434 research outputs found
Planar diagrams from optimization
We propose a new toy model of a heteropolymer chain capable of forming planar
secondary structures typical for RNA molecules. In this model the sequential
intervals between neighboring monomers along a chain are considered as quenched
random variables. Using the optimization procedure for a special class of
concave--type potentials, borrowed from optimal transport analysis, we derive
the local difference equation for the ground state free energy of the chain
with the planar (RNA--like) architecture of paired links. We consider various
distribution functions of intervals between neighboring monomers (truncated
Gaussian and scale--free) and demonstrate the existence of a topological
crossover from sequential to essentially embedded (nested) configurations of
paired links.Comment: 10 pages, 10 figures, the proof is added. arXiv admin note: text
overlap with arXiv:1102.155
The interaction between humic acid and naphthalene after exposure to visible and UV light
Dissolved organic matter plays an important role in pollution migration from human waste to aquatic environments. In this study, the effect of humic acid (HA) on the photo-chemical transformation of naphthalene by irradiation model solar and UV light was reported using fluorescence quenching titrations. It was calculated the interactions between naphthalene and humic acids. It is found that the molecular complex of humic acid and naphthalene is more stable to UV irradiation, compared with the model solar radiation. The application of molecular fluorescence spectrometry is a useful sensitive tool evaluate intermolecular HA and naphthalene interactions. © (2015) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only
Pressure on charged domain walls and additional imprint mechanism in ferroelectrics
The impact of free charges on the local pressure on a charged ferroelectric
domain wall produced by an electric field has been analyzed. A general formula
for the local pressure on a charged domain wall is derived considering full or
partial compensation of bound polarization charges by free charges. It is shown
that the compensation can lead to a very strong reduction of the pressure
imposed on the wall from the electric field. In some cases this pressure can be
governed by small nonlinear effects. It is concluded that the free charge
compensation of bound polarization charges can lead to substantial reduction of
the domain wall mobility even in the case when the mobility of free charge
carriers is high. This mobility reduction gives rise to an additional imprint
mechanism which may play essential role in switching properties of
ferroelectric materials. The effect of the pressure reduction on the
compensated charged domain walls is illustrated for the case of 180-degree
ferroelectric domain walls and of 90-degree ferroelectric domain walls with the
head-to-head configuration of the spontaneous polarization vectors.Comment: subm. to PRB. This verion is extended by appendi
Exact solution of the Bernoulli matching model of sequence alignment
Through a series of exact mappings we reinterpret the Bernoulli model of
sequence alignment in terms of the discrete-time totally asymmetric exclusion
process with backward sequential update and step function initial condition.
Using earlier results from the Bethe ansatz we obtain analytically the exact
distribution of the length of the longest common subsequence of two sequences
of finite lengths . Asymptotic analysis adapted from random matrix theory
allows us to derive the thermodynamic limit directly from the finite-size
result.Comment: 13 pages, 4 figure
Inelastic Decay of Electrons in the Shockley-type Metal-Organic Interface States
We present a theoretical study of lifetimes of interface states (IS) on
metal-organic interfaces PTCDA/Ag(111), NTCDA/Ag(111), PFP/Ag(111), and
PTCDA/Ag(100), describing and explaining the recent experimental data. By means
of unfolding the band structure of one of the interfaces under study onto the
Ag(111) Brillouin zone we demonstrate, that the Brillouin zone folding upon
organic monolayer deposition plays a minor role in the phase space for electron
decay, and hence weakly affects the resulting lifetimes. The presence of the
unoccupied molecular states below the IS gives a small contribution to the IS
decay rate mostly determined by the change of the phase space of bulk states
upon the energy shift of the IS. The calculated lifetimes follow the
experimentally observed trends. In particular, we explain the trend of the
unusual increase of the IS lifetimes with rising temperature.Comment: 8 pages, 5 figure
Influence of humic acid on the naphthalene photochemical transformation upon irradiation with visible and UV light
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