One Particle and Two Particle Distributions in the Liquid-Vapour Interface

Liquid-vapour interface for a simple fluid modelled by the Lennard-Jones potential was treated by the first two mernbers of the Born-Green-Yvon-Bogolyubov hierarchy. The pair of coupled integral equations was solved numerically to get the density profile and the pair correlation function in the inhomogeneous region. It was found that one can get a significant result for the pair correlation function if the monotonous density profile is inserted in the equation determining the pair correlation function. On the other hand, we did not succeed in getting a convergentsolution for the density profile. This means that some further efforts will be necessary to overcome the difficulties connected with the unstable numerical procedures

Percolation Transitions in Sticky Disk Systems. A Molecular Dynamics Study

Molecular dynamics computer simulation was performed on the systems consisting of 100 two dimensional particles interacting with the hard core square well potential. Calculations were performed for various combinations of the parameters defining the attractive part of the potentials and for various densities. The pairs e and A, denoting the depth and width of the potential well, were chosen in such a way that the systems approached Baxter’s limit of sticky or adhesive potential with infinite depth and zero width of the well, provided that the product A exp(e/kT) remained finite. The results of the simulation gave support to the claims based on the analysis of higher order virial coefficients that the system of adhesive particles does not possess thermodynamic stability. The results show that the approach of the system towards equilibrium slows down when approaching the limit of stickiness and, besides, systems close to the sticky limit show a tendency to aggregation and collapse towards the crystal structure, which raises doubts about the regularity of the percolation problem of sticky systems

Trinucleotide repeats in human genome and exome

Trinucleotide repeats (TNRs) are of interest in genetics because they are used as markers for tracing genotype–phenotype relations and because they are directly involved in numerous human genetic diseases. In this study, we searched the human genome reference sequence and annotated exons (exome) for the presence of uninterrupted triplet repeat tracts composed of six or more repeated units. A list of 32 448 TNRs and 878 TNR-containing genes was generated and is provided herein. We found that some triplet repeats, specifically CNG, are overrepresented, while CTT, ATC, AAC and AAT are underrepresented in exons. This observation suggests that the occurrence of TNRs in exons is not random, but undergoes positive or negative selective pressure. Additionally, TNR types strongly determine their localization in mRNA sections (ORF, UTRs). Most genes containing exon-overrepresented TNRs are associated with gene ontology-defined functions. Surprisingly, many groups of genes that contain TNR types coding for different homo-amino acid tracts associate with the same transcription-related GO categories. We propose that TNRs have potential to be functional genetic elements and that their variation may be involved in the regulation of many common phenotypes; as such, TNR polymorphisms should be considered a priority in association studies

Triplet repeat RNA structure and its role as pathogenic agent and therapeutic target

This review presents detailed information about the structure of triplet repeat RNA and addresses the simple sequence repeats of normal and expanded lengths in the context of the physiological and pathogenic roles played in human cells. First, we discuss the occurrence and frequency of various trinucleotide repeats in transcripts and classify them according to the propensity to form RNA structures of different architectures and stabilities. We show that repeats capable of forming hairpin structures are overrepresented in exons, which implies that they may have important functions. We further describe long triplet repeat RNA as a pathogenic agent by presenting human neurological diseases caused by triplet repeat expansions in which mutant RNA gains a toxic function. Prominent examples of these diseases include myotonic dystrophy type 1 and fragile X-associated tremor ataxia syndrome, which are triggered by mutant CUG and CGG repeats, respectively. In addition, we discuss RNA-mediated pathogenesis in polyglutamine disorders such as Huntington's disease and spinocerebellar ataxia type 3, in which expanded CAG repeats may act as an auxiliary toxic agent. Finally, triplet repeat RNA is presented as a therapeutic target. We describe various concepts and approaches aimed at the selective inhibition of mutant transcript activity in experimental therapies developed for repeat-associated diseases

Percolation Transitions in Sticky Disk Systems. A Molecular Dynamics Study

Molecular dynamics computer simulation was performed on the systems consisting of 100 two dimensional particles interacting with the hard core square well potential. Calculations were performed for various combinations of the parameters defining the attractive part of the potentials and for various densities. The pairs e and A, denoting the depth and width of the potential well, were chosen in such a way that the systems approached Baxter’s limit of sticky or adhesive potential with infinite depth and zero width of the well, provided that the product A exp(e/kT) remained finite. The results of the simulation gave support to the claims based on the analysis of higher order virial coefficients that the system of adhesive particles does not possess thermodynamic stability. The results show that the approach of the system towards equilibrium slows down when approaching the limit of stickiness and, besides, systems close to the sticky limit show a tendency to aggregation and collapse towards the crystal structure, which raises doubts about the regularity of the percolation problem of sticky systems

One Particle and Two Particle Distributions in the Liquid-Vapour Interface

Liquid-vapour interface for a simple fluid modelled by the Lennard-Jones potential was treated by the first two mernbers of the Born-Green-Yvon-Bogolyubov hierarchy. The pair of coupled integral equations was solved numerically to get the density profile and the pair correlation function in the inhomogeneous region. It was found that one can get a significant result for the pair correlation function if the monotonous density profile is inserted in the equation determining the pair correlation function. On the other hand, we did not succeed in getting a convergentsolution for the density profile. This means that some further efforts will be necessary to overcome the difficulties connected with the unstable numerical procedures

Mutational dynamics of short tandem repeats in human genome

The evolutionary dynamics of short tandem repeats of nucleotide sequences of the human genome is studied. It is shown that a model due to which the evolutionary repeat dynamics consists of elongations and shortenings of the repeats, combined with point mutations, is degenerate in the sense that an ambiguity exists regarding the role of point mutations and slippage asymmetry. By introducing a measure of the correlations between the positions of the repeats along the DNA sequences we were able to remove the degeneracy and to show that the slippage events which are the main factor in repeat evolution exhibit more frequent shortenings than elongations