Biomedical subjects

A Wynveen

Publications and source records attributed to A Wynveen.

5 recordsLinked to original sources

PubMed2006

Interactions of polarizable media in water: a molecular dynamics approach.

We investigate the interactions of polarizable solutes in water as a function of the solute permittivity. A generic and computationally efficient simulation methodology for the investigation of systems involving dielectric discontinuities is introduced. We report results for interactions between two polarizable cylindrical solutes of nanometer dimensions, which demonstrate that the interactions between the solutes strongly depend on the solute permittivity epsilon. For low permittivity, epsilon approximately 1-2, the interactions are dominated by surface tension forces whose origin lies in the formation of a vapor cavity between the two hydrophobic solutes. This effect leads to a drying transition, where the intersolute force changes discontinuously at a specific solute-solute separation. We find that a moderate permittivity, epsilon approximately 20, enhances the solvation of the polarizable objects inhibiting this drying transition. In the limit of moderately high permittivity, the interactions are dominated by solvation forces. These forces are much larger than those calculated using macroscopic models of dielectrics, which consider water as a continuum dielectric medium. Our results emphasize the importance of including the solvent explicitly to investigate dielectric discontinuities and interactions between polarizable media in water.

Biopolymers↗

PubMed2005

Statistical mechanics of columnar DNA assemblies.

Many physical systems can be mapped onto solved or "solvable" models of magnetism. In this work, we have mapped the statistical mechanics of columnar phases of ideally helical rigid DNA--subject to the earlier found unusual, frustrated pair potential (A.A. Kornyshev, S. Leikin, J. Chem. Phys. 107, 3656 (1997))--onto an exotic, unknown variant of the XY model on a fixed or restructurable lattice. Here, the role of the "spin" is played by the azimuthal orientation of the molecules. We have solved this model using a Hartree-Fock approximation, ground-state calculations, and finite-temperature Monte Carlo simulations. We have found peculiar spin order transitions, which may also be accompanied by positional restructuring, from hexagonal to rhombohedric lattices. Some of these have been experimentally observed in dense columnar aggregates. Note that DNA columnar phases are of great interest in biophysical research, not only because they are a useful in vitro tool for the study of DNA condensation, but also since these structures have been detected in living matter. Within the approximations made, our study provides insight into the statistical mechanics of these systems.

Computer Simulation↗

PubMed2004

DNA-DNA interaction beyond the ground state.

The electrostatic interaction potential between DNA duplexes in solution is a basis for the statistical mechanics of columnar DNA assemblies. It may also play an important role in recombination of homologous genes. We develop a theory of this interaction that includes thermal torsional fluctuations of DNA using field-theoretical methods and Monte Carlo simulations. The theory extends and rationalizes the earlier suggested variational approach which was developed in the context of a ground state theory of interaction of nonhomologous duplexes. It shows that the heuristic variational theory is equivalent to the Hartree self-consistent field approximation. By comparison of the Hartree approximation with an exact solution based on the QM analogy of path integrals, as well as Monte Carlo simulations, we show that this easily analytically-tractable approximation works very well in most cases. Thermal fluctuations do not remove the ability of DNA molecules to attract each other at favorable azimuthal conformations, neither do they wash out the possibility of electrostatic "snap-shot" recognition of homologous sequences, considered earlier on the basis of ground state calculations. At short distances DNA molecules undergo a "torsional alignment transition," which is first order for nonhomologous DNA and weaker order for homologous sequences.

Base Pairing↗

PubMed2004

Nonlinear effects in the torsional adjustment of interacting DNA.

DNA molecules in solution, having negatively charged phosphates and countercations readsorbed on its surface, possess a distinct charge separation motif to interact electrostatically. If their double-helical structure were ideal, duplexes in parallel juxtaposition could choose azimuthal alignment providing attraction, or at least a reduction of repulsion, between them. But duplexes are not perfect staircases and the distortions of their helical structure correlate with their base pair texts. If the patterns of distortions on the opposing molecules are uncorrelated, the mismatch will accumulate as a random walk and attraction vanishes. Based on this idea, a model of recognition of homologous sequences has been proposed [A. A. Kornyshev and S. Leikin, Phys. Rev. Lett. 86, 3666 (2001)]. But DNA has torsional elasticity. How will this help to relax a mismatch between the charge distributions on two nonhomologous DNA's? In the same work, the solution of this problem has been mapped onto a frustrated sine Gordon equation in a nonlocal random field (where the latter represents a pattern of twist angle distortions on the opposing molecules), but the results had been obtained in the limit of torsionally rigid molecules. In the present paper, by solving this equation numerically, we find a strongly nonlinear relaxation mechanism which utilizes static kink-soliton modes triggered by the "random field." In the range of parameters where the solitons do not emerge, we find good agreement with the results of a variational study [A. G. Cherstvy, A. A. Kornyshev, and S. Leikin, J. Phys. Chem. B (to be published)]. We reproduce the first-order transitions in the interaxial separation dependence, but detect also second-order or weak first-order transitions for shorter duplexes. The recognition energy between two nonhomologous DNA sequences is calculated as a function of interaxial separation and the length of juxtaposition. The soliton-caused kinky length dependence is discussed in connection with plots of recombination frequency as a function of the length of homology.

Binding Sites↗

PubMed2003

Dynamics of low-energy helium vapor pulses.

We report results of experiments in which pulses of helium vapor are produced by a current pulse in a chromium film covered with superfluid helium at around 0.3 K. The pulses were detected by a titanium bolometer operating at 0.47 K. The shape of the detected signal is a strong function of the power of the initiating current pulse. For low powers the signal from a single current pulse also contains a single peak, but for higher powers, a single current pulse produces two and then at the highest powers, three peak signals. To analyze the origin of these phenomena we report results of hybrid gas-dynamics and hydrodynamics simulations, which demonstrate that the signals arise from shock waves formed in the vapor. The shock waves form due to the presence of a gradient in the small ambient background of helium vapor in the chamber and are extremely sensitive to the pulse power.

Journal Article↗