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V V Anshelevich

Publications and source records attributed to V V Anshelevich.

14 recordsLinked to original sources
PubMed1991

Computer simulation of DNA supercoiling.

We treat supercoiled DNA within a wormlike model with excluded volume. A modified Monte Carlo approach has been used, which allowed computer statistical-mechanical simulations of moderately and highly supercoiled DNA molecules. Even highly supercoiled molecules do not have a regular shape, though with an increase in writhing the chains look more and more like branched interwound helixes. The averaged writhing (Wr) approximately 0.7 delta Lk. The superhelical free energy F is calculated as a function of the linking number. Lk. The calculations have shown that the generally accepted quadratic dependence of F on Lk is valid for a variety of conditions, though it is by no means universal. Significant deviations from the quadratic dependence are expected at high superhelical density under ionic conditions where the effective diameter of DNA is small. The results are compared with the available experimental data.

Computer Simulation↗
PubMed1989

On the ability of neural networks to perform generalization by induction.

The ability of neural networks to perform generalization by induction is the ability to learn an algorithm without the benefit of complete information about it. We consider the properties of networks and algorithms that determine the efficiency of generalization. These properties are described in quantitative terms. The most effective generalization is shown to be achieved by networks with the least admissible capacity. General conclusions are illustrated by computer simulations for a three-layered neural network. We draw a quantitative comparison between the general equations and specific results reported here and elsewhere.

Algorithms↗
PubMed1989

Neural network models for promoter recognition.

The problem of recognition of promoter sites in the DNA sequence has been treated with models of learning neural networks. The maximum network capacity admissible for this problem has been estimated on the basis of the total of experimental data available on the determined promoter sequences. The model of a block neural network has been constructed to satisfy this estimate and rules have been elaborated for its learning and testing. The learning process involves a small (of the order of 10%) part of the total set of promoter sequences. During this procedure the neural network develops a system of distinctive features (key words) to be used as a reference in identifying promoters against the background of random sequences. The learning quality is then tested with the whole set. The efficiency of promoter recognition has been found to amount to 94 to 99%. The probability of an arbitrary sequence being identified as a promoter is 2 to 6%.

Base Sequence↗
PubMed1989

Variance of writhe for wormlike DNA rings with excluded volume.

We have calculated the variance of the equilibrium distribution of a circular wormlike polymer chain over the writhing number, less than (Wr)2 greater than, with allowance for the excluded volume effects. Within this model the less than (Wr)2 greater than value is a function of the number of Kuhn statistical segments, n, and the chain diameter, d measured in Kuhn statistical lengths, b. Simulated DNA chains varied from 200 to 10,000 base pairs and the d value varied from 0.02 to 0.2. Theory predicts a considerable ionic strength dependence of the DNA superhelix energy as a consequence of the change in the DNA diameter. A comparison with the available experimental data has yielded an estimate of the DNA torsional rigidity, the Kuhn statistical length, and the effective diameter of the double helix under conditions of the complete screening of the DNA electrostatic potential.

DNA↗
PubMed1988

Effect of excluded volume on topological properties of circular DNA.

We have performed computer simulations of closed polymer chains with allowance for the excluded volume effects within the framework of the free-joint model. The probability of knot formation, the linking probability of a pair of chains and the variance in the writhing number proved to be significantly affected by the excluded volume effects. This is true even for DNA with completely screened charges for which the b/d ratio (where b is the Kuhn statistical length and d is the diameter of the double helix) is as large as 50. Allowance for the electrostatic repulsion (change of the DNA effective diameter d) further increases the effects. The most dramatic dependence on d is found for the probability of knot formation. The data on the dependence of the variance of writhing, mean value of (WR)2, on d indicate that the DNA superhelix energy should be significantly ionic strength-dependent. Special calculations have shown that the free-joint model underestimates the mean value of (Wr)2 value by about 20% as compared with the wormlike model.

DNA, Circular↗
PubMed1988

A theoretical study of formation of DNA noncanonical structures under negative superhelical stress.

The development of statistical mechanical models of the formation of noncanonical structures in circular DNA and the finding of the energy parameters for these models made it possible to predict the appearance of such structures in a DNA with any given sequence. It does not seem feasible, however, to perform such calculations for DNA sequences of considerable length by allowing for all the possible states. We propose a special algorithm for calculating the thermodynamic characteristics of various conformational rearrangements in DNA that occur under negative supercoilings, allowing for several possible states of each base pair in the chain. Calculations have been performed for a number of natural DNAs. According to these calculations, the most likely noncanonical structures in DNA under normal conditions are cruciform structures and the Z form. The results of the calculations are compared with the experimental data reported in the literature. State diagrams have been computed for a number of inserts in circular DNA that can adopt both the cruciform conformation and the left-handed helical Z form.

Algorithms↗
PubMed1986

The effect of sequence heterogeneity on DNA melting kinetics.

We consider kinetics of the cooperative melting of DNA sections situated at the edge of the helix. Accurate calculations based on the real sequences of such sections demonstrate that their internal heterogeneity has a drastic effect on the melting kinetics. Allowance for the internal heterogeneity increases the relaxation time by several orders of magnitude as compared with a model based on the assumption of equal base-pair stability within a section. The relaxation times obtained are in good agreement with the experimental data of Suyama and Wada (A. Suyama and A. Wada, Biopolymers, 23, 409 (1984)). An analysis of the melting process revealed some simple sequence characteristics that determine its rate. An examination of the temperature dependence of the relaxation time led to a distinct interpretation of the apparent activation energies of the denaturation and renaturation. The relaxation time proved to reach its maximum near the equilibrium melting point of the section examined.

Base Sequence↗
PubMed1985

Torsional and bending rigidity of the double helix from data on small DNA rings.

We have calculated the variance of equilibrium distribution of a circular wormlike polymer chain over the writhing number, [Wr)2), as a function of the number of Kuhn statistical segments, n. For large n these data splice well with our earlier results obtained for a circular freely jointed polymer chain. Assuming that [delta Lk)2) = [delta Tw)2) we have compared our results with experimental data on the chain length dependence of the [delta Lk)2) value recently obtained by Horowitz and Wang for small DNA rings. This comparison has shown an excellent agreement between theory and experiment and yielded a reliable estimate of the torsional and bending rigidity parameters. Namely, the torsional rigidity constant is C = 3.0.10(-19) erg cm, and the bending rigidity as expressed in terms of the DNA persistence length is a = 500 A. The obtained value of C agrees well with earlier estimates by Shore and Baldwin as well as by Horowitz and Wang whereas the a value is in accord with the data of Hagerman. We have found the data of Shore and Baldwin on the chain length dependence of the [delta Lk)2) value to be entirely inconsistent with our theorectical results.

Chemical Phenomena↗
PubMed1985

Application of polyelectrolyte theory to the study of the B-Z transition in DNA (1).

We have used the polyelectrolyte theory to study the ionic strength dependence of the B-Z equilibrium in DNA. A DNA molecule is molded as an infinitely long continuously charged cylinder of radius a with reduced linear charge density q. The parameters a and q for the B and Z forms were taken from X-ray data: aB = 1nm, qB = 4.2, aZ = 0.9 nm and qZ = 3.9. A simple theory shows that at low ionic strengths (when Debye screening length rD much greater than a) the electrostatic free energy difference FelBZ = FelZ - FelB increases with increasing ionic strength since qB greater than qZ. At high ionic strengths (when rD much less than a) the FelBZ would go on growing with increasing ionic strength if the inequality qB/aB greater than qZ/aZ were valid. In the converse case when qZ/qB greater than aZ/aB the FelBZ value decreases with increasing salt concentration at high ionic strength. Since X-ray data correspond to the latter case, theory predicts that the FelBZ value reaches a maximum at an intermediate ionic strength of about 0.1 M (where rD approximately a). We also performed rigorous calculations based on the Poisson-Boltzmann equation. These calculations have confirmed the above criterion of nonmonotonous behaviour of the FelBZ value as a function of ionic strength. Different theoretical predictions for the B-Z transition in linear and superhelical molecules are discussed. Theory predicts specifically that at a very low ionic strength the Z form may prove to be more stable than the B form.(ABSTRACT TRUNCATED AT 250 WORDS)

DNA↗
PubMed1979

Statistical mechanics of supercoils and the torsional stiffness of the DNA double helix.

The distribution of closed unknotted polymer chains over the writhing number is calculated by the Monte-Carlo method. For circular duplex DNA the variance of the distribution equals approximately half the observed variance of equilibrium distribution over the linking number. The balance which arises from fluctuations in DNA twisting makes it possible to estimate the torsional stiffness of the double helix.

DNA, Superhelical↗
PubMed1979

Fluctuations in superhelical DNA.

The effect of superhelicity on the base-pair opening probability and on the probability of occurrence of cruciform states in palindromic regions is theoretically treated. The calculations show that below the superhelix density value of -sigma=0.05 superhelicity does not appreciably affect the characteristics of DNA secondary structure fluctuations. In the range of physiological superhelix densities sigma (-sigma=0.05-0.09) the base-pair opening probability markedly increases. However, within this range of sigma the base-pairs are opened only transiently and permanently open regions are not formed. Permanently opened regions appear at higher negative superhelix densities (-sigma greater than 0.10). At the values of -sigma higher than 0.06 a cruciform structure in the palindromic region centred in position 3965 proves to be the most probable fluctuational disturbance in the 0x174 duplex DNA. Different experimental approaches used for probing the fluctuations in superhelical DNA have been analysed. The results suggest that most direct quantitative information can be derived from data on the nicking of closed DNA by single strand-specific endonucleases. Such data (Wang, 1974) accord with the results of theoretical calculations. Calculations show that, due to base-pair opening, the total free energy of superhelical DNA should depend parabolically on sigma only up to some critical value of sigma=sigmac. If negative superhelicity exceeds this critical value, which under physiological conditions proves to be -sigma=0.085, the free energy should increase linearly with -sigma. The biological role of supercoiling is discussed in the light of obtained results.

Base Sequence↗
PubMedDate not supplied

[The ability of neuronal networks to generalize using an induction method].

Inductive generalization means the ability of a neural network to learn a given algorithm using incomplete information about it. A consideration based on the information theory leads to a simple equation connecting characteristics of the network with those of the algorithm to be learned. The main conclusion is that the most efficient generalization is achieved on the networks with minimal complexity sufficient for realization of the algorithm under consideration. The obtained equation is compared with the results of computer simulations for a universal neural network obtained in the present paper as well as by other workers. A good agreement is observed between theoretical predictions for generalization efficacy and results of computer simulations.

Generalization, Response↗