arXiv subjects

Joachim Dzubiella

Publications and source records attributed to Joachim Dzubiella.

86 records · Page 5Linked to original sources

arXiv2015

Curvature Dependence of Hydrophobic Hydration Dynamics

We investigate the curvature-dependence of water dynamics in the vicinity of hydrophobic spherical solutes using molecular dynamics simulations. For both, the lateral and perpendicular diffusivity as well as for H-bond kinetics of water in the first hydration shell, we find a non-monotonic solute-size dependence, exhibiting extrema close to the well-known structural crossover length scale for hydrophobic hydration. Additionally, we find an apparently anomalous diffusion for water moving parallel to the surface of small solutes, which, however, can be explained by topology effects. The intimate connection between solute curvature, water structure and dynamics has implications for our understanding of hydration dynamics at heterogeneous biomolecular surfaces.

cond-mat.soft↗

arXiv2014

Anisotropic Electrostatic Friction of Organic Molecules on ZnO Surfaces

We study the long-time self-diffusion of a single conjugated organic para-sexiphenyl (p-6P) molecule physisorbed on the inorganic ZnO $\left(10\overline{1}0\right)$ surface by means of all-atom molecular dynamics computer simulations. We find strongly anisotropic diffusion processes in which the diffusive motion along the polar [0001] direction of the surface can be many orders of magnitudes slower at relevant experimental temperatures than in the perpendicular direction. The observation can be rationalized by the underlying charge pattern of the electrostatically heterogeneous surface which imposes direction-dependent energy barriers to the motion of the molecule. Furthermore, the diffusive behavior is found to be normal and Arrhenius-like, governed by thermally activated energy barrier crossings. The detailed analysis of the underlying potential energy landscape shows, however, that in general the activation barriers cannot be estimated from idealized zero-temperature trajectories but must include the conformational and positional excursion of the molecule along its pathway. Furthermore, the corresponding (Helmholtz) free energy barriers are significantly smaller than the pure energetic barriers with implications on absolute rate prediction at experimentally relevant temperatures. Our findings suggest that adequately engineered substrate charge patterns could be possibly harvested to select desired growth modes of hybrid interfaces for optoelectronic device engineering.

cond-mat.mtrl-sci↗

arXiv2014

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.

physics.bio-ph↗

arXiv2013

Thermodynamic Description of the LCST of Charged Thermoresponsive Copolymers

The dependence of the lower critical solution temperature (LCST) of charged, thermosensitive copolymers on their charge fraction and the salt concentration is investigated by employing systematic cloud-point experiments and analytical theory. The latter is based on the concept of the Donnan equilibrium incorporated into a thermodynamic expansion of a two-state free energy around a charge-neutral reference homopolymer and should be applicable for weakly charged (or highly salted) polymer systems. Very good agreement is found between the theoretical description and the experiments for aqueous solutions of the responsive copolymer poly(NIPAM-co-EVImBr) for a wide range of salt concentrations and charge fractions up to 8%, using only two global, physical fitting parameters.

cond-mat.soft↗

arXiv2012

Rationalizing polymer swelling and collapse under repulsive to highly attractive cosolvent conditions

The collapse and swelling behavior of a generic homopolymer is studied using implicit-solvent, explicit-cosolvent Langevin dynamics computer simulations for varying interaction strengths. The systematic investigation reveals that polymer swelling is maximal if both monomer-monomer and monomer-cosolute interactions are weakly attractive. In the most swollen state the cosolute density inside the coil is remarkably bulk-like and homogenous. Highly attractive monomer-cosolute interactions, however, are found to induce a collapse of the chain which, in contrast to the collapsed case induced by purely repulsive cosolvents, exhibits a considerably enhanced cosolute density within the globule. Thus, collapsed states, although appearing similar on a first glance, may result from very different mechanisms with distinct final structural and thermodynamics properties. Two theoretical models, one based on an effective one-component description where the cosolutes have been integrated out, and a fully two-component Flory -- de Gennes like model, support the simulation findings above and serve for interpretation. In particular, the picture is supported that collapse in highly attractive cosolvents is driven by crosslinking-like bridging effects, while the ratio of attraction width to cosolute size plays a critical role behind this mechanism. Only if polymer-cosolute interactions are not too short-ranged swelling effects should be observable. Our findings may be important for the interpretation of the effects of cosolutes on polymer and protein conformational structure, in particular for highly attractive interaction combinations, such as provided by urea, GdmCl, NaI, or NaClO4 near peptide-like moieties.

cond-mat.soft↗

arXiv2012

Sorption of proteins to charged microgels: characterizing binding isotherms and driving forces

We present a set of Langmuir binding models in which electrostatic cooperativity effects to protein sorption is incorporated in the spirit of Guoy-Chapman-Stern models, where the global substrate (microgel) charge state is modified by bound reactants (charged proteins). Application of this approach to lysozyme sorption to oppositely charged core-shell microgels allows us to extract the intrinsic, binding affinity of the protein to the gel, which is salt-concentration independent and mostly hydrophobic in nature. The total binding affinity is found to be mainly electrostatic in nature, changes many orders of magnitude during the sorption process, and is significantly influenced by osmotic deswelling effects. The intrinsic binding affinity is determined to be about 7 kBT for our system. We additionally show that Langmuir binding models and those based on excludedvolume interactions are formally equivalent for low to moderate protein packing, if the nature of the bound state is consistently defined. Having appreciated this, a more quantitative interpretation of binding isotherms in terms of separate physical interactions is possible in future for a wide variety of experimental approaches.

cond-mat.soft↗

arXiv2011

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.

cond-mat.soft↗

arXiv2010

Ion-specificity in α-helical folding kinetics

The influence of the salts KCl, NaCl, and NaI at molar concentrations on the α-helical folding kinetics of the alanine-based oligopeptide Ace-AEAAAKEAAAKA-Nme is investigated by means of (explicit-water) molecular dynamics simulations and a diffusional analysis. The mean first passage times for folding and unfolding are found to be highly salt-specific. In particular, the folding times increase about one order of magnitude for the sodium salts. The drastic slowing down can be traced back to long-lived, compact configurations of the partially folded peptide, in which sodium ions are tightly bound by several carbonyl and carboxylate groups. This multiple trapping is found to lead to a non-exponential residence time distribution of the cations in the first solvation shell of the peptide. The analysis of α-helical folding in the framework of diffusion in a reduced (one-dimensional) free energy landscape further shows that the salt not only specifically modifies equilibrium properties, but also induces kinetic barriers due to individual ion binding. In the sodium salts, for instance, the peptide's configurational mobility (or "diffusivity") can decrease about one order of magnitude. This study demonstrates the highly specific action of ions and highlights the intimate coupling of intramolecular friction and solvent effects in protein folding.

cond-mat.soft↗

arXiv2010

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 variation, some having an activation barrier, 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.

physics.bio-ph↗

arXiv2009

Ionic force field optimization based on single-ion and ion-pair solvation properties

Molecular dynamics simulations of ionic solutions depend sensitively on the force fields employed for the ions. To resolve the fine differences between ions of the same valence and roughly similar size and in particular to correctly describe ion-specific effects, it is clear that accurate force fields are necessary. In the past, optimization strategies for ionic force fields either considered single-ion properties (such as the solvation free energy at infinite dilution or the ion-water structure) or ion-pair properties (in the form of ion-ion distribution functions). In this paper we investigate strategies to optimize ionic force fields based on single-ion and ion-pair properties simultaneously. To that end, we simulate five different salt solutions, namely CsCl, KCl, NaI, KF, and CsI, at finite ion concentration. The force fields of these ions are systematically varied under the constraint that the single-ion solvation free energy matches the experimental value, which reduces the two-dimensional $\{σ,ε\}$ parameter space of the Lennard Jones interaction to a one dimensional line for each ion. From the finite-concentration simulations, the pair-potential is extracted and the osmotic coefficient is calculated, which is compared to experimental data. We find a strong dependence of the osmotic coefficient on the force field, which is remarkable as the single-ion solvation free energy and the ion-water structure remain invariant under the parameter variation. Optimization of the force field is achieved for the cations Cs$^+$ and K$^+$, while for the anions I$^-$ and F$^-$ the experimental osmotic coefficient cannot be reached. This suggests that in the long run, additional parameters might have to be introduced into the modeling, for example by modified mixing rules.

physics.chem-ph↗

arXiv2008

Sequence-specific size, structure, and stability of tight protein knots

Approximately 1% of the known protein structures display knotted configurations in their native fold but their function is not understood. It has been speculated that the entanglement may inhibit mechanical protein unfolding or transport, e.g., as in cellular threading or translocation processes through narrow biological pores. Here we investigate tigh peptide knot (TPK) characteristics in detail by pulling selected 3_1 and 4_1-knotted peptides using all-atom molecular dynamics computer simulations. We find that the 3_1 and 4_1-TPK lengths are typically Delta l~4.7 nm and 6.9 nm, respectively, for a wide range of tensions (F < 1.5 nN), pointing to a pore diameter of ~2 nm below which a translocated knotted protein might get stuck. The 4_1-knot length is in agreement with recent AFM pulling experiments. Detailed TPK characteristics however, may be sequence-specific: we find a different size and structural behavior in polyglycines, and, strikingly, a strong hydrogen bonding and water molecule trapping capability of hydrophobic TPKs due to side chain shielding of the polar TPK core. Water capturing and release is found to be controlla ble by the tightening force in a few cases. These mechanisms result into a sequence-specific 'locking' and metastability of TPKs what might lead to a blocking of knotted peptide transport at designated sequence-positions. Intriguingly, macroscopic tight 4_1-knot structures are reproduced microscopically ('figure-of-eight' vs. the 'pretzel') and can be tuned by sequence in contrast to mathematical predictions. Our findings may explain a function of knots in native proteins, challenge previous studies on macromolecular knots, and may find use in bio- and nanotechnology.

physics.bio-ph↗

arXiv2008

Salt-specific stability and denaturation of a short salt-bridge forming alpha-helix

The structure of a single alanine-based Ace-AEAAAKEAAAKA-Nme peptide in explicit aqueous electrolyte solutions (NaCl, KCl, NaI, and KF) at large salt concentrations (3-4 M) is investigated using 1 microsecond molecular dynamics (MD) computer simulations. The peptide displays 71 alpha-helical structure without salt and destabilizes with the addition of NaCl in agreement with experiments of a somewhat longer version. It is mainly stabilized by direct and indirect (i+4)EK salt bridges between the Lys and Glu side chains and a concomitant backbone shielding mechanism. NaI is found to be a stronger denaturant than NaCl, while the potassium salts hardly show influence. Investigation of the molecular structures reveals that consistent with recent experiments Na+ has a much stronger affinity to side chain carboxylates and backbone carbonyls than K+, thereby weakening salt bridges and secondary structure hydrogen bonds. At the same time the large I- has a considerable affinity to the nonpolar alanine in line with recent observations of a large propensity of I- to adsorb to simple hydrophobes, and thereby 'assists' Na+ in its destabilizing action. In the denatured states of the peptide novel long-lived (10-20 ns) 'loop'-configurations are observed in which single Na+ ions and water molecules are hydrogen-bonded to multiple backbone carbonyls. In an attempt to analyze the denaturation behavior within the preferential interaction formalism, we find indeed that for the strongest denaturant, NaI, the protein is least hydrated. Additionally, a possible indication for protein denaturation might be a preferential solvation of the first solvation shell of the peptide backbone by the destabilizing cosolute (sodium).

physics.bio-ph↗

arXiv2007

Interface dynamics of microscopic cavities in water

An analytical description of the interface motion of a collapsing nanometer-sized spherical cavity in water is presented by a modification of the Rayleigh-Plesset equation in conjunction with explicit solvent molecular dynamics simulations. Quantitative agreement is found between the two approaches for the time-dependent cavity radius $R(t)$ at different solvent conditions while in the continuum picture the solvent viscosity has to be corrected for curvature effects. The typical magnitude of the interface or collapse velocity is found to be given by the ratio of surface tension and fluid viscosity, $v\simeqγ/η$, while the curvature correction accelerates collapse dynamics on length scales below the equilibrium crossover scales ($\sim$1nm). The study offers a starting point for an efficient implicit modeling of water dynamics in aqueous nanoassembly and protein systems in nonequilibrium.

cond-mat.soft↗

arXiv2007

Non-equilibrium sedimentation of colloids on the particle scale

We investigate sedimentation of model hard sphere-like colloidal dispersions confined in horizontal capillaries using laser scanning confocal microscopy, dynamical density functional theory, and Brownian dynamics computer simulations. For homogenized initial states we obtain quantitative agreement of the results from the respective approaches for the time evolution of the one-body density distribution and the osmotic pressure on the walls. We demonstrate that single particle information can be obtained experimentally in systems that were initialized further out-of-equilibrium such that complex lateral patterns form.

cond-mat.soft↗