45 research outputs found
Universal reduction of pressure between charged surfaces by long-wavelength surface charge modulation
We predict theoretically that long-wavelength surface charge modulations
universally reduce the pressure between the charged surfaces with counterions
compared with the case of uniformly charged surfaces with the same average
surface charge density. The physical origin of this effect is the fact that
surface charge modulations always lead to enhanced counterion localization near
the surfaces, and hence, fewer charges at the midplane. We confirm the last
prediction with Monte Carlo simulations.Comment: 8 pages 1 figure, Europhys. Lett., in pres
Statistically enhanced self-attraction of random patterns
In this work we develop a theory of interaction of randomly patterned
surfaces as a generic prototype model of protein-protein interactions. The
theory predicts that pairs of randomly superimposed identical (homodimeric)
random patterns have always twice as large magnitude of the energy fluctuations
with respect to their mutual orientation, as compared with pairs of different
(heterodimeric) random patterns. The amplitude of the energy fluctuations is
proportional to the square of the average pattern density, to the square of the
amplitude of the potential and its characteristic length, and scales linearly
with the area of surfaces. The greater dispersion of interaction energies in
the ensemble of homodimers implies that strongly attractive complexes of random
surfaces are much more likely to be homodimers, rather than heterodimers. Our
findings suggest a plausible physical reason for the anomalously high fraction
of homodimers observed in real protein interaction networks.Comment: Submitted to PR
Counterions at charge-modulated substrates
We consider counterions in the presence of a single planar surface with a
spatially inhomogeneous charge distribution using Monte-Carlo simulations and
strong-coupling theory. For high surface charges, multivalent counterions, or
pronounced substrate charge modulation the counterions are laterally correlated
with the surface charges and their density profile deviates strongly from the
limit of a smeared-out substrate charge distribution, in particular exhibiting
a much increased laterally averaged density at the surface.Comment: 7 page
Charge Fluctuations and Counterion Condensation
We predict a condensation phenomenon in an overall neutral system, consisting
of a single charged plate and its oppositely charged counterions. Based on the
``two-fluid'' model, in which the counterions are divided into a ``free'' and a
``condensed'' fraction, we argue that for high surface charge, fluctuations can
lead to a phase transition in which a large fraction of counterions is
condensed. Furthermore, we show that depending on the valence, the condensation
is either a first-order or a smooth transition.Comment: 16 pages, 1 figure, accepted to be published in PR
Slow fluctuations in enhanced Raman scattering and surface roughness relaxation
We propose an explanation for the recently measured slow fluctuations and
``blinking'' in the surface enhanced Raman scattering (SERS) spectrum of single
molecules adsorbed on a silver colloidal particle. We suggest that these
fluctuations may be related to the dynamic relaxation of the surface roughness
on the nanometer scale and show that there are two classes of roughness with
qualitatively different dynamics. The predictions agree with measurements of
surface roughness relaxation. Using a theoretical model for the kinetics of
surface roughness relaxation in the presence of charges and optical electrical
fields, we predict that the high-frequency electromagnetic field increases both
the effective surface tension and the surface diffusion constant and thus
accelerates the surface smoothing kinetics and time scale of the Raman
fluctuations in manner that is linear with the laser power intensity, while the
addition of salt retards the surface relaxation kinetics and increases the time
scale of the fluctuations. These predictions are in qualitative agreement with
the Raman experiments
Hydration interactions: aqueous solvent effects in electric double layers
A model for ionic solutions with an attractive short-range pair interaction
between the ions is presented. The short-range interaction is accounted for by
adding a quadratic non-local term to the Poisson-Boltzmann free energy. The
model is used to study solvent effects in a planar electric double layer. The
counter-ion density is found to increase near the charged surface, as compared
with the Poisson-Boltzmann theory, and to decrease at larger distances. The ion
density profile is studied analytically in the case where the ion distribution
near the plate is dominated only by counter-ions. Further away from the plate
the density distribution can be described using a Poisson-Boltzmann theory with
an effective surface charge that is smaller than the actual one.Comment: 11 Figures in 13 files + LaTex file. 20 pages. Accepted to Phys. Rev.
E. Corrected typos and reference
Controlling the temperature sensitivity of DNA-mediated colloidal interactions through competing linkages
We propose a new strategy to improve the self-assembly properties of
DNA-functionalised colloids. The problem that we address is that
DNA-functionalised colloids typically crystallize in a narrow temperature
window, if at all. The underlying reason is the extreme sensitivity of
DNA-mediated interactions to temperature or other physical control parameters.
We propose to widen the window for colloidal crystallization by exploiting the
competition between DNA linkages with different nucleotide sequences, which
results in a temperature-dependent switching of the dominant bond type.
Following such a strategy, we can decrease the temperature dependence of
DNA-mediated self assembly to make systems that can crystallize in a wider
temperature window than is possible with existing systems of DNA functionalised
colloids. We report Monte Carlo simulations that show that the proposed
strategy can indeed work in practice for real systems and specific, designable
DNA sequences. Depending on the length ratio of the different DNA constructs,
we find that the bond switching is either energetically driven (equal length or
`symmetric' DNA) or controlled by a combinatorial entropy gain (`asymmetric'
DNA), which results from the large number of possible binding partners for each
DNA strand. We provide specific suggestions for the DNA sequences with which
these effects can be achieved experimentally
Extent of Structural Asymmetry in Homodimeric Proteins: Prevalence and Relevance
Most homodimeric proteins have symmetric structure. Although symmetry is known to confer structural and functional advantage, asymmetric organization is also observed. Using a non-redundant dataset of 223 high-resolution crystal structures of biologically relevant homodimers, we address questions on the prevalence and significance of asymmetry. We used two measures to quantify global and interface asymmetry, and assess the correlation of several molecular and structural parameters with asymmetry. We have identified rare cases (11/223) of biologically relevant homodimers with pronounced global asymmetry. Asymmetry serves as a means to bring about 2∶1 binding between the homodimer and another molecule; it also enables cellular signalling arising from asymmetric macromolecular ligands such as DNA. Analysis of these cases reveals two possible mechanisms by which possible infinite array formation is prevented. In case of homodimers associating via non-topologically equivalent surfaces in their tertiary structures, ligand-dependent mechanisms are used. For stable dimers binding via large surfaces, ligand-dependent structural change regulates polymerisation/depolymerisation; for unstable dimers binding via smaller surfaces that are not evolutionarily well conserved, dimerisation occurs only in the presence of the ligand. In case of homodimers associating via interaction surfaces with parts of the surfaces topologically equivalent in the tertiary structures, steric hindrance serves as the preventive mechanism of infinite array. We also find that homodimers exhibiting grossly symmetric organization rarely exhibit either perfect local symmetry or high local asymmetry. Binding of small ligands at the interface does not cause any significant variation in interface asymmetry. However, identification of biologically relevant interface asymmetry in grossly symmetric homodimers is confounded by the presence of similar small magnitude changes caused due to artefacts of crystallisation. Our study provides new insights regarding accommodation of asymmetry in homodimers