44 research outputs found
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 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