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R Podgornik

Publications and source records attributed to R Podgornik.

18 recordsLinked to original sources
PubMed2006

Screening and fundamental length scales in semidilute Na-DNA aqueous solutions.

The fundamental length scales in semidilute Na-DNA aqueous solutions have been investigated by dielectric spectroscopy. The low- and the high-frequency relaxation modes are studied in detail. The length scale of the high-frequency relaxation mode at high DNA concentrations can be identified with the de Gennes-Pfeuty-Dobrynin correlation length of polyelectrolytes in semidilute solution, whereas at low DNA concentrations and in the low added salt limit the length scale shows an unusual exponent reminiscent of semidilute polyelectrolyte chains with hydrophobic backbone. The length scale of the low-frequency relaxation mode corresponds to a Gaussian chain composed of correlation blobs in the low added salt limit, and to the Odijk-Skolnick-Fixman value of the single chain persistence length in the high added salt limit.

DNA↗
PubMed2006

Nonadditivity in van der Waals interactions within multilayers.

Working at the macroscopic continuum level, we investigate effective van der Waals interactions between two layers within a multilayer assembly. By comparing the pair interactions between two layers with effective pair interactions within an assembly we assess the significant consequences of nonadditivity of van der Waals interactions. This allows us to evaluate the best numerical estimate to date for the Hamaker coefficient of van der Waals interactions in lipid-water multilamellar systems.

Algorithms↗
PubMed2004

van der Waals interactions across stratified media.

Working at the Lifshitz level, we investigate the van der Waals interactions across a series of layers with a periodic motif. We derive the complete form of the van der Waals interaction as an explicit function of the number of periodic layers. We then compare our result with an approximation based on an anisotropic-continuum representation of the stratified medium. Satisfactory agreement between discrete-layer and continuum models is reached only for thicknesses of ten or more layers.

Journal Article↗
PubMed2001

Positional, reorientational, and bond orientational order in DNA mesophases.

We investigate the orientational order of transverse polarization vectors of long, stiff polymer molecules and their coupling to bond orientational and positional order in high density mesophases. Homogeneous ordering of transverse polarization vector promotes distortions in the hexatic phase, whereas inhomogeneous ordering precipitates crystallization of the 2D sections with different orientations of the transverse polarization vector on each molecule in the unit cell. We propose possible scenarios for going from the hexatic phase, through the distorted hexatic phase, to the crystalline phase with an orthorhombic unit cell observed experimentally for the case of DNA.

Crystallization↗
PubMed2001

Osmotic properties of DNA: critical evaluation of counterion condensation theory.

The osmotic coefficient of B-DNA in water may, in dilute solutions, deviate by as much as 100% from predictions based on a simple line-charge "counterion condensation" theory. In contrast, a cell model description of the ionic atmosphere near a cylindrical polyelectrolyte predicts osmotic properties that are in surprisingly good harmony with all available experimental findings over a wide range of DNA concentrations. We argue that the neglect of molecular features, such as finite radius, makes line-charge condensation theory inapplicable at all but impractically low polyelectrolyte concentrations.

Cells↗
PubMed2000

Refusing to twist: demonstration of a line hexatic phase in DNA liquid crystals

We report conclusive high resolution small angle x-ray scattering evidence that long DNA fragments form an untwisted line hexatic phase between the cholesteric and the crystalline phases. The line hexatic phase is a liquid-crystalline phase with long-range hexagonal bond-orientational order, long-range nematic order, but liquidlike, i.e., short-range, positional order. So far, it has not been seen in any other three dimensional system. By line-shape analysis of x-ray scattering data we found that positional order decreases when the line hexatic phase is compressed. We suggest that such anomalous behavior is a result of the chiral nature of DNA molecules.

Journal Article↗
PubMed2000

Pseudo-casimir structural force drives spinodal dewetting in nematic liquid crystals

We analyze theoretically the fluctuation-induced force in thin nematic films subject to competing surface interactions, and we find that the force is attractive at small distances and repulsive otherwise. The results provide a consistent interpretation of a recent study of spinodal dewetting of 5CB on a silicon wafer [F. Vandenbrouck et al., Phys. Rev. Lett. 82, 2693 (1999)], implying that this experiment can be regarded as the first observation of the pseudo-Casimir effect in liquid crystals.

Journal Article↗
PubMed2000

Pseudo-Casimir effect in nematic liquid crystals in frustrating geometries

We study theoretically the fluctuation-induced structural force in nematic systems frustrated by external fields. We focus on the uniform director structure in the hybrid-aligned film characterized by opposing surface fields and in the Freedericksz cell where frustration arises from competing bulk and surface fields. We find that frustration gives rise to several interesting features of the interaction, including a crossover from attraction at small distances to repulsion at large distances. The fluctuation-induced interaction is enhanced substantially by frustration, the enhancement being progressively stronger on approaching the transition from uniform to distorted structure. At the structural transition the interaction diverges and we show that the pretransitional singularity is universal.

Journal Article↗
PubMed1999

Buckling, fluctuations, and collapse in semiflexible polyelectrolytes.

We present a systematic statistical mechanical analysis of the conformational properties of a stiff polyelectrolyte chain with intrachain attractions that are due to counterion correlations. We show that the mean-field solution corresponds to an Euler-like buckling instability. The effect of the conformational fluctuations on the buckling instability is investigated, first, qualitatively, within the harmonic ("semiclassical") theory, then, systematically, within a 1/d expansion, where d denotes the dimension of embedding space. Within the "semiclassical" approximation, we predict that the effect of fluctuations is to renormalize the effective persistence length to smaller values, but not to change the nature of the mean-field (i.e., buckling) behavior. Based on the 1/d expansion we are, however, led to conclude that thermal fluctuations are responsible for a change of the buckling behavior which is turned into a polymer collapse. A phase diagram is constructed in which a sequence of collapse transitions terminates at a buckling instability that occurs at a place that varies with the magnitude of the bare persistence length of the polymer chain, as well as with the strength and range of the attractive potential.

Chromosome Structures↗
PubMed1998

DNA--DNA interactions.

The forces that govern DNA double helix organization are being finally systematically measured. The non-specific longer-range interactions--such as electrostatic interactions, hydration, and fluctuation forces--that treat DNA as a featureless rod are reasonably well recognized. Recently, specific interactions--such as those controlled by condensing agents or those consequent to helical structure-are beginning to be recognized, quantified and tested.

Base Composition↗
PubMed1997

On a possible microscopic mechanism underlying the vapor pressure paradox.

We investigate the free energy and the profile of the displacement field in a stack of sterically interacting smectic multilayers bounded by surfaces under tension. We show that this tension can lead to a significant change in the multilayer free energy. It creates an additional long-range attraction (a pseudo-Casimir attraction) of the van der Waals type and leads to a perturbation in the spatial profile of the displacement field fluctuations. This perturbation can extend to macroscopic distances into the multilayer, away from the perturbing surfaces. The lowering of the free energy of the layers varies explicitly as an inverse power of the thickness of the stack, but also depends implicitly on the bare interactions between the smectic layers. One may regard this lowered energy as being due to a kind of mechanical van der Waals force. We investigate in detail the characteristics and magnitude of the free energy as well as the fluctuations in the displacement field for some typical situations of underlying interlamellar interactions.

Chemical Phenomena↗
PubMed1996

Bond orientational order, molecular motion, and free energy of high-density DNA mesophases.

By equilibrating condensed DNA arrays against reservoirs of known osmotic stress and examining them with several structural probes, it has been possible to achieve a detailed thermodynamic and structural characterization of the change between two distinct regions on the liquid-crystalline phase diagram: (i) a higher density hexagonally packed region with long-range bond orientational order in the plane perpendicular to the average molecular direction and (ii) a lower density cholesteric region with fluid-like positional order. X-ray scattering on highly ordered DNA arrays at high density and with the helical axis oriented parallel to the incoming beam showed a sixfold azimuthal modulation of the first-order diffraction peak that reflects the macroscopic bond-orientational order. Transition to the less-dense cholesteric phase through osmotically controlled swelling shows the loss of this bond orientational order, which had been expected from the change in optical birefringence patterns and which is consistent with a rapid onset of molecular positional disorder. This change in order was previously inferred from intermolecular force measurements and is now confirmed by 31P NMR. Controlled reversible swelling and compaction under osmotic stress, spanning a range of densities between approximately 120 mg/ml to approximately 600 mg/ml, allow measurement of the free-energy changes throughout each phase and at the phase transition, essential information for theories of liquid-crystalline states.

DNA↗
PubMed1995

Watching molecules crowd: DNA double helices under osmotic stress.

Simultaneous measurements on the packing and energetics of high-density liquid crystalline DNA phases show that the crowding of long DNA polyelectrolytes at ever increasing concentrations is accomplished through straightening of the random coils that the double helix assumes in dilute solution. X-ray scattering by ordered phases reveals that the local straightening of the molecules is also accompanied by their progressive immobilization and confinement within the molecular 'cages' created by neighboring molecules. These effects can be clearly observed through the measured energies of DNA packing under osmotic stress and through the changes in structural and dynamic characteristics of X-ray scattering from DNA in ordered arrays at different concentrations. The character of the confinement of large DNA motions for a wide range of DNA concentrations is dominated by the soft potentials of direct interaction. We do not see the power-law variation of energy vs. volume expected from space-filling fluctuations of molecules that enjoy no interaction except the hard clash of steric repulsion. Rather, in highly concentrated DNA mesophases we see a crowding of molecules through electrostatic or hydration repulsion that confines their movements and positions. This view is based on directly measured packing energies as well as on concurrently measured structural parameters while the DNA double helices are condensed under an externally applied osmotic pressure.

DNA↗
PubMed1994

Parametrization of direct and soft steric-undulatory forces between DNA double helical polyelectrolytes in solutions of several different anions and cations.

Directly measured forces between DNA helices in ordered arrays have been reduced to simple force coefficients and mathematical expressions for the interactions between pairs of molecules. The tabulated force parameters and mathematical expressions can be applied to parallel molecules or, by transformation, to skewed molecules of variable separation and mutual angle. This "toolbox" of intermolecular forces is intended for use in modelling molecular interactions, assembly, and conformation. The coefficients characterizing both the exponential hydration and the electrostatic interactions depend strongly on the univalent counterion species in solution, but are only weakly sensitive to anion type and temperature (from 5 to 50 degrees C). Interaction coefficients for the exponentially varying hydration force seen at spacings less than 10 to 15 A between surfaces are extracted directly from pressure versus interaxial distance curves. Electrostatic interactions are only observed at larger spacings and are always coupled with configurational fluctuation forces that result in observed exponential decay lengths that are twice the expected Debye-Huckel length. The extraction of electrostatic force parameters relies on a theoretical expression describing steric forces of molecules "colliding" through soft exponentially varying direct interactions.

Animals↗