Statics and Dynamics of Strongly Charged Soft Matter

Soft matter materials, such as polymers, membranes, proteins, are often electrically charged. This makes them water soluble, which is of great importance in technological application and a prerequisite for biological function. We discuss a few static and dynamic systems that are dominated by charge effects. One class comprises complexation between oppositely charged objects, for example the adsorption of charged ions or charged polymers (such as DNA) on oppositely charged substrates of different geometry. The second class comprises effective interactions between similarly charged objects. Here the main theme is to understand the experimental finding that similarly and highly charged bodies attract each other in the presence of multi-valent counterions. This is demonstrated using field-theoretic arguments as well as Monte-Carlo simulations for the case of two homogeneously charged bodies. Realistic surfaces, on the other hand, are corrugated and also exhibit modulated charge distributions, which is important for static properties such as the counterion-density distribution, but has even more pronounced consequences for dynamic properties such as the counterion mobility. More pronounced dynamic effects are obtained with highly condensed charged systems in strong electric fields. Likewise, an electrostatically collapsed highly charged polymer is unfolded and oriented in strong electric fields. At the end of this review, we give a very brief account of the behavior of water at planar surfaces and demonstrate using ab-initio methods that specific interactions between oppositely charged groups cause ion-specific effects that have recently moved into the focus of interest.Comment: 61 pages, 31 figures, Physics Reports (2005)-in press (high quality figures available from authors

Controlled DNA compaction within chromatin: the tail-bridging effect

We study the mechanism underlying the attraction between nucleosomes, the fundamental packaging units of DNA inside the chromatin complex. We introduce a simple model of the nucleosome, the eight-tail colloid, consisting of a charged sphere with eight oppositely charged, flexible, grafted chains that represent the terminal histone tails. We demonstrate that our complexes are attracted via the formation of chain bridges and that this attraction can be tuned by changing the fraction of charged monomers on the tails. This suggests a physical mechanism of chromatin compaction where the degree of DNA condensation can be controlled via biochemical means, namely the acetylation and deacetylation of lysines in the histone tails.Comment: 4 pages, 5 figures, submitte

Phase Diagram of Chiral Biopolymer Wigner Crystals

We study the statistical mechanics of counterion Wigner crystals associated with hexagonal bundles of chiral biopolymers. We show that, due to spontaneous chiral symmetry breaking induced by frustration, these Wigner crystals would be chiral even if the biopolymers themselves were not chiral. Using a duality transformation of the model onto a "spin-charge" Hamiltonian, we show that melting of the Wigner crystal is due to the unbinding of screw dislocations and that the melting temperature has a singular dependence on the intrinsic chirality of the biopolymers. Finally, we report that, if electrostatic interactions are strongly screened, the counterions can condense in the form of an intermediate achiral Wigner solid phase that melts by the unbinding of fractional topological charges.Comment: 43 pages, 13 figure

The low-density/high-density liquid phase transition for model globular proteins

The effect of molecule size (excluded volume) and the range of interaction on the surface tension, phase diagram and nucleation properties of a model globular protein is investigated using a combinations of Monte Carlo simulations and finite temperature classical Density Functional Theory calculations. We use a parametrized potential that can vary smoothly from the standard Lennard-Jones interaction characteristic of simple fluids, to the ten Wolde-Frenkel model for the effective interaction of globular proteins in solution. We find that the large excluded volume characteristic of large macromolecules such as proteins is the dominant effect in determining the liquid-vapor surface tension and nucleation properties. The variation of the range of the potential only appears important in the case of small excluded volumes such as for simple fluids. The DFT calculations are then used to study homogeneous nucleation of the high-density phase from the low-density phase including the nucleation barriers, nucleation pathways and the rate. It is found that the nucleation barriers are typically only a few $k_{B}T$ and that the nucleation rates substantially higher than would be predicted by Classical Nucleation Theory.Comment: To appear in Langmui

Partially Annealed Disorder and Collapse of Like-Charged Macroions

Charged systems with partially annealed charge disorder are investigated using field-theoretic and replica methods. Charge disorder is assumed to be confined to macroion surfaces surrounded by a cloud of mobile neutralizing counterions in an aqueous solvent. A general formalism is developed by assuming that the disorder is partially annealed (with purely annealed and purely quenched disorder included as special cases), i.e., we assume in general that the disorder undergoes a slow dynamics relative to fast-relaxing counterions making it possible thus to study the stationary-state properties of the system using methods similar to those available in equilibrium statistical mechanics. By focusing on the specific case of two planar surfaces of equal mean surface charge and disorder variance, it is shown that partial annealing of the quenched disorder leads to renormalization of the mean surface charge density and thus a reduction of the inter-plate repulsion on the mean-field or weak-coupling level. In the strong-coupling limit, charge disorder induces a long-range attraction resulting in a continuous disorder-driven collapse transition for the two surfaces as the disorder variance exceeds a threshold value. Disorder annealing further enhances the attraction and, in the limit of low screening, leads to a global attractive instability in the system.Comment: 21 pages, 2 figure

Renormalized Surface Charge Density for a Strongly Charged Plate in Asymmetric Electrolytes: Asymptotic Exact Results in Poisson Boltzmann Theory

The Poisson-Boltzmann equation for a strongly charged plate inside a generic charge-asymmetric electrolyte is solved using the method of asymptotic matching. Both near field and far field asymptotic behaviors of the potential are systematically analyzed. Using these expansions, the renormalized surface charge density is obtained as an asymptotic series in terms of the bare surface charge density.Comment: 11 pages, 4 eps figure

Single-molecule experiments in biological physics: methods and applications

I review single-molecule experiments (SME) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize individual molecules and measure microscopic forces. Using SME it is possible to: manipulate molecules one at a time and measure distributions describing molecular properties; characterize the kinetics of biomolecular reactions and; detect molecular intermediates. SME provide the additional information about thermodynamics and kinetics of biomolecular processes. This complements information obtained in traditional bulk assays. In SME it is also possible to measure small energies and detect large Brownian deviations in biomolecular reactions, thereby offering new methods and systems to scrutinize the basic foundations of statistical mechanics. This review is written at a very introductory level emphasizing the importance of SME to scientists interested in knowing the common playground of ideas and the interdisciplinary topics accessible by these techniques. The review discusses SME from an experimental perspective, first exposing the most common experimental methodologies and later presenting various molecular systems where such techniques have been applied. I briefly discuss experimental techniques such as atomic-force microscopy (AFM), laser optical tweezers (LOT), magnetic tweezers (MT), biomembrane force probe (BFP) and single-molecule fluorescence (SMF). I then present several applications of SME to the study of nucleic acids (DNA, RNA and DNA condensation), proteins (protein-protein interactions, protein folding and molecular motors). Finally, I discuss applications of SME to the study of the nonequilibrium thermodynamics of small systems and the experimental verification of fluctuation theorems. I conclude with a discussion of open questions and future perspectives.Comment: Latex, 60 pages, 12 figures, Topical Review for J. Phys. C (Cond. Matt

Stability of strong polyelectrolyte-macroion complexes

We investigate the thermodynamic stability of complexes formed by one semiflexible charged polymer wrapped around an oppositely charged sphere. Choosing parameters for DNA and histones, we determine all conformational eigen-modes and the corresponding eigen-value spectrum of the complexed chain, from which the free energy of complexation and thus the reaction constant is obtained. The resulting complexation diagram exhibits qualitative agreement with experimental results as a function of salt and DNA/histone concentration

Interactions between polyelectrolyte-macroion complexes

We consider structures formed by one semiflexible polyelectrolyte (PE) and one oppositely charged sphere and calculate the interaction between two such complexes within the ground-state approximation, where the PE assumes its optimal configuration. Using parameters appropriate for DNA-histone systems, we find the second virial coefficient of inter-complex interactions to be negative for intermediate salt concentrations within the range where stable complexes are formed, in agreement with experiments. A simple screened monopole-dipole model reproduces these findings