Branko Borštnik - Academia.edu (original) (raw)

Papers by Branko Borštnik

Research paper thumbnail of Model calculation of the gas diffusion through the polymer bulk

Die Makromolekulare Chemie, Mar 11, 2003

A model calculation of the diffusion of a noble gas (Ar) through the polyethylene bulk is perform... more A model calculation of the diffusion of a noble gas (Ar) through the polyethylene bulk is performed on the molecular scale. The amorphous phase of the polymer chains is generated by computer calculation and the potential field due to the penetrating atom is evaluated. The diffusion process across the barriers is simulated to obtain the value of the diffusion constant. Es wird eine Modellrechnung fur die Diffusion eines Edelgases (Ar) durch festes Polyathylen im molekularen Masstab durchgefuhrt. Die amorphe Phase der Polymerketten wird mit Hilfe von Computerberechnungen nachgebildet und das Potentialfeld, das durch die eindringenden Atome erzeugt wird, bestimmt. Der Diffusionsprozes wird simuliert, um die Diffusionskonstante zu erhalten.

Research paper thumbnail of The influence of the intermolecular interactions on the high frequency vibrations of polyethylene in the amorphous region

Die Makromolekulare Chemie, 1973

Research paper thumbnail of Bioinformatical Analysis of Point Mutations in Human Genome

Point Mutation, 2012

levels of validation are possible, but only a limited number of snps fulfill the most stringent v... more levels of validation are possible, but only a limited number of snps fulfill the most stringent validation criteria.

Research paper thumbnail of Diffusion of gas through polymer bulk: Computer simulation approach

Journal of Polymer Science: Polymer Symposia, 1973

The diffusion of a gas through the polymer (polyethylene) bulk is calculated in two steps. In the... more The diffusion of a gas through the polymer (polyethylene) bulk is calculated in two steps. In the first part, the amorphous phase of the polymer chains, at appropriate temperature and density, is generated using the Monte Carlo method on the tetrahedral lattice. The ground state is then obtained by the inclusion of the interchain forces. Using the energy surfaces from the first part, the energy barriers, modified by the interaction detween gas molecules (argon) and the polymer chains, are deduced. These values are the basis for the calculation of the diffusion coefficient.

Research paper thumbnail of Temperature dependence of the infrared bands in polyvinylacetate

Spectrochimica Acta Part A: Molecular Spectroscopy, 1973

Abstract Temperature dependence of the infrared band in polyvinylacetate is used to deduce the ac... more Abstract Temperature dependence of the infrared band in polyvinylacetate is used to deduce the activation energy of the CH 3 rotation.

Research paper thumbnail of Correlation energy in hydrogen bonded systems: a semiempirical approach

Journal of Molecular Structure, 1975

Research paper thumbnail of Torsional barrier calculations for p-halogenobenzaldehydes by the SCF-P-P-P method

Journal of Molecular Structure, 1968

Research paper thumbnail of Intensity and width of infrared A-H stretching bands in hydrogen-bonded systems

Journal of Molecular Structure, 1971

Abstract The intensity of the ir absorption band of an A-H stretching mode interacting with a low... more Abstract The intensity of the ir absorption band of an A-H stretching mode interacting with a low frequency A·B motion is calculated as the thermodynamic average over contributions from various R AB distances.

Research paper thumbnail of Dispersion study of a hydrogen-bonded complex

Journal of Molecular Structure, 1971

Research paper thumbnail of Liquid water structure at the wall. RISM approach

Journal of Molecular Liquids, 1991

Abstract Reference interaction site model was used to study the structure of liquid water at the ... more Abstract Reference interaction site model was used to study the structure of liquid water at the plane wall. The calculations were performed for extremely dilute solution of spherically symmetric particles in water. In the limiting procedure in which the diameter of the solute was let to approach large values, the resulting solute-solvent distribution functions represent the density profiles for water oxygens and hydrogens next to the plane wall. On the basis of this information the orientational distribution functions were calculated. The results predict rather strong density oscillations in the vicinity of the wall, much stronger than one obtains by computer simulation techniques.

Research paper thumbnail of Percolation of randomly centered rods and spheres

Journal of Mathematical Chemistry, 1991

The percolation properties of randomly centered rods and spheres are studied. The approach is bas... more The percolation properties of randomly centered rods and spheres are studied. The approach is based on the detailed study of frequencies of cluster occurrences. For random rods, the analytic expressions are derived for all cluster frequencies. It is then shown that one-dimensional systems of random rods exhibit critical behaviour with?c = 8,? = 1. For randomly centered spheres, we designed

Research paper thumbnail of Molecular dynamics simulation of liquid-solid transition in two dimensions

Journal of Crystal Growth, 1973

Research paper thumbnail of Study of Diffusion Coefficients in Mixtures of Lennard-Jones Molecules in the Liquid Range

The Journal of Chemical Physics, 1971

Research paper thumbnail of On the Monte Carlo method for sticky disks

The Journal of Chemical Physics, 1994

It is shown that the finding of Stell [J. Stat. Phys. 63, 1203 (1991)] that sticky systems are no... more It is shown that the finding of Stell [J. Stat. Phys. 63, 1203 (1991)] that sticky systems are not thermodynamically stable has for the consequence that custom tailored Monte Carlo methods, which sample the configurational phase space in an apparently successful way, break down if the methods are generalized in such a way that several particles instead of one particle are moved simultaneously to new position. Due to diverging integrals which are supposed to determine the probability of clusters with maximal connectivity, one can expect the system would always proceed toward the state of maximal degree of aggregation without respect to the strength of the potential.

Research paper thumbnail of On the Probability of Codon-Codon Mutational Replacements

Journal of Chemical Information and Modeling, 1997

... Journal of Chemical ... As it is known for decades since King and Jukes 9 published the paper... more ... Journal of Chemical ... As it is known for decades since King and Jukes 9 published the paper which became a cornerstone of the theory of neutral evolution, the amino acid composition of proteins is roughly determined by the number of codons by which a particular amino acid is ...

Research paper thumbnail of From interactions to structures and thermodynamic properties

International Journal of Quantum Chemistry, 2000

The standard paradigm of statistical thermodynamics is explored for five model systems. Three sys... more The standard paradigm of statistical thermodynamics is explored for five model systems. Three systems belong to the class of lattice models and two to the class of models with hard-core interaction potentials. The methodology is based on the concept of clusters. It is shown that the study of clusters in the lattice site percolation problem can give us valuable information about the Ising model and also about another Ising-type spin model which is introduced in the study. In the field of hard-core systems the concept of clusters is realized in the form of virial expansion and applied to the problem of stability of hard-sphere mixtures and also to the problem of the existence of a thermodynamic limit for the model of adhesive spheres. c 2000 John Wiley & Sons, Inc. Int J Quantum Chem 80: 416-424, 2000

Research paper thumbnail of Tandem Repeats in Protein Coding Regions of Primate Genes

Genome Research, 2002

Tandem repeats in GenBank primate nucleotide sequences annotated as protein coding regions are an... more Tandem repeats in GenBank primate nucleotide sequences annotated as protein coding regions are analyzed. It is found that only trinucleotide repeats show repeat enrichment well above the threshold of statistical significance. The statistics are improved by a simultaneous search for repeats on both the amino acid and nucleotide levels. The results of the analyses of natural sequences are interpreted by comparing them with the results of the computer simulation of the model dedicated to protein coding regions. According to the simulation results, a limited set of trinucleotides, that is, cgg, ccg, cag, and gaa repeats coding for polyalanine, polyglycine, polyproline, polyglutamine, and polylysine are prone to proliferation. It is also found that within the repeat regions slippage is more frequent by a factor of 10 than point mutations, whereas the ratio of silent versus recognizable point mutations is approximately the same as elsewhere in coding regions. The trinucleotide repeats cov...

Research paper thumbnail of Mutational dynamics of short tandem repeats in human genome

Europhysics Letters (EPL), 2004

The evolutionary dynamics of short tandem repeats of nucleotide sequences of the human genome is ... more 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.

Research paper thumbnail of Analysis of Apparent 1/ f α Spectrum in DNA Sequences

Europhysics Letters (EPL), 1993

The question whether the correlations in DNA sequences are long ranged or short ranged is address... more The question whether the correlations in DNA sequences are long ranged or short ranged is addressed by an extensive analysis of genetic sequences. Our results do not support the notion of critical properties of sequential distribution of nucleotides. Continuous segments of DNA (chromosomes) can be viewed as a mosaic structure of shorter segments with distinct functional role and, consequently, with

Research paper thumbnail of Variation of cluster properties in lattice percolation problem: A prototype of phase transition

The European Physical Journal B, 2000

: Properties of clusters appearing in the site percolation problem on square and cubic lattices... more : Properties of clusters appearing in the site percolation problem on square and cubic lattices are expressed in a way that emphasizes the thermodynamic analogy. It is shown that the analog of the specific heat exhibits expected critical behaviour as a function of the analog of the temperature. The results support the notion that the partition of the specific heat

Research paper thumbnail of Model calculation of the gas diffusion through the polymer bulk

Die Makromolekulare Chemie, Mar 11, 2003

A model calculation of the diffusion of a noble gas (Ar) through the polyethylene bulk is perform... more A model calculation of the diffusion of a noble gas (Ar) through the polyethylene bulk is performed on the molecular scale. The amorphous phase of the polymer chains is generated by computer calculation and the potential field due to the penetrating atom is evaluated. The diffusion process across the barriers is simulated to obtain the value of the diffusion constant. Es wird eine Modellrechnung fur die Diffusion eines Edelgases (Ar) durch festes Polyathylen im molekularen Masstab durchgefuhrt. Die amorphe Phase der Polymerketten wird mit Hilfe von Computerberechnungen nachgebildet und das Potentialfeld, das durch die eindringenden Atome erzeugt wird, bestimmt. Der Diffusionsprozes wird simuliert, um die Diffusionskonstante zu erhalten.

Research paper thumbnail of The influence of the intermolecular interactions on the high frequency vibrations of polyethylene in the amorphous region

Die Makromolekulare Chemie, 1973

Research paper thumbnail of Bioinformatical Analysis of Point Mutations in Human Genome

Point Mutation, 2012

levels of validation are possible, but only a limited number of snps fulfill the most stringent v... more levels of validation are possible, but only a limited number of snps fulfill the most stringent validation criteria.

Research paper thumbnail of Diffusion of gas through polymer bulk: Computer simulation approach

Journal of Polymer Science: Polymer Symposia, 1973

The diffusion of a gas through the polymer (polyethylene) bulk is calculated in two steps. In the... more The diffusion of a gas through the polymer (polyethylene) bulk is calculated in two steps. In the first part, the amorphous phase of the polymer chains, at appropriate temperature and density, is generated using the Monte Carlo method on the tetrahedral lattice. The ground state is then obtained by the inclusion of the interchain forces. Using the energy surfaces from the first part, the energy barriers, modified by the interaction detween gas molecules (argon) and the polymer chains, are deduced. These values are the basis for the calculation of the diffusion coefficient.

Research paper thumbnail of Temperature dependence of the infrared bands in polyvinylacetate

Spectrochimica Acta Part A: Molecular Spectroscopy, 1973

Abstract Temperature dependence of the infrared band in polyvinylacetate is used to deduce the ac... more Abstract Temperature dependence of the infrared band in polyvinylacetate is used to deduce the activation energy of the CH 3 rotation.

Research paper thumbnail of Correlation energy in hydrogen bonded systems: a semiempirical approach

Journal of Molecular Structure, 1975

Research paper thumbnail of Torsional barrier calculations for p-halogenobenzaldehydes by the SCF-P-P-P method

Journal of Molecular Structure, 1968

Research paper thumbnail of Intensity and width of infrared A-H stretching bands in hydrogen-bonded systems

Journal of Molecular Structure, 1971

Abstract The intensity of the ir absorption band of an A-H stretching mode interacting with a low... more Abstract The intensity of the ir absorption band of an A-H stretching mode interacting with a low frequency A·B motion is calculated as the thermodynamic average over contributions from various R AB distances.

Research paper thumbnail of Dispersion study of a hydrogen-bonded complex

Journal of Molecular Structure, 1971

Research paper thumbnail of Liquid water structure at the wall. RISM approach

Journal of Molecular Liquids, 1991

Abstract Reference interaction site model was used to study the structure of liquid water at the ... more Abstract Reference interaction site model was used to study the structure of liquid water at the plane wall. The calculations were performed for extremely dilute solution of spherically symmetric particles in water. In the limiting procedure in which the diameter of the solute was let to approach large values, the resulting solute-solvent distribution functions represent the density profiles for water oxygens and hydrogens next to the plane wall. On the basis of this information the orientational distribution functions were calculated. The results predict rather strong density oscillations in the vicinity of the wall, much stronger than one obtains by computer simulation techniques.

Research paper thumbnail of Percolation of randomly centered rods and spheres

Journal of Mathematical Chemistry, 1991

The percolation properties of randomly centered rods and spheres are studied. The approach is bas... more The percolation properties of randomly centered rods and spheres are studied. The approach is based on the detailed study of frequencies of cluster occurrences. For random rods, the analytic expressions are derived for all cluster frequencies. It is then shown that one-dimensional systems of random rods exhibit critical behaviour with?c = 8,? = 1. For randomly centered spheres, we designed

Research paper thumbnail of Molecular dynamics simulation of liquid-solid transition in two dimensions

Journal of Crystal Growth, 1973

Research paper thumbnail of Study of Diffusion Coefficients in Mixtures of Lennard-Jones Molecules in the Liquid Range

The Journal of Chemical Physics, 1971

Research paper thumbnail of On the Monte Carlo method for sticky disks

The Journal of Chemical Physics, 1994

It is shown that the finding of Stell [J. Stat. Phys. 63, 1203 (1991)] that sticky systems are no... more It is shown that the finding of Stell [J. Stat. Phys. 63, 1203 (1991)] that sticky systems are not thermodynamically stable has for the consequence that custom tailored Monte Carlo methods, which sample the configurational phase space in an apparently successful way, break down if the methods are generalized in such a way that several particles instead of one particle are moved simultaneously to new position. Due to diverging integrals which are supposed to determine the probability of clusters with maximal connectivity, one can expect the system would always proceed toward the state of maximal degree of aggregation without respect to the strength of the potential.

Research paper thumbnail of On the Probability of Codon-Codon Mutational Replacements

Journal of Chemical Information and Modeling, 1997

... Journal of Chemical ... As it is known for decades since King and Jukes 9 published the paper... more ... Journal of Chemical ... As it is known for decades since King and Jukes 9 published the paper which became a cornerstone of the theory of neutral evolution, the amino acid composition of proteins is roughly determined by the number of codons by which a particular amino acid is ...

Research paper thumbnail of From interactions to structures and thermodynamic properties

International Journal of Quantum Chemistry, 2000

The standard paradigm of statistical thermodynamics is explored for five model systems. Three sys... more The standard paradigm of statistical thermodynamics is explored for five model systems. Three systems belong to the class of lattice models and two to the class of models with hard-core interaction potentials. The methodology is based on the concept of clusters. It is shown that the study of clusters in the lattice site percolation problem can give us valuable information about the Ising model and also about another Ising-type spin model which is introduced in the study. In the field of hard-core systems the concept of clusters is realized in the form of virial expansion and applied to the problem of stability of hard-sphere mixtures and also to the problem of the existence of a thermodynamic limit for the model of adhesive spheres. c 2000 John Wiley & Sons, Inc. Int J Quantum Chem 80: 416-424, 2000

Research paper thumbnail of Tandem Repeats in Protein Coding Regions of Primate Genes

Genome Research, 2002

Tandem repeats in GenBank primate nucleotide sequences annotated as protein coding regions are an... more Tandem repeats in GenBank primate nucleotide sequences annotated as protein coding regions are analyzed. It is found that only trinucleotide repeats show repeat enrichment well above the threshold of statistical significance. The statistics are improved by a simultaneous search for repeats on both the amino acid and nucleotide levels. The results of the analyses of natural sequences are interpreted by comparing them with the results of the computer simulation of the model dedicated to protein coding regions. According to the simulation results, a limited set of trinucleotides, that is, cgg, ccg, cag, and gaa repeats coding for polyalanine, polyglycine, polyproline, polyglutamine, and polylysine are prone to proliferation. It is also found that within the repeat regions slippage is more frequent by a factor of 10 than point mutations, whereas the ratio of silent versus recognizable point mutations is approximately the same as elsewhere in coding regions. The trinucleotide repeats cov...

Research paper thumbnail of Mutational dynamics of short tandem repeats in human genome

Europhysics Letters (EPL), 2004

The evolutionary dynamics of short tandem repeats of nucleotide sequences of the human genome is ... more 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.

Research paper thumbnail of Analysis of Apparent 1/ f α Spectrum in DNA Sequences

Europhysics Letters (EPL), 1993

The question whether the correlations in DNA sequences are long ranged or short ranged is address... more The question whether the correlations in DNA sequences are long ranged or short ranged is addressed by an extensive analysis of genetic sequences. Our results do not support the notion of critical properties of sequential distribution of nucleotides. Continuous segments of DNA (chromosomes) can be viewed as a mosaic structure of shorter segments with distinct functional role and, consequently, with

Research paper thumbnail of Variation of cluster properties in lattice percolation problem: A prototype of phase transition

The European Physical Journal B, 2000

: Properties of clusters appearing in the site percolation problem on square and cubic lattices... more : Properties of clusters appearing in the site percolation problem on square and cubic lattices are expressed in a way that emphasizes the thermodynamic analogy. It is shown that the analog of the specific heat exhibits expected critical behaviour as a function of the analog of the temperature. The results support the notion that the partition of the specific heat