 pN respectively) that indicate some force-induced structural rearrangements within the ssDNA. Because the stacking of adenines forms a spiral structure within ssDNA, Marszalek's team suggests that the two plateaus represent the unraveling of the helix as the base-stacking interactions sever. Thus, the measurements directly captured, for the first time, the strength of base stacking interactions in DNA in the absence of base-pairing, a significant contribution to understanding the forces that stabilize DNA structure.
***
Non-Abelian Josephson Currents
Quantum mechanics is most commonly used to describe physics on microscopic
scales, those of atoms and nuclei. Superconductivity, on the other hand, may
be thought of as a macroscopic manifestation of quantum physics for a
collection of particles where electric currents flow without resistance. In
the absence of coupling between the two superconducting regions, there is a
separate symmetry for the each of the regions. The Josephson effect occurs
when electrical currents spontaneously flow through a normal barrier
separating two superconducting regions. The wave functions describing the
states of the separate superconducting regions are coupled across the
barrier and the current depends on the phase difference of the two wave
functions. This causes a loss of symmetry from the uncoupled system of
superconductors. This paper explores the possibility of similar junctions in
more complex systems, possibly including high-density quark matter present
in neutron stars and some forms of high-temperature superconductors studied
in recent times. Such systems have multi-component wave functions,
describing many possible phases of the system. The corresponding
transformations that leave the dynamical equations describing the physics of
the system invariant in this case are non-abelian. The transformations
describing the symmetry of the system depend on the order in which they are
done. Here there is a much richer set of circumstances, depending on the
more complicated order parameter-wave function and on the non-abelian
counterpart of the electric and magnetic fields in the ordinary Josephson
effect. The coupling again reduces the symmetry and the consequences of the
reduced symmetry are the subject of this paper. There are different fashions
in which the Josephson currents could flow depending on the way the two
sides of the junction are coupled. So it appears that the same quantum
mechanical phenomena that are observed in ordinary Josephson junctions
produced as sandwiches between superconducting and normal regions in the
laboratory can be observed in other far more complicated systems, some
possibly as large as neutron stars and perhaps the very early universe.
***
New laws for self-organized island growth on surfaces
How many islands form when atoms are deposited randomly onto a smooth
surface and find themselves via a complex interplay of diffusion,
nucleation and aggregation processes? This question has been answered a
long time ago for deposition of one type of atom. An extended theory
developed in the recent issue ... of Physical Review Letters now
allows one to predict the island density when different types of atoms
are co-deposited with varying stoichiometries. In this multi-component
case the situation becomes more diverse due to the fact that islands
of the same size exhibit different stabilities in dependence of their
specific composition. The extended theory can be applied to adjust the
number of islands in self-organized nanostructuring. It furthermore
gives access to numerous growth parameters. In particular, binding
energies between different species can be determined by evaluation of
measured island densities.
***
Force microscopy overtones for nanoimaging
Our paper describes a new atomic force microscopy (AFM) method for achieving subnm
resolution on native membranes by exploiting higher harmonics in the oscillating
movement of a cantilever. The mechanism behind this method can be better understood by
drawing an analogy to music:
A driven non-linear oscillator, such as the human voice, a blown wind instrument, or a
bowed violin string and also an AFM cantilever tapping on a sample, will oscillate in a
periodic, non-sinusoidal manner. This generates the impression of sound at integer multiple
frequencies of the fundamental known as harmonics. The overall combination of the
instrument's specific harmonics is what determines the timbre ("flavour of sound") of that
instrument. Timbre is what gives the listener the ability to distinguish different instruments
that play the same note at the same volume in a band or orchestra, and what gives the scientist
the ability to distinguish different sample elasticity.
In our study a point mass model was introduced, to qualitatively explain the origin of
these harmonic contributions, and this model was compared to experimental findings. In order
to demonstrate the great potential of this novel method, the 2nd harmonic amplitude in the
movement of an AFM cantilever was recorded during scanning a bacterial surface proteinlayer
and a layer of human rhinovirus under physiological conditions. A lateral resolution of
~0.5 nm was obtained, one order of magnitude higher than the resolution in the
simultaneously recorded topography image.
***
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Radioactive decay of beryllium(Be)-7 speeds up at 5 Kelvin by almost 1.5%
when the Be-7 stays inside C60 cage. This is the largest shift yet seen
in a chemically and/or metallically induced modification of the Be-7 lifetime.
In this case, one of the orbital electrons, usually from the K or L shell,
is captured by a proton in the Be nucleus, forming a neutron and a neutrino
(EC decay). The 1.5% difference between the EC decay rate
inside C60 (52.4 days) and inside other materials (53.2 days) represents
a strong environmental effect on the Be-7 EC decay rate, caused by
the different electronic wave-functions. This finding may suggest
that the Be-7 atoms stay at the center (potential minimum)
of the C60 at 5 Kelvin and the L shell electrons can be fully restricted to
the Be
nucleus as if they were isolated without chemical bond in vacuum.
The magnitude may be the achievable largest value in laboratories on earth.
A schematic view of the closed K and L electron shells when the Be-7 is
inside C60 is shown in the figure.
