5,161 research outputs found
Stretching of a single-stranded DNA: Evidence for structural transition
Recent experiments have shown that the force-extension (F-x) curve for
single-stranded DNA (ssDNA) consisting only of adenine [poly(dA)] is
significantly different from thymine [poly(dT)]. Here, we show that the base
stacking interaction is not sufficient to describe the F-x curves as seen in
the experiments. A reduction in the reaction co-ordinate arising from the
formation of helix at low forces and an increase in the distance between
consecutive phosphates of unstacked bases in the stretched state at high force
in the proposed model, qualitatively reproduces the experimentally observed
features. The multi-step plateau in the F-x curve is a signature of structural
change in ssDNA.Comment: 10 pages, 4 figure
Does changing the pulling direction give better insight into biomolecules?
Single molecule manipulation techniques reveal that the mechanical resistance
of a protein depends on the direction of the applied force. Using a lattice
model of polymers, we show that changing the pulling direction leads to
different phase diagrams. The simple model proposed here indicates that in one
case the system undergoes a transition akin to the unzipping of a
sheet, while in the other case the transition is of a shearing (slippage)
nature. Our results are qualitatively similar to experimental results. This
demonstrates the importance of varying the pulling direction since this may
yield enhanced insights into the molecular interactions responsible for the
stability of biomolecules.Comment: RevTeX v4, 10 pages with 6 eps figure
Spin-glass-like state in GdCu: role of phase separation and magnetic frustration
We report investigations on the ground state magnetic properties of
intermetallic compound GdCu through dc magnetization measurements. GdCu
undergoes first order martensitic type structural transition over a wide
temperature window of coexisting phases. The high temperature cubic and the low
temperature orthorhombic phases have different magnetic character and they show
antiferromagnetic and helimagnetic orderings below 145 K and 45 K respectively.
We observe clear signature of a glassy magnetic phase below the helimagnetic
ordering temperature, which is marked by thermomagnetic irreversibility, aging
and memory effects. The glassy magnetic phase in GdCu is found to be rather
intriguing with its origin lies in the interfacial frustration due to distinct
magnetic character of the coexisting phases.Comment: Physical Review B 83, 134427 (2011
Intermodal entanglement in Raman processes
The operator solution of a completely quantum mechanical Hamiltonian of the
Raman processes is used here to investigate the possibility of obtaining
intermodal entanglement between different modes involved in the Raman processes
(e.g. pump mode, Stokes mode, vibration (phonon) mode and anti-Stokes mode).
Intermodal entanglement is reported between a) pump mode and anti-Stokes mode,
b) pump mode and vibration (phonon) mode c) Stokes mode and vibration phonon
mode, d) Stokes mode and anti-stokes mode in the stimulated Raman processes for
the variation of the phase angle of complex eigenvalue of pump
mode . Some incidents of intermodal entanglement in the spontaneous and the
partially spontaneous Raman processes are also reported. Further it is shown
that the specific choice of coupling constants may produce genuine entanglement
among Stokes mode, anti-Stokes mode and vibration-phonon mode. It is also shown
that the two mode entanglement not identified by Duan's criterion may be
identified by Hillery-Zubairy criteria. It is further shown that intermodal
entanglement, intermodal antibunching and intermodal squeezing are independent
phenomena.Comment: 11 pages, 4 figure
Problems Affecting Labor
Much experimental work has been devoted in comparing the folding behavior of proteins sharing the same fold but different sequence. The recent design of proteins displaying very high sequence identities but different 3D structure allows the unique opportunity to address the protein-folding problem from a complementary perspective. Here we explored by ℙ-value analysis the pathways of folding of three different heteromorphic pairs, displaying increasingly high-sequence identity (namely, 30%, 77%, and 88%), but different structures called G A (a 3-α helix fold) and G B (an α/β fold). The analysis, based on 132 site-directed mutants, is fully consistent with the idea that protein topology is committed very early along the pathway of folding. Furthermore, data reveals that when folding approaches a perfect two-state scenario, as in the case of the G A domains, the structural features of the transition state appear very robust to changes in sequence composition. On the other hand, when folding is more complex and multistate, as for the G Bs, there are alternative nuclei or accessible pathways that can be alternatively stabilized by altering the primary structure. The implications of our results in the light of previous work on the folding of different members belonging to the same protein family are discussed
Manufacturer's pricing strategies in cooperative and non-cooperative advertising supply chain under retail competition
This article studies the manufacturer's pricing strategy in a supply chain with a single manufacturer and two competing retailers. The manufacturer, as a Stackelberg leader specifies wholesale prices to two retailers who face advertisement dependent demand. Based on this gaming structure, two mathematical models are developed - the cooperative advertising model where manufacturer shares a fraction of retailers' advertising costs and the non-cooperative advertising model where manufacturer does not share any retailer's advertising expenses. The optimal strategies of the manufacturer and retailers are determined and a numerical example is taken to illustrate the theoretical results derived. We show that cooperative advertising policy is beneficial not only for the participating entities but also for the entire supply chain
KSZ tomography and the bispectrum
Several statistics have been proposed for measuring the kSZ effect by
combining the small-scale CMB with galaxy surveys. We review five such
statistics, and show that they are all mathematically equivalent to the optimal
bispectrum estimator of type . Reinterpreting these kSZ
statistics as special cases of bispectrum estimation makes many aspects
transparent, for example optimally weighting the estimator, or incorporating
photometric redshift errors. We analyze the information content of the
bispectrum and show that there are two observables: the small-scale
galaxy-electron power spectrum , and the large-scale
galaxy-velocity power spectrum . The cosmological constraining power
of the kSZ arises from its sensitivity to fluctuations on large length scales,
where its effective noise level can be much better than galaxy surveys.Comment: 39 page
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
Force induced triple point for interacting polymers
We show the existence of a force induced triple point in an interacting
polymer problem that allows two zero-force thermal phase transitions. The phase
diagrams for three different models of mutually attracting but self avoiding
polymers are presented. One of these models has an intermediate phase and it
shows a triple point but not the others. A general phase diagram with
multicritical points in an extended parameter space is also discussed.Comment: 4 pages, 8 figures, revtex
Structural domain and spin ordering induced glassy magnetic phase in single layered manganite PrSrMnO
The single layered manganite PrSrMnO undergoes
structural transition from high temperature tetragonal phase to low temperature
orthorhombic phase below room temperature. The orthorhombic phase was reported
to have two structural variants with slightly different lattice parameters and
Mn-3 levels show orbital ordering within both the variants, albeit having
mutually perpendicular ordering axis. In addition to orbital ordering, the
orthorhombic variants also order antiferromagnetically with different N\'eel
temperatures. Our magnetic investigation on the polycrystalline sample of
PrSrMnO shows large thermal hysteresis indicating the
first order nature of the tetragonal to orthorhombic transition. We observe
magnetic memory, large relaxation, frequency dependent ac susceptbility and
aging effects at low temperature, which indicate spin glass like magnetic
ground state in the sample. The glassy magnetic state presumably arises from
the interfacial frustration of orthorhombic domains with orbital and spin
orderings playing crucial role toward the competing magnetic interactions.Comment: 6 pages, 4 figures, Accepted in Europhysics Letter
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