Biomedical subjects

Roland R Netz

Publications and source records attributed to Roland R Netz.

10 recordsLinked to original sources

PubMed2006

Scaling and universality in the counterion-condensation transition at charged cylinders.

Counterions at charged rodlike polymers exhibit a condensation transition at a critical temperature (or, equivalently, at a critical linear charge density for polymers), which dramatically influences various static and dynamic properties of charged polymer solutions. We address the critical and universal aspects of this transition for counterions at a single charged cylinder in two and three spatial dimensions using numerical and analytical methods. By introducing a Monte Carlo sampling method in logarithmic radial scale, we are able to numerically simulate the critical limit of infinite system size (corresponding to the infinite-dilution limit) within tractable equilibration times. The critical exponents are determined for the inverse moments of the counterionic density profile (which play the role of the order parameters and represent the mean inverse localization length of counterions) both within mean-field theory and within Monte Carlo simulations. In three dimensions (3D), we demonstrate that correlation effects (neglected within mean-field theory) lead to an excessive accumulation of counterions near the charged cylinder below the critical temperature (i.e., in the condensation phase), while surprisingly, the critical region exhibits universal critical exponents in accordance with mean-field theory. Also in contrast with the typical trend in bulk critical phenomena, where fluctuations become more enhanced in lower dimensions, we demonstrate, using both numerical and analytical approaches, that mean-field theory becomes exact for the two-dimensional (2D) counterion-cylinder system at all temperatures (Manning parameters), when the number of counterions tends to infinity. For a finite number of particles, however, the 2D problem displays a series of peculiar singular points (with diverging heat capacity), which reflect successive delocalization events of individual counterions from the central cylinder. In both 2D and 3D, the heat capacity shows a universal jump at the critical point and the internal energy develops a pronounced peak. The asymptotic behavior of the energy peak location is used to determine the critical temperature, which is also found to be in agreement with the mean-field prediction.

Journal Article↗

PubMed2006

Pumping fluids with periodically beating grafted elastic filaments.

Using Brownian dynamics simulations, we investigate the pumping efficiency of an array of periodically beating semiflexible filaments that are grafted to a surface. Full hydrodynamic interactions among and within filaments and no slip at the surface are considered. Optimal pumping is obtained for a characteristic ratio of applied forward-backward torques and filament persistence length. For independently driven filaments, phase locking between neighboring filaments occurs autonomously via hydrodynamic coupling, giving rise to significantly enhanced pumping efficiency.

Biological Clocks↗

PubMed2006

Electro-osmosis at inhomogeneous charged surfaces: hydrodynamic versus electric friction.

Electrokinetic methods are efficient in probing the electrostatic surface properties of charged systems. However, anomalies observed in experiments indicate that the classical electrokinetic theory should be reconsidered. Using Green's function methods and hydrodynamic simulations, we investigate electro-osmosis driven by electric-field-induced ion motion near a charged planar substrate with smooth or rough boundary. First, a reformulation of electro-osmotic theory for planar charged surfaces employing Green's functions shows that the Helmholtz-Smoluchowski (HS) relation between electrostatic potential and solvent velocity is exact for smooth surfaces, even in the presence of ion correlations. Deviations from HS theory are caused by combined hydrodynamic and electric surface friction, as our hydrodynamic simulations of ions at smooth and corrugated charged surfaces in lateral electric fields demonstrate. Within the simulations, hydrodynamic interactions are treated in the continuum limit and the presence of a no-slip boundary condition at the surface is taken into account. While electrofriction is relevant in highly charged system and/or for multivalent ions, hydrodynamic friction is dominant in systems with moderate surface charge density and/or low ionic valency. We also derive the effective electrokinetic surface charge from the electro-osmotic solvent profiles, which is substantially reduced when compared with the bare value and shows qualitative agreement with the experimental tendency.

Journal Article↗

PubMed2006

Propulsion with a rotating elastic nanorod.

The dynamics of a rotating elastic filament is investigated using Stokesian simulations. The filament, straight and tilted with respect to its rotation axis for small driving torques, undergoes at a critical torque a strongly discontinuous shape bifurcation to a helical state. It induces a substantial forward propulsion whatever the sense of rotation: a nanomechanical force-rectification device is established.

Bacteria↗

PubMed2006

Dissimilar kinetic behavior of electrically manipulated single- and double-stranded DNA tethered to a gold surface.

We report on the electrical manipulation of single- and double-stranded oligodeoxynucleotides that are end tethered to gold surfaces in electrolyte solution. The response to alternating repulsive and attractive electric surface fields is studied by time-resolved fluorescence measurements, revealing markedly distinct dynamics for the flexible single-stranded and stiff double-stranded DNA, respectively. Hydrodynamic simulations rationalize this finding and disclose two different kinetic mechanisms: stiff polymers undergo rotation around the anchoring pivot point; flexible polymers, on the other hand, are pulled onto the attracting surface segment by segment.

Computer Simulation↗

PubMed2005

Counterions at charged cylinders: criticality and universality beyond mean-field theory.

The counterion-condensation transition at charged cylinders is studied using Monte Carlo simulations. Employing logarithmically rescaled radial coordinates, large system sizes are tractable and the critical behavior is determined by a combined finite-size and finite-ion-number analysis. Critical counterion localization exponents are introduced and found to be in accord with mean-field theory both in two (2D) and three (3D) dimensions. In 3D, the heat capacity shows a universal jump at the transition, while in 2D, it consists of discrete peaks where single counterions successively condense.

Journal Article↗

PubMed2005

Counterion density profiles at charged flexible membranes.

Counterion distributions at charged flexible membranes are studied using analytical and simulation methods in both Poisson-Boltzmann and strong-coupling limits. The softer the membrane, the more smeared out the counterion-density profile becomes and counterions penetrate through the mean-membrane surface location, in agreement with anomalous scattering results. Repulsion between membrane charges enhances protrusions and induces short-scale membrane roughening.

Biopolymers↗

PubMed2005

Highly stretched single polymers: atomic-force-microscope experiments versus ab-initio theory.

Experimental single-molecule stretching curves for three backbone architectures (single-stranded DNA, various types of peptides, polyvinylamine) are quantitatively compared with corresponding quantum-chemical (zero-temperature) ab-initio calculations in the high-force range of up to two nanonewtons. For high forces, quantitative agreement is obtained with the contour length of the polymers as the only fitting parameter. For smaller forces, the effects of chain fluctuations are accounted for by using recent theoretical results for the stretching response of a freely-rotating-chain model.

Computer Simulation↗

PubMed2004

Water at hydrophobic substrates: curvature, pressure, and temperature effects.

We studied the water density profile close to spherical and planar hydrophobic objects using molecular dynamics (MD) simulations. For normal pressure and room temperature, the depletion layer thickness of a planar substrate is approximately 2.5 Angstroms. Even for quite large spherical solutes with a radius of R = 18 Angstroms, the depletion layer thickness is reduced by 30%, which shows that substrate curvature and roughness is an experimentally important factor. Rising temperature leads to a substantial increase of the depletion layer thickness. The compressibility of the depletion layer is found to be surprisingly small and only approximately 5 times higher than that of bulk water. A high electrostatic surface potential of 0.5 V is found, which presumably plays an important role in the presence of charged solutes, since it can promote adsorption into the interfacial layer.

Journal Article↗

PubMed2002

Poisson-Boltzmann theory for membranes with mobile charged lipids and the pH-dependent interaction of a DNA molecule with a membrane.

We consider a planar stiff model membrane consisting of mobile surface groups whose state of charge depends on the pH and the ionic composition of the adjacent electrolyte solution. To calculate the mean-field interaction potential between a charged object and such a model membrane, one needs to solve a Poisson-Boltzmann boundary value problem. We here derive and discuss the boundary condition at the membrane surface, a condition that is generally appropriate for biological membranes where two charge-regulating mechanisms are present at the same time: the pH-dependent chemical charge regulation and a regulation through the in-plane mobility of the surface groups. As an application of this general formalism, we consider the specific example of a single DNA molecule, approximated by a cylinder with smeared-out surface charges, interacting with such a model membrane. We study the effect that the two competing charge-regulating mechanisms have on the DNA/membrane interaction and the distribution of surface ions in the plane of the membrane. We find that, at short DNA-membrane distances, membrane fluidity can have a considerable impact on the DNA adsorption behavior and can lead to such counterintuitive phenomena as the adsorption of a negatively charged DNA onto a (on average) negatively charged membrane.

DNA↗