arXiv subjects

J. Dzubiella

Publications and source records attributed to J. Dzubiella.

At least 19 recordsLinked to original sources

arXiv2009

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 semi-quantitatively.

cond-mat.soft↗

arXiv2008

Tightening the knot in phytochrome by single molecule atomic force microscopy

A growing number of proteins have been shown to adopt knotted folds. Yet the biological roles and biophysical properties of these knots remain poorly understood. We have used protein engineering and atomic force microscopy to explore single-molecule mechanics of the figure-of-eight knot in the chromophore-binding domain of the red/far red photoreceptor, phytochrome. Under load, apo phytochrome unfolds at forces of ~47 pN, while phytochrome carrying its covalently bound tetrapyrrole chromophore unfolds at ~73 pN. These forces are among the lowest measured in mechanical protein unfolding, hence the presence of the knot does not automatically indicate a super-stable protein. Our experiments reveal a stable intermediate along the mechanical unfolding pathway, reflecting sequential unfolding of two distinct subdomains in phytochrome, potentially the GAF and PAS domains. For the first time, our experiments allow direct determination of knot size under load. In the unfolded chain, the tightened knot is reduced to 17 amino acids, resulting in apparent shortening of the polypeptide chain by 6.2 nm. Steered molecular dynamics simulations corroborate this number. Finally, we found that covalent phytochrome dimers created for these experiments retain characteristic photoreversibility, unexpectedly arguing against dramatic rearrangement of the native GAF dimer interface upon photoconversion.

physics.bio-ph↗

arXiv2008

Application of the level-set method to the implicit solvation of nonpolar molecules

A level-set method is developed for numerically capturing the equilibrium solute-solvent interface that is defined by the recently proposed variational implicit solvent model (Dzubiella, Swanson, and McCammon, Phys. Rev. Lett. {\bf 104}, 527 (2006) and J. Chem.\Phys. {\bf 124}, 084905 (2006)). In the level-set method, a possible solute-solvent interface is represented by the zero level-set (i.e., the zero level surface) of a level-set function and is eventually evolved into the equilibrium solute-solvent interface. The evolution law is determined by minimization of a solvation free energy {\it functional} that couples both the interfacial energy and the van der Waals type solute-solvent interaction energy. The surface evolution is thus an energy minimizing process, and the equilibrium solute-solvent interface is an output of this process. The method is implemented and applied to the solvation of nonpolar molecules such as two xenon atoms, two parallel paraffin plates, helical alkane chains, and a single fullerene $C_{60}$. The level-set solutions show good agreement for the solvation energies when compared to available molecular dynamics simulations. In particular, the method captures solvent dewetting (nanobubble formation) and quantitatively describes the interaction in the strongly hydrophobic plate system.

physics.chem-ph↗

arXiv2006

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.

cond-mat.stat-mech↗

arXiv2005

Coupling hydrophobic, dispersion, and electrostatic contributions in continuum solvent models

Recent studies of the hydration of micro- and nanoscale solutes have demonstrated a strong {\it coupling} between hydrophobic, dispersion and electrostatic contributions, a fact not accounted for in current implicit solvent models. We present a theoretical formalism which accounts for coupling by minimizing the Gibbs free energy with respect to a solvent volume exclusion function. The solvent accessible surface is output of our theory. Our method is illustrated with the hydration of alkane-assembled solutes on different length scales, and captures the strong sensitivity to the particular form of the solute-solvent interactions in agreement with recent computer simulations.

physics.chem-ph↗

arXiv2005

Accurate description of 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

cond-mat.soft↗

arXiv2004

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 B_2*. Comparisons to Brownian dynamics simulations excluding HI show excellent agreement up to bulk number densities of B_2* rho_0 < 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.

cond-mat.soft↗

arXiv2004

A 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 which 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, while the opposite trend is predicted for the fluid--fluid interfacial tension.

cond-mat.soft↗

arXiv2004

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.

cond-mat.soft↗

arXiv2004

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.

cond-mat.soft↗

arXiv2003

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.

cond-mat.stat-mech↗

arXiv2003

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.

cond-mat.soft↗

arXiv2003

Depletion forces in non-equilibrium

The concept of effective depletion forces between two fixed big colloidal particles in a bath of small particles is generalized to a non-equilibrium 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 non-equilibrium forces violate Newton's third law, are non-conservative and strongly anisotropic, featuring both strong attractive and repulsive domains.

cond-mat.soft↗

arXiv2003

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

We report Molecular Dynamics (MD) 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.

physics.bio-ph↗

arXiv2003

Thermodynamic perturbation theory of the phase behaviour of colloid / interacting polymer mixtures

We use thermodynamic perturbation theory to calculate the free energies and resulting phase diagrams of binary systems of spherical colloidal particles and interacting polymer coils in good solvent within an effective one-component representation of such mixtures, whereby the colloidal particles interact via a polymer-induced depletion potential. MC simulations are used to test the convergence of the high temperature expansion of the free energy. The phase diagrams calculated for several polymer to colloid size ratios differ considerably from the results of similar calculations for mixtures of colloids and ideal (non-interacting) polymers, and are in good overall agreement with the results of an explicit two-component representation of the same system, which includes more than two-body depletion forces.

cond-mat.soft↗

arXiv2003

Mean-field dynamical density functional theory

We examine the out-of-equilibrium dynamical evolution of density profiles of ultrasoft particles under time-varying external confining potentials in three spatial dimensions. The theoretical formalism employed is the dynamical density functional theory (DDFT) of Marini Bettolo Marconi and Tarazona [J. Chem. Phys. {\bf 110}, 8032 (1999)], supplied by an equilibrium excess free energy functional that is essentially exact. We complement our theoretical analysis by carrying out extensive Brownian Dynamics simulations. We find excellent agreement between theory and simulations for the whole time evolution of density profiles, demonstrating thereby the validity of the DDFT when an accurate equilibrium free energy functional is employed.

cond-mat.soft↗

arXiv2002

Polyelectrolyte-colloid complexes: polarizability and effective interaction

We theoretically study the polarizability and the interactions of neutral complexes consisting of a semi-flexible polyelectrolyte adsorbed onto an oppositely charged spherical colloid. In the systems we studied, the bending energy of the chain is small compared to the Coulomb energy and the chains are always adsorbed on the colloid. We observe that the polarizability is large for short chains and small electrical fields and shows a non-monotonic behavior with the chain length at fixed charge density. The polarizability has a maximum for a chain length equal to half of the circumference of the colloid. For long chains we recover the polarizability of a classical conducting sphere. For short chains, the existence of a permanent dipole moment of the complexes leads to a van der Waal's-type long-range attraction between them. This attractive interaction vanishes for long chains (i.e., larger than the colloidal size), where the permanent dipole moment is negligible. For short distances the complexes interact with a deep short-ranged attraction which is due to energetic bridging for short chains and entropic bridging for long chains. Exceeding a critical chain length eventually leads to a pure repulsion. This shows that the stabilization of colloidal suspensions by polyelectrolyte adsorption is strongly dependent on the chain size relative to the colloidal size: for long chains the suspensions are always stable (only repulsive forces between the particles), while for mid-sized and short chains there is attraction between the complexes and a salting-out can occur.

cond-mat.soft↗

arXiv2002

Pattern formation in colloidal mixtures under external driving fields

The influence of an external field acting differently on the two constituents of a binary colloidal mixture performing Brownian dynamics is investigated by computer simulations and a simple theory. In our model, one half of the particles ($A$-particles) are pulled by an external force ${\vec F}^{(A)}$ while the other half of them ($B$-particles) are pulled by an external force ${\vec F}^{(B)}$. If ${\vec F}^{(A)}$ and ${\vec F}^{(B)}$ are parallel and the field-free state is a mixed fluid, previous simulations (J. Dzubiella et al, Phys. Rev. E {\bf 65} 021402 (2002)) have shown a nonequilibrium pattern formation involving lanes of $A$ or $B$ particles only which are sliding against each other in the direction of the external forces. In this paper, we generalize the situation both to non-parallel external forces and to field-free crystalline states. For non-parallel forces, lane formation is also observed but with an orientation {\it tilted} with respect to the external forces. If the field-free state is crystalline, a continuous increase of the parallel external forces yields a novel {\it reentrant freezing} behavior: the crystal first melts mechanically via the external force and then recrystallizes into demixed crystalline lanes sliding against each other.

cond-mat.soft↗