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 $X,Y$. 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