Swelling of cross-linked polyelectrolyte gels

The European Physical Journal E - A model of a cross-linked polyelectrolyte gel has been examined using Monte Carlo simulations. The simple model contained a charged defect-free network represented...     

Dipolar Order in Molecular Fluids: I. Toward an Understanding

The origin behind the dipolar order in molecular fluids is investigated by using a simple dipolar fluid and Monte Carlo simulation technique. A penalty function is employed to separately manipulate the positional and orientational structure of the fluid. By considering the distance-dependent Kirkwood function G _k, which in turn is related to the dielectric permittivity of the fluid, it is observed that both positional and orientational ordering are involved to establish dipolar order.     

Dipolar Order in Molecular Fluids: II. Molecular Influence

The influence on the short-range packing in dipolar fluids by molecular shape and by additional higher order electrostatic moments has been investigated by molecular dynamic simulations. The dipole polarization was found to decrease as the particles were elongated parallel to the dipole and to increase for elongation perpendicular to the dipole, eventually forming a nematic order. The addition of a quadrupole lead to a reduction of the polarization, and the influence of an axial octupole was weaker and more complex. Both a decrease and an increase of the polarization is possible depending on the relative dipole–dipole and octupole–octupole interaction strengths and the relative direction of the symmetry axes of the moments. These observations were attributed to the different parity of a dipole and a quadrupole and the same parity of a dipole and an axial octupole under reflection. In addition, further insights into the formation of dipole polarization were obtained. Short polar and long equatorial radii and strong dipole–dipole interaction are particle properties that promote a fluid with a high dipole polarization.     

MOLSIM: A modular molecular simulation software

The modular software MOLSIM for all‐atom molecular and coarse‐grained simulations is presented with focus on the underlying concepts used. The software possesses four unique features: (1) it is an integrated software for molecular dynamic, Monte Carlo, and Brownian dynamics simulations; (2) simulated objects are constructed in a hierarchical fashion representing atoms, rigid molecules and colloids, flexible chains, hierarchical polymers, and cross‐linked networks; (3) long‐range interactions involving charges, dipoles and/or anisotropic dipole polarizabilities are handled either with the standard Ewald sum, the smooth particle mesh Ewald sum, or the reaction‐field technique; (4) statistical uncertainties are provided for all calculated observables. In addition, MOLSIM supports various statistical ensembles, and several types of simulation cells and boundary conditions are available. Intermolecular interactions comprise tabulated pairwise potentials for speed and uniformity and many‐body interactions involve anisotropic polarizabilities. Intramolecular interactions include bond, angle, and crosslink potentials. A very large set of analyses of static and dynamic properties is provided. The capability of MOLSIM can be extended by user‐providing routines controlling, for example, start conditions, intermolecular potentials, and analyses. An extensive set of case studies in the field of soft matter is presented covering colloids, polymers, and crosslinked networks. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Monte Carlo simulations of the hydrophobic effect in aqueous electrolyte solutions

The hydrophobic interaction between two methane molecules in salt-free and high salt-containing aqueous solutions and the structure in such solutions have been investigated using an atomistic model solved by Monte Carlo simulations. Monovalent salt representing NaCl and divalent salt with the same nonelectrostatic properties as the monovalent salt have been used to examine the influence of the valence of the salt species. In salt-free solution the effective interaction between the two methane molecules displayed a global minimum at close contact of the two methane molecules and a solvent-separated secondary minimum. In 3 and 5 M monovalent salt solution the potential of mean force became slightly more attractive, and in a 3 M divalent salt solution the attraction became considerably stronger. The structure of the aqueous solutions was determined by radial distribution functions and angular probability functions. The distortion of the native water structure increased with ion valence. The increase of the hydrophobic attraction was associated with (i) a breakdown of the tetrahedral structure formed by neighboring water molecules and of the hydrogen bonds between them and (i) the concomitant increase of the solution density.     

Macroion solutions in the cell model studied by field theory and Monte Carlo simulations

Aqueous solutions of charged spherical macroions with variable dielectric permittivity and their associated counterions are examined within the cell model using a field theory and Monte Carlo simulations. The field theory is based on separation of fields into short- and long-wavelength terms, which are subjected to different statistical-mechanical treatments. The simulations were performed by using a new, accurate, and fast algorithm for numerical evaluation of the electrostatic polarization interaction. The field theory provides counterion distributions outside a macroion in good agreement with the simulation results over the full range from weak to strong electrostatic coupling. A low-dielectric macroion leads to a displacement of the counterions away from the macroion.     

Residue-specific pKa determination of lysine and arginine side chains by indirect 15N and 13C NMR spectroscopy: application to apo calmodulin

Electrostatic interactions in proteins can be probed experimentally through determination of residue-specific acidity constants. We describe here triple-resonance NMR techniques for direct determination of lysine and arginine side-chain protonation states in proteins. The experiments are based on detection of nonexchangeable protons over the full range of pH and temperature and therefore are well suited for pKa determination of individual amino acid side chains. The experiments follow the side-chain 15Nzeta (lysine) and 15Nepsilon or 13Czeta (arginine) chemical shift, which changes due to sizable changes in the heteronuclear electron distribution upon (de)protonation. Since heteronuclear chemical shifts are overwhelmed by the charge state of the amino acid side chain itself, these methods supersede 1H-based NMR in terms of accuracy, sensitivity, and selectivity. Moreover, the 15Nzeta and 15Nepsilon nuclei may be used to probe changes in the local electrostatic environment. Applications to three proteins are described: apo calmodulin, calbindin D9k, and FKBP12. For apo calmodulin, residue-specific pKa values of lysine side chains were determined to fall between 10.7 and 11.2 as a result of the high net negative charge on the protein surface. Ideal two-state titration behavior observed for all lysines indicates the absence of significant direct charge interactions between the basic residues. These results are compared with earlier studies based on chemical modification.     

Interaction between colloids with grafted diblock polyampholytes

The interaction between composite colloidal particles composed of a spherical core and grafted AB-diblock polyampholytes (diblock copolymers with oppositely charged blocks) are investigated by using a coarse-grained model solved with Monte Carlo simulations. The B block is end-grafted onto the core of the colloid and its linear charge density is varied, whereas the linear charge density of the A block is fixed. The brush structure of a single colloid, the mean force between two colloids, and the structure of solutions of such colloids have been determined for different linear charge densities of the B blocks and block lengths. Many features of the present system are controlled by the charge of the B blocks. In the limit of uncharged B blocks, (i) the grafted chains are stretched and form an extended polyelectrolyte brush, (ii) a strong repulsive force is operating between two colloids, (iii) and the solution is thermodynamic stable and displays strong spatial correlation among the colloids. In the limit where the charges of the two types of blocks exactly compensate each other, (i) the chains are collapsed and form a polyelectrolyte complex surrounding the cores, (ii) an attractive force appears between two colloids, and (iii) strong colloid clustering appears in the solution. These features become more pronounced as the length of the polymer blocks is increased, and a phase instability occurs at sufficiently long chains. A comparison with properties for other related colloidal particles is also provided.