526 research outputs found
How interface geometry dictates water's thermodynamic signature in hydrophobic association
As a common view the hydrophobic association between molecular-scale binding
partners is supposed to be dominantly driven by entropy. Recent calorimetric
experiments and computer simulations heavily challenge this established
paradigm by reporting that water's thermodynamic signature in the binding of
small hydrophobic ligands to similar-sized apolar pockets is enthalpy-driven.
Here we show with purely geometric considerations that this controversy can be
resolved if the antagonistic effects of concave and convex bending on water
interface thermodynamics are properly taken into account. A key prediction of
this continuum view is that for fully complementary binding of the convex
ligand to the concave counterpart, water shows a thermodynamic signature very
similar to planar (large-scale) hydrophobic association, that is,
enthalpy-dominated, and hardly depends on the particular pocket/ligand
geometry. A detailed comparison to recent simulation data qualitatively
supports the validity of our perspective down to subnanometer scales. Our
findings have important implications for the interpretation of thermodynamic
signatures found in molecular recognition and association processes.
Furthermore, traditional implicit solvent models may benefit from our view with
respect to their ability to predict binding free energies and entropies.Comment: accepted for publication in J. Stat. Phys., special issue on
water&associated liquid
Equilibrium structure and fluctuations of suspensions of colloidal dumbbells
We investigate the structure and equilibrium linear-response dynamics of
suspensions of hard colloidal dumbbells using Brownian Dynamics computer
simulations. The focus lies on the dense fluid and plastic crystal states of
the colloids with investigated aspect (elongation-to-diameter) ratios varying
from the hard sphere limit up to 0.39, which is roughly the stability limit of
the plastic crystal phase. We find expected structural changes with larger
elongation with respect to the hard sphere reference case and very localized
orientational correlations, typically just involving next-neighbor couplings.
These relatively weak correlations are also reflected in only minor effects on
the translational and rotational diffusion coefficients for most of the
investigated elongations. However, the linear response shear viscosity exhibits
a dramatic increase at high packing fractions () beyond a
critical anisotropy factor of about which is surprising in
view of the relatively weak changes found before on the level of colloidal
self-dynamics. We suspect that even for the small investigated anisotropies,
newly occurring, collective rotational-translational couplings must be made
responsible for the slow time scales appearing in the plastic crystal.Comment: Molecular Physics 201
Competition of hydrophobic and Coulombic interactions between nano-sized solutes
The solvation of charged, nanometer-sized spherical solutes in water, and the
effective, solvent-induced force between two such solutes are investigated by
constant temperature and pressure Molecular Dynamics simulations of model
solutes carrying various charge patterns. The results for neutral solutes agree
well with earlier findings, and with predictions of simple macroscopic
considerations: substantial hydrophobic attraction may be traced back to strong
depletion (``drying'') of the solvent between the solutes. This hydrophobic
attraction is strongly reduced when the solutes are uniformly charged, and the
total force becomes repulsive at sufficiently high charge; there is a
significant asymmetry between anionic and cationic solute pairs, the latter
experiencing a lesser hydrophobic attraction. The situation becomes more
complex when the solutes carry discrete (rather than uniform) charge patterns.
Due to antagonistic effects of the resulting hydrophilic and hydrophobic
``patches'' on the solvent molecules, water is once more significantly depleted
around the solutes, and the effective interaction reverts to being mainly
attractive, despite the direct electrostatic repulsion between solutes.
Examination of a highly coarse-grained configurational probability density
shows that the relative orientation of the two solutes is very different in
explicit solvent, compared to the prediction of the crude implicit solvent
representation. The present study strongly suggests that a realistic modeling
of the charge distribution on the surface of globular proteins, as well as the
molecular treatment of water are essential prerequisites for any reliable study
of protein aggregation.Comment: 20 pages, 25 figure
Reduction of the hydrophobic attraction between charged solutes in water
We examine the effective force between two nanometer scale solutes in water
by Molecular Dynamics simulations. Macroscopic considerations predict a strong
reduction of the hydrophobic attraction between solutes when the latter are
charged. This is confirmed by the simulations which point to a surprising
constancy of the effective force between oppositely charged solutes at contact,
while like charged solutes lead to significantly different behavior between
positive and negative pairs. The latter exhibit the phenomenon of ``like-charge
attraction" previously observed in some colloidal dispersions.Comment: 4 pages, 5 figure
Communication: Resonance reaction in diffusion-influenced bimolecular reactions
We investigate the influence of a stochastically fluctuating step-barrier potential on bimolecular reaction rates by exact analytical theory and stochastic simulations. We demonstrate that the system exhibits a new "resonant reaction" behavior with rate enhancement if an appropriately defined fluctuation decay length is of the order of the system size. Importantly, we find that in the proximity of resonance, the standard reciprocal additivity law for diffusion and surface reaction rates is violated due to the dynamical coupling of multiple kinetic processes. Together, these findings may have important repercussions on the correct interpretation of various kinetic reaction problems in complex systems, as, e.g., in biomolecular association or catalysis
Dynamic density functional theory of protein adsorption on polymer-coated nanoparticles
We present a theoretical model for the description of the adsorption kinetics
of globular proteins onto charged core-shell microgel particles based on
Dynamic Density Functional Theory (DDFT). This model builds on a previous
description of protein adsorption thermodynamics [Yigit \textit{et al},
Langmuir 28 (2012)], shown to well interpret the available calorimetric
experimental data of binding isotherms. In practice, a spatially-dependent
free-energy functional including the same physical interactions is built, and
used to study the kinetics via a generalised diffusion equation. To test this
model, we apply it to the case study of Lysozyme adsorption on PNIPAM coated
nanoparticles, and show that the dynamics obtained within DDFT is consistent
with that extrapolated from experiments. We also perform a systematic study of
the effect of various parameters in our model, and investigate the loading
dynamics as a function of proteins' valence and hydrophobic adsorption energy,
as well as their concentration and that of the nanoparticles. Although we
concentrated here on the case of adsorption for a single protein type, the
model's generality allows to study multi-component system, providing a reliable
instrument for future studies of competitive and cooperative adsorption effects
often encountered in protein adsorption experiments.Comment: Submitted to Soft Matte
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