How the diffusivity profile reduces the arbitrariness of protein folding free energies.

The concept of a protein diffusing in its free-energy folding landscape has been fruitful for both theory and experiment. Yet the choice of the reaction coordinate (RC) introduces an undesirable degree of arbitrariness into the problem. We analyze extensive simulation data of an alpha-helix in explicit water solvent as it stochastically folds and unfolds. The free-energy profiles for different RCs exhibit significant variations, some having an activation barrier, while others not. We show that this variation has little effect on the predicted folding kinetics if the diffusivity profiles are properly taken into account. This kinetic quasi-universality is rationalized by an RC rescaling, which, due to the reparameterization invariance of the Fokker-Planck equation, allows the combination of free-energy and diffusivity effects into a single function, the rescaled free-energy profile. This rescaled free energy indeed shows less variation among different RCs than the bare free energy and diffusivity profiles separately do, if we properly distinguish between RCs that contain knowledge of the native state and those that are purely geometric in nature. Our method for extracting diffusivity profiles is easily applied to experimental single molecule time series data and might help to reconcile conflicts that arise when comparing results from different experimental probes for the same protein.

Dewetting-controlled binding of ligands to hydrophobic pockets.

We report on a combined atomistic molecular dynamics simulation and implicit solvent analysis of a generic hydrophobic pocket-ligand (host-guest) system. The approaching ligand induces complex wetting-dewetting transitions in the weakly solvated pocket. The transitions lead to bimodal solvent fluctuations which govern magnitude and range of the pocket-ligand attraction. A recently developed implicit water model, based on the minimization of a geometric functional, captures the sensitive aqueous interface response to the concave-convex pocket-ligand configuration semiquantitatively.

Tuning colloidal interactions in subcritical solvents by solvophobicity: explicit versus implicit modeling.

The distance-resolved effective interaction between two colloidal particles in a subcritical solvent is explored both by an explicit and implicit modeling. An implicit solvent approach based on a simple thermodynamic interface model is tested against grand-canonical Monte Carlo computer simulations using explicit Lennard-Jones solvent molecules. Close to liquid-gas coexistence, a joint gas bubble surrounding the colloidal particle pair yields an effective attraction between the colloidal particles, the strength of which can be vastly tuned by the solvophobicity of the colloids. The implicit model is in good agreement with our explicit computer simulations, thus enabling an efficient modeling and evaluation of colloidal interactions and self-assembly in subcritical solvent environments.

Ion specific correlations in bulk and at biointerfaces.

Ion specific effects are ubiquitous in any complex colloidal or biological fluid in bulk or at interfaces. The molecular origins of these 'Hofmeister effects' are not well understood and their theoretical description poses a formidable challenge to the modeling and simulation community. On the basis of the combination of atomistically resolved molecular dynamics (MD) computer simulations and statistical mechanics approaches, we present a few selected examples of specific electrolyte effects in bulk, at simple neutral and charged interfaces, and on a short α-helical peptide. The structural complexity in these strongly Coulomb-correlated systems is highlighted and analyzed in the light of available experimental data. While in general the comparison of MD simulations to experiments often lacks quantitative agreement, mostly because molecular force fields and coarse-graining procedures remain to be optimized, the consensus as regards trends provides important insights into microscopic hydration and binding mechanisms.

Density profiles and solvation forces for a Yukawa fluid in a slit pore.

The effect of varying wall-particle and particle-particle interactions on the density profiles near a single wall and the solvation forces between two walls immersed in a fluid of particles is investigated by grand canonical Monte Carlo simulations. Attractive and repulsive particle-particle and particle-wall interactions are modeled by a versatile hard-core Yukawa form. These simulation results are compared to theoretical calculations using the hypernetted chain integral equation technique, as well as with fundamental measure density functional theory (DFT), where particle-particle interactions are either treated as a first order perturbation using the radial distribution function or else with a DFT based on the direct-correlation function. All three theoretical approaches reproduce the main trends fairly well, but exhibit inconsistent accuracy, particularly for attractive particle-particle interactions. We show that the wall-particle and particle-particle attractions can couple together to induce a nonlinear enhancement of the adsorption and a related "repulsion through attraction" effect for the effective wall-wall forces. We also investigate the phenomenon of bridging, where an attractive wall-particle interaction induces strongly attractive solvation forces.

Coupling hydrophobicity, dispersion, and electrostatics in continuum solvent models.

An implicit solvent model is presented that couples hydrophobic, dispersion, and electrostatic solvation energies by minimizing the system Gibbs free energy with respect to the solvent volume exclusion function. The solvent accessible surface is the output of the theory. The method is illustrated with the solvation of simple solutes on different length scales and captures the sensitivity of hydration to the particular form of the solute-solvent interactions in agreement with recent computer simulations.

Coupling nonpolar and polar solvation free energies in implicit solvent models.

Recent studies on the solvation of atomistic and nanoscale solutes indicate that a strong coupling exists between the hydrophobic, dispersion, and electrostatic contributions to the solvation free energy, a facet not considered in current implicit solvent models. We suggest a theoretical formalism which accounts for coupling by minimizing the Gibbs free energy of the solvent with respect to a solvent volume exclusion function. The resulting differential equation is similar to the Laplace-Young equation for the geometrical description of capillary interfaces but is extended to microscopic scales by explicitly considering curvature corrections as well as dispersion and electrostatic contributions. Unlike existing implicit solvent approaches, the solvent accessible surface is an output of our model. The presented formalism is illustrated on spherically or cylindrically symmetrical systems of neutral or charged solutes on different length scales. The results are in agreement with computer simulations and, most importantly, demonstrate that our method captures the strong sensitivity of solvent expulsion and dewetting to the particular form of the solvent-solute interactions.

Bulk and interfacial properties in colloid-polymer mixtures.

Large-scale Monte Carlo simulations of a phase-separating colloid-polymer mixture are performed and compared to recent experiments. The approach is based on effective interaction potentials in which the central monomers of self-avoiding polymer chains are used as effective coordinates. By incorporating polymer nonideality together with soft colloid-polymer repulsion, the predicted binodal is in excellent agreement with recent experiments. In addition, the interfacial tension as well as the capillary length are in quantitative agreement with experimental results obtained at a number of points in the phase-coexistence region, without the use of any fit parameters.

Electric-field-controlled water and ion permeation of a hydrophobic nanopore.

The permeation of hydrophobic, cylindrical nanopores by water molecules and ions is investigated under equilibrium and out-of-equilibrium conditions by extensive molecular-dynamics simulations. Neglecting the chemical structure of the confining pore surface, we focus on the effects of pore radius and electric field on permeation. The simulations confirm the intermittent filling of the pore by water, reported earlier under equilibrium conditions for pore radii larger than a critical radius R(c). Below this radius, water can still permeate the pore under the action of a strong electric field generated by an ion concentration imbalance at both ends of the pore embedded in a structureless membrane. The water driven into the channel undergoes considerable electrostriction characterized by a mean density up to twice the bulk density and by a dramatic drop in dielectric permittivity which can be traced back to a considerable distortion of the hydrogen-bond network inside the pore. The free-energy barrier to ion permeation is estimated by a variant of umbrella sampling for Na(+), K(+), Ca(2+), and Cl(-) ions, and correlates well with known solvation free energies in bulk water. Starting from an initial imbalance in ion concentration, equilibrium is gradually restored by successive ion passages through the water-filled pore. At each passage the electric field across the pore drops, reducing the initial electrostriction, until the pore, of radius less than R(c), closes to water and hence to ion transport, thus providing a possible mechanism for voltage-dependent gating of hydrophobic pores.

Substrate concentration dependence of the diffusion-controlled steady-state rate constant.

The Smoluchowski approach to diffusion-controlled reactions is generalized to interacting substrate particles by including the osmotic pressure and hydrodynamic interactions of the nonideal particles in the Smoluchoswki equation within a local-density approximation. By solving the strictly linearized equation for the time-independent case with absorbing boundary conditions, we present an analytic expression for the diffusion-limited steady-state rate constant for small substrate concentrations in terms of an effective second virial coefficient B2*. Comparisons to Brownian dynamics simulations excluding hydrodynamic interactions show excellent agreement up to bulk number densities of B2*rho0 < approximately = 0.4 for hard sphere and repulsive Yukawa-like interactions between the substrates. Our study provides an alternative way to determine the second virial coefficient of interacting macromolecules experimentally by measuring their steady-state rate constant in diffusion-controlled reactions at low densities.

Density-functional study of interfacial properties of colloid-polymer mixtures.

Interfacial properties of colloid-polymer mixtures are examined within an effective one-component representation, where the polymer degrees of freedom are traced out, leaving a fluid of colloidal particles interacting via polymer-induced depletion forces. Restriction is made to zero-, one-, and two-body effective potentials, and a free energy functional is used that treats colloid excluded volume correlations within Rosenfeld's fundamental measure theory, and depletion-induced attraction within first-order perturbation theory. This functional allows a consistent treatment of both ideal and interacting polymers. The theory is applied to surface properties near a hard wall, to the depletion interaction between two walls, and to the fluid-fluid interface of demixed colloid-polymer mixtures. The results of the present theory compare well with predictions of a fully two-component representation of mixtures of colloids and ideal polymers (the Asakura-Oosawa model) and allow a systematic investigation of the effects of polymer-polymer interactions on interfacial properties. In particular, the wall surface tension is found to be significantly larger for interacting than for ideal polymers, whereas the opposite trend is predicted for the fluid-fluid interfacial tension.

Competition of hydrophobic and Coulombic interactions between nanosized 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.

Reentrance effect in the lane formation of driven colloids.

Recently it has been shown that a strongly interacting colloidal mixture consisting of oppositely driven particles undergoes a nonequilibrium transition towards lane formation provided the driving strength exceeds a threshold value. We predict here a reentrance effect in lane formation: for fixed high driving force and increasing particle densities, there is first a transition towards lane formation which is followed by another transition back to a state with no lanes. Our result is obtained both by Brownian dynamics computer simulations and by a phenomenological dynamical density functional theory.

Electric field-controlled water permeation coupled to ion transport through a nanopore.

We report molecular dynamics simulations of a generic hydrophobic nanopore connecting two reservoirs which are initially at different Na(+) concentrations, as in a biological cell. The nanopore is impermeable to water under equilibrium conditions, but the strong electric field caused by the ionic concentration gradient drives water molecules in. The density and structure of water in the pore are highly field dependent. In a typical simulation run, we observe a succession of cation passages through the pore, characterized by approximately bulk mobility. These ion passages reduce the electric field, until the pore empties of water and closes to further ion transport, thus providing a possible mechanism for biological ion channel gating.

Depletion forces in nonequilibrium.

The concept of effective depletion forces between two fixed big colloidal particles in a bath of small particles is generalized to a nonequilibrium situation where the bath of small Brownian particles is flowing around the big particles with a prescribed velocity. In striking contrast to the equilibrium case, the nonequilibrium forces violate Newton's third law; they are nonconservative and strongly anisotropic, featuring both strong attractive and repulsive domains.

Dynamic density functional study of a driven colloidal particle in polymer solutions.

The dynamic density functional (DDF) theory and standard Brownian dynamics simulations (BDS) are used to study the drifting effects of a colloidal particle in a polymer solution, both for ideal and interacting polymers. The structure of the stationary density distributions and the total induced current are analyzed for different drifting rates. We find good agreement with the BDS, which gives support to the assumptions of the DDF theory. The qualitative aspect of the density distribution are discussed and compared to recent results for driven colloids in one-dimensional channels and to analytical expansions for the ideal solution limit.

Lane formation in colloidal mixtures driven by an external field.

The influence of an external field on a binary colloidal mixture performing Brownian dynamics in a solvent is investigated by nonequilibrium computer simulations and simple theory. In our model, one half of the particles are pushed into the field direction while the other half of them are pulled into the opposite direction. For increasing field strength, we show that the system undergoes a nonequilibrium phase transition from a disordered state to a state characterized by lane formation parallel to the field direction. The lanes are formed by the same kind of particles moving collectively with the field. Lane formation accelerates particle transport parallel to the field direction but suppresses massively transport perpendicular to the field. We further show that lane formation also occurs in a time-dependent oscillatory field. If the frequency of the external field exceeds a critical value, however, the system exhibits a transition back to the disordered state. Our results can be experimentally verified in binary colloidal suspensions exposed to external fields under nonequilibrium conditions.

Phase separation in star-polymer-colloid mixtures.

We examine the demixing transition in star-polymer-colloid mixtures for star arm numbers f=2,6,16,32 and different star-polymer-colloid size ratios 0.18< or =q< or =0.50. Theoretically, we solve the thermodynamically self-consistent Rogers-Young integral equations for binary mixtures using three effective pair potentials obtained from direct molecular computer simulations. The numerical results show a spinodal instability. The demixing binodals are approximately calculated and found to be consistent with experimental observations.

Sedimentation profiles of systems with reentrant melting behavior.

We examine sedimentation density profiles of star polymer solutions as an example of colloidal systems in sedimentation equilibrium that exhibit reentrant melting in their bulk phase diagram. Phase transitions between a fluid and a fluid with an intercalated solid are observed below a critical gravitational strength alpha*. Characteristics of the two fluid-solid interfaces in the density profiles occurring in Monte Carlo simulations for alpha

Topological defects in nematic droplets of hard spherocylinders

Using computer simulations we investigate the microscopic structure of the singular director field within a nematic droplet. As a theoretical model for nematic liquid crystals we take hard spherocylinders. To induce an overall topological charge, the particles are either confined to a two-dimensional circular cavity with homeotropic boundary or to the surface of a three-dimensional sphere. Both systems exhibit half-integer topological point defects. The isotropic defect core has a radius of the order of one particle length and is surrounded by free-standing density oscillations. The effective interaction between two defects is investigated. All results should be experimentally observable in thin sheets of colloidal liquid crystals.