Transfer matrix solution of the Wako-Sait\^o-Mu\~noz-Eaton model augmented by arbitrary short range interactions

The Wako-Sait{\^o}-Mu\~noz-Eaton (WSME) model, initially introduced in the theory of protein folding, has also been used in modeling the RNA folding and some epitaxial phenomena. The advantage of this model is that it admits exact solution in the general inhomogeneous case (Bruscolini and Pelizzola, 2002) which facilitates the study of realistic systems. However, a shortcoming of the model is that it accounts only for interactions within continuous stretches of native bonds or atomic chains while neglecting interstretch (interchain) interactions. But due to the biopolymer (atomic chain) flexibility, the monomers (atoms) separated by several non-native bonds along the sequence can become closely spaced. This produces their strong interaction. The inclusion of non-WSME interactions into the model makes the model more realistic and improves its performance. In this study we add arbitrary interactions of finite range and solve the new model by means of the transfer matrix technique. We can therefore exactly account for the interactions which in proteomics are classified as medium- and moderately long-range ones.Comment: 15 pages, 2 figure

Bose-Einstein correlations at LEP and Tevatron energies

Using the Bose-Einstein correlations (BEC) implemented in PYTHIA we investigated a possibility of the CDF experiment at the Tevatron to see the two-particle correlations in the final state of interactions. The approach based on quantum field theory at finite temperature was applied to the ALEPH data at LEP, and the BEC important parameters were retrieved.Comment: 5 pages, 4 figures, 1 table. Based on the talk gived at The 6th international workshop on very high multiplicity physics, JINR Dubna, 16-17 april 2005. In Table 1. the sign of error adde

Constraints on the intrinsic charm content of the proton from recent ATLAS data

Constraints on the intrinsic charm probability \wccm = P_{{\mathrm{c}\bar \mathrm{c}} / \mathrm{p}} in the proton are obtained for the first time from LHC measurements. The ATLAS Collaboration data for the production of prompt photons, accompanied by a charm-quark jet in pp collisions at $\sqrt s = 8$ TeV, are used. The upper limit \mbox{\wccm < 1.93~\%} is obtained at the 68~\% confidence level. This constraint is primarily determined from the theoretical scale and systematical experimental uncertainties. Suggestions for reducing these uncertainties are discussed. The implications of intrinsic heavy quarks in the proton for future studies at the LHC are also discussed.Comment: 6 pages, 4 figure

An exactly solvable model for a beta-hairpin with random interactions

I investigate a disordered version of a simplified model of protein folding, with binary degrees of freedom, applied to an ideal beta-hairpin structure. Disorder is introduced by assuming that the contact energies are independent and identically distributed random variables. The equilibrium free-energy of the model is studied, performing the exact calculation of its quenched value and proving the self-averaging feature.Comment: 9 page

Plasma electrons above Saturn's main rings: CAPS observations

We present observations of thermal ( similar to 0.6 - 100eV) electrons observed near Saturn's main rings during Cassini's Saturn Orbit Insertion (SOI) on 1 July 2004. We find that the intensity of electrons is broadly anticorrelated with the ring optical depth at the magnetic footprint of the field line joining the spacecraft to the rings. We see enhancements corresponding to the Cassini division and Encke gap. We suggest that some of the electrons are generated by photoemission from ring particle surfaces on the illuminated side of the rings, the far side from the spacecraft. Structure in the energy spectrum over the Cassini division and A-ring may be related to photoelectron emission followed by acceleration, or, more likely, due to photoelectron production in the ring atmosphere or ionosphere

Theory of temperature dependence of the Fermi surface-induced splitting of the alloy diffuse-scattering intensity peak

The explanation is presented for the temperature dependence of the fourfold intensity peak splitting found recently in diffuse scattering from the disordered Cu3Au alloy. The wavevector and temperature dependence of the self-energy is identified as the origin of the observed behaviour. Two approaches for the calculation of the self-energy, the high-temperature expansion and the alpha-expansion, are proposed. Applied to the Cu3Au alloy, both methods predict the increase of the splitting with temperature, in agreement with the experimental results.Comment: 4 pages, 3 EPS figures, RevTeX, submitted to J. Phys. Condens. Matter (Letter to the Editor

Accelerated kinetic Monte Carlo algorithm for diffusion limited kinetics

If a stochastic system during some periods of its evolution can be divided into non-interacting parts, the kinetics of each part can be simulated independently. We show that this can be used in the development of efficient Monte Carlo algorithms. As an illustrative example the simulation of irreversible growth of extended one dimensional islands is considered. The new approach allowed to simulate the systems characterized by parameters superior to those used in previous simulations.Comment: 4 pages, 4 figures, to be published in Phys. Rev.