Jens Smiatek

Properties of compatible solutes in aqueous solution.

We have performed Molecular Dynamics simulations of ectoine, hydroxyectoine and urea in explicit solvent. Special attention has been spent on the local surrounding structure of water molecules. Our results indicate that ectoine and hydroxyectoine are able to accumulate more water molecules than urea by a pronounced ordering due to hydrogen bonds. We have validated that the charging of the molecules is of main importance resulting in a well defined hydration sphere. The influence of a varying salt concentration is also investigated. Finally we present experimental results of a DPPC monolayer phase transition that validate our numerical findings.

Osmolyte Effects: Impact on the Aqueous Solution around Charged and Neutral Spheres

We have performed atomistic molecular dynamics simulations to study the solvation characteristics of model spheres for low concentrations of urea and hydroxyectoine in aqueous solution. The spheres are either positively or negatively charged with a valency of one or charge neutral. Our results illustrate that the presence of osmolytes influences the solvation properties of the spheres significantly. We have conducted a detailed investigation of water properties like the mean dipolar relaxation times, water orientation parameters around the spheres, dielectric constants, preferential binding behavior, water self-diffusion coefficients, and free energies of solvation by thermodynamic integration to study the influence of osmolytes in detail. Our findings indicate that several factors like the charge of the spheres as well as the characteristics of the osmolytes significantly influence the thermodynamic and dynamic properties of the local water shell and the solvation process with regard to varying enthalpic and entropic contributions.

Mesoscopic simulations of the counterion-induced electro-osmotic flow: A comparative study

We present mesoscopic simulations of the counterion-induced electro-osmotic flow in different electrostatic coupling regimes. Two simulation methods are compared, dissipative particle dynamics (DPD) and coupled lattice-Boltzmann/molecular dynamics (LB/MD). A general mapping scheme to match DPD to LB/MD is developed. For the weak coupling regime, analytic expressions for the flow profiles in the presence of partial-slip as well as no-slip boundary conditions are derived from the Poisson-Boltzmann and Stokes equations, which are in good agreement with the numerical results. The influence of electrofriction and partial slip on the flow profiles is discussed.

Mesoscopic Simulations of Electroosmotic Flow and Electrophoresis in Nanochannels

Abstract We review recent dissipative particle dynamics (DPD) simulations of electrolyte flow in nanochannels. A method is presented by which the slip length δ B at the channel boundaries can be tuned systematically from negative to infinity by introducing suitably adjusted wall-fluid friction forces. Using this method, we study electroosmotic flow (EOF) in nanochannels for varying surface slip conditions and fluids of different ionic strength. Analytic expressions for the flow profiles are derived from the Stokes equation, which are in good agreement with the numerical results. Finally, we investigate the influence of EOF on the effective mobility of polyelectrolytes in nanochannels. The relevant quantity characterizing the effect of slippage is found to be the dimensionless quantity κ δ B , where 1 / κ is an effective electrostatic screening length at the channel boundaries.

Separation of chiral particles in micro or nanofluidic channels

We propose a method to separate enantiomers in microfluidic or nanofluidic channels. It requires flow profiles that break chiral symmetry and have regions with high local shear. Such profiles can be generated in channels confined by walls with different hydrodynamic boundary conditions (e.g., slip lengths). Because of a nonlinear hydrodynamic effect, particles with different chirality migrate at different speeds and can be separated. The mechanism is demonstrated by computer simulations. We investigate the influence of thermal fluctuations (i.e., the Péclet number) and show that the effect disappears in the linear response regime. The details of the microscopic flow are important and determine which volume forces are necessary to achieve separation.

Concentration dependent effects of urea binding to poly(N-isopropylacrylamide) brushes: a combined experimental and numerical study

The binding effects of osmolytes on the conformational behavior of grafted polymers are studied in this work. In particular, we focus on the interactions between urea and poly(N-isopropylacrylamide) (PNIPAM) brushes by monitoring the ellipsometric brush thickness for varying urea concentrations over a broad temperature range. The interpretation of the obtained data is supported by atomistic molecular dynamics simulations, which provide detailed insights into the experimentally observed concentration-dependent effects on PNIPAM-urea interaction. In particular, in the low concentration regime (cu ≤ 0.5 mol L(-1)) a preferential exclusion of urea from PNIPAM chains is observed, while in the high concentration regime (2 ≤ cu ≤ 7 mol L(-1)) a preferential binding of the osmolyte to the polymer surface is found. In both regimes, the volume phase transition temperature (Ttr) decreases with increasing urea concentration. This phenomenon derives from two different effects depending on urea concentration: (i) for cu ≤ 0.5 mol L(-1), the decrease of Ttr is explained by a decrease of the chemical potential of bulk water in the surrounding aqueous phase; (ii) for cu ≥ 2 mol L(-1), the lower Ttr is explained by the favorable replacement of water molecules by urea, which can be regarded as a cross-linker between adjacent PNIPAM chains. Significant effects of the concentration-dependent urea binding on the brush conformation are noticed: at cu = 0.5 mol L(-1), although urea is loosely embedded between the hydrated polymer chains, it enhances the brush swelling by excluded volume effects. Beyond 0.5 mol L(-1), the stronger interaction between PNIPAM and urea reduces the chain hydration, which in combination with cross-linking of monomer units induces the shrinkage of the polymer brush.

The solvation and ion condensation properties for sulfonated polyelectrolytes in different solvents : a computational study

In contrast to the broad knowledge about aqueous polyelectrolyte solutions, less is known about the properties in aprotic and apolar solvents. We therefore investigate the behavior of sulfonated polyelectrolytes in sodium form in the presence of different solvents via all-atom molecular dynamics simulations. The results clearly reveal strong variations in ion condensation constants and polyelectrolyte conformations for different solvents like water, dimethyl sulfoxide (DMSO) and chloroform. The binding free energies of the solvent contacts with the polyelectrolyte groups validate the influence of different solvent qualities. With regard to the ion condensation behavior, the numerical findings show that the explicit values for the condensation constants depend on the preferential binding coefficient as derived by the evaluation of Kirkwood–Buff integrals. Surprisingly, the smallest ion condensation constant is observed for DMSO compared to water, whereas in the presence of chloroform, virtually no free ions are present, which is in good agreement to the donor number concept. In contrast to the results for the low condensation constants, the sodium conductivity in DMSO is smaller compared to water. We are able to relate this result to the observed smaller diffusion coefficient for the sodium ions in DMSO.

Polyelectrolyte electrophoresis in nanochannels: a dissipative particle dynamics simulation.

We present mesoscopic dissipative particle dynamics-simulations of polyelectrolyte electrophoresis in confined nanogeometries for varying salt concentration and surface slip conditions. Special attention is given to the influence of electroosmotic flow on the migration of the polyelectrolyte. The effective polyelectrolyte mobility is found to depend strongly on the boundary properties, that is, the slip length and the width of the electric double layer. Analytic expressions for the electroosmotic mobility and the total mobility are derived that are in good agreement with the numerical results. The relevant quantity characterizing the effect of slippage is found to be the dimensionless quantity kappa delta(B), where delta(B) is the slip length, and kappa(-1) is an effective electrostatic screening length at the channel boundaries.

Stable conformations of a single stranded deprotonated DNA i-motif.

We present molecular dynamics simulations of a single stranded deprotonated DNA i-motif in explicit solvent. Our results indicate that hairpin structures are stable equilibrium conformations at 300 K. The entropic preference of these configurations is explained by strong water ordering effects due to the present number of hydrogen bonds. We observe a full unfolding at higher temperatures in good agreement with experimental results.

Calculation of free energy landscapes: A histogram reweighted metadynamics approach

We present an efficient method for the calculation of free energy landscapes. Our approach involves a history‐dependent bias potential, which is evaluated on a grid. The corresponding free energy landscape is constructed via a histogram reweighting procedure a posteriori. Because of the presence of the bias potential, it can be also used to accelerate rare events. In addition, the calculated free energy landscape is not restricted to the actual choice of collective variables and can in principle be extended to auxiliary variables of interest without further numerical effort. The applicability is shown for several examples. We present numerical results for the alanine dipeptide and the Met‐Enkephalin in explicit solution to illustrate our approach. Furthermore, we derive an empirical formula that allows the prediction of the computational cost for the ordinary metadynamics variant in comparison with our approach, which is validated by a dimensionless representation.