5,062 research outputs found
The attractive nonlinear delta-function potential
We solve the continuous one-dimensional Schr\"{o}dinger equation for the case
of an inverted {\em nonlinear} delta-function potential located at the origin,
obtaining the bound state in closed form as a function of the nonlinear
exponent. The bound state probability profile decays exponentially away from
the origin, with a profile width that increases monotonically with the
nonlinear exponent, becoming an almost completely extended state when this
approaches two. At an exponent value of two, the bound state suffers a
discontinuous change to a delta-like profile. Further increase of the exponent
increases again the width of the probability profile, although the bound state
is proven to be stable only for exponents below two. The transmission of plane
waves across the nonlinear delta potential increases monotonically with the
nonlinearity exponent and is insensitive to the sign of its opacity.Comment: submitted to Am. J. of Phys., sixteen pages, three figure
Force induced stretched state: Effects of temperature
A model of self avoiding walks with suitable constraint has been developed to
study the effect of temperature on a single stranded DNA (ssDNA) in the
constant force ensemble. Our exact calculations for small chains show that the
extension (reaction co-ordinate) may increase or decrease with the temperature
depending upon the applied force. The simple model developed here which
incorporates semi-microscopic details of base direction provide an explanation
of the force induced transitions in ssDNA as observed in experiments.Comment: 5 pages, 8 figures, RevTex
Effects of Eye-phase in DNA unzipping
The onset of an "eye-phase" and its role during the DNA unzipping is studied
when a force is applied to the interior of the chain. The directionality of the
hydrogen bond introduced here shows oscillations in force-extension curve
similar to a "saw-tooth" kind of oscillations seen in the protein unfolding
experiments. The effects of intermediates (hairpins) and stacking energies on
the melting profile have also been discussed.Comment: RevTeX v4, 9 pages with 7 eps figure
Searching for cavities of various densities in the Earth's crust with a low-energy electron-antineutrino beta-beam
We propose searching for deep underground cavities of different densities in
the Earth's crust using a long-baseline electron-antineutrino disappearance
experiment, realized through a low-energy beta-beam with highly-enhanced
luminosity. We focus on four cases: cavities with densities close to that of
water, iron-banded formations, heavier mineral deposits, and regions of
abnormal charge accumulation that have been posited to appear prior to the
occurrence of an intense earthquake. The sensitivity to identify cavities
attains confidence levels higher than and for exposures
times of 3 months and 1.5 years, respectively, and cavity densities below 1 g
cm or above 5 g cm, with widths greater than 200 km. We
reconstruct the cavity density, width, and position, assuming one of them known
while keeping the other two free. We obtain large allowed regions that improve
as the cavity density differs more from the Earth's mean density. Furthermore,
we demonstrate that knowledge of the cavity density is important to obtain
O(10%) error on the width. Finally, we introduce an observable to quantify the
presence of a cavity by changing the orientation of the electron-antineutrino
beam, with which we are able to identify the presence of a cavity at the
to C.L.Comment: 7 pages, 5 figures; matches published versio
Theory of High-Force DNA Stretching and Overstretching
Single molecule experiments on single- and double stranded DNA have sparked a
renewed interest in the force-extension of polymers. The extensible Freely
Jointed Chain (FJC) model is frequently invoked to explain the observed
behavior of single-stranded DNA. We demonstrate that this model does not
satisfactorily describe recent high-force stretching data. We instead propose a
model (the Discrete Persistent Chain, or ``DPC'') that borrows features from
both the FJC and the Wormlike Chain, and show that it resembles the data more
closely. We find that most of the high-force behavior previously attributed to
stretch elasticity is really a feature of the corrected entropic elasticity;
the true stretch compliance of single-stranded DNA is several times smaller
than that found by previous authors. Next we elaborate our model to allow
coexistence of two conformational states of DNA, each with its own stretch and
bend elastic constants. Our model is computationally simple, and gives an
excellent fit through the entire overstretching transition of nicked,
double-stranded DNA. The fit gives the first values for the elastic constants
of the stretched state. In particular we find the effective bend stiffness for
DNA in this state to be about 10 nm*kbt, a value quite different from either
B-form or single-stranded DNAComment: 33 pages, 11 figures. High-quality figures available upon reques
DNA unzipped under a constant force exhibits multiple metastable intermediates
Single molecule studies, at constant force, of the separation of
double-stranded DNA into two separated single strands may provide information
relevant to the dynamics of DNA replication. At constant applied force, theory
predicts that the unzipped length as a function of time is characterized by
jumps during which the strands separate rapidly, followed by long pauses where
the number of separated base pairs remains constant. Here, we report previously
uncharacterized observations of this striking behavior carried out on a number
of identical single molecules simultaneously. When several single lphage
molecules are subject to the same applied force, the pause positions are
reproducible in each. This reproducibility shows that the positions and
durations of the pauses in unzipping provide a sequence-dependent molecular
fingerprint. For small forces, the DNA remains in a partially unzipped state
for at least several hours. For larger forces, the separation is still
characterized by jumps and pauses, but the double-stranded DNA will completely
unzip in less than 30 min
Dynamic force spectroscopy of DNA hairpins. II. Irreversibility and dissipation
We investigate irreversibility and dissipation in single molecules that
cooperatively fold/unfold in a two state manner under the action of mechanical
force. We apply path thermodynamics to derive analytical expressions for the
average dissipated work and the average hopping number in two state systems. It
is shown how these quantities only depend on two parameters that characterize
the folding/unfolding kinetics of the molecule: the fragility and the
coexistence hopping rate. The latter has to be rescaled to take into account
the appropriate experimental setup. Finally we carry out pulling experiments
with optical tweezers in a specifically designed DNA hairpin that shows
two-state cooperative folding. We then use these experimental results to
validate our theoretical predictions.Comment: 28 pages, 12 figure
Synthesis studies of secondary forest productivity in the Amazon: field data, remote sensing, modeling approaches.
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