Numerical Simulations and Analysis of Thermally Excited Waves in Plasma Crystals

A numerical model for a 2D-monolayer plasma crystal was established using the Box_tree code. Box_tree is a Barnes_Hut tree code which has proven effective in modeling systems composed of large numbers of particles. Thermally excited waves in this plasma crystal were numerically simulated and dispersion relations for both the longitudinal and transverse wave modes were found. These were compared with the dispersion relations extrapolated from experiment as well as a theory based on harmonic approximation. The results were found to agree with theoretical dispersion relations under different wave propagation directions with different particle charges and over a range of 0.9<k<5.Comment: 7 pages, Presented at COSPAR '0

Implementation of analytical Hartree-Fock gradients for periodic systems

We describe the implementation of analytical Hartree-Fock gradients for periodic systems in the code CRYSTAL, emphasizing the technical aspects of this task. The code is now capable of calculating analytical derivatives with respect to nuclear coordinates for systems periodic in 0, 1, 2 and 3 dimensions (i.e. molecules, polymers, slabs and solids). Both closed-shell restricted and unrestricted Hartree-Fock gradients have been implemented. A comparison with numerical derivatives shows that the forces are highly accurate.Comment: accepted by Comp. Phys. Com

A minimum principle in mRNA editing ?

mRNA editing of sequences of many species is analyzed. The nature of the inserted nucleotides and the position of the insertion sites, once fixed the edited peptide chain, are explained by introducing a minimum principle in the framework of the crystal basis model of the genetic code introduced by the authors.Comment: revised extended version - includes analysis on more dat

Sum rules of codon usage probabilities

In the crystal basis model of the genetic code, it is deduced that the sum of usage probabilities of the codons with C and A in the third position for the quartets and/or sextets is independent of the biological species for vertebrates. A comparison with experimental data shows that the prediction is satisfied within about 5 %.Comment: 7 page