Molecular dynamics simulations of aqueous urea solutions: Study of dimer stability and solution structure, and calculation of the total nitrogen radial distribution function GN(r

Molecular dynamics simulations have been performed in order to study the structure of two molal urea solutions in D2O. Several initial dimer configurations were considered for an adequate sampling of phase space. Eventually all of them appeared to be unstable, when system size and periodic boundary conditions are chosen properly, even after a very careful equilibration. The total nitrogen scattering function GN(r), calculated from these simulations, is in good agreement with neutron scattering experiments when both intra- and intermolecular correlations are considered and the experimental truncation ripples are introduced by a Fourier transform of GN(r) back and forth. The simple pair potential model that we used gives results in good agreement with experiments and with a much more involved potential model, recently described in the literature [J. Chem. Phys. 95, 8419 (1991)]

Representations of coarse-grained potentials for polymer simulations

In order to be able to simulate long time and large space scale properties of polymer melts one has to resort to coarse grained models, for example by subdividing all polymers into parts and restricting attention to the center of mass positions and velocities of these parts. The dynamics of these variables is governed by Langevin equations in which the free energy obtained by integrating the remaining variables provides the potential of the conservative forces. In general this leads to many particle interactions on the coarse-grained level. Methods suggested in the literature to represent these many particle interactions by effective two body interactions are reviewed and a new method, based on the Gibbs-Bogoliubov inequality, is proposed. The reason why none of these methods is able to reproduce the pressure of the underlying atomistic model is discussed

A single particle model to simulate the dynamics of entangled polymer melts

We present a computer simulation model of polymer melts representing each chain as one single particle. Besides the position coordinate of each particle, we introduce a parameter nij for each pair of particles i and j within a specified distance from each other. These numbers, called entanglement numbers, describe the deviation of the system of ignored coordinates from its equilibrium state for the given configuration of the centers of mass of the polymers. The deviations of the entanglement numbers from their equilibrium values give rise to transient forces, which, together with the conservative forces derived from the potential of mean force, govern the displacements of the particles. We have applied our model to a melt of C800H1602 chains at 450 K and have found good agreement with experiments and more detailed simulations. Properties addressed in this paper are radial distribution functions, dynamic structure factors, and linear as well as nonlinear rheological properties

From wave function to crystal morphology: application to urea and alpha-glycine

In this paper the relation between the molecular electron density distribution and the crystal growth morphology is investigated. Accurate charge densities derived from ab initio quantum chemical calculations were partitioned into multipole moments, to calculate the electrostatic contribution to the intermolecular interaction energy. For urea and alpha-glycine the F-faces or connected nets were determined according to the Hartman-Perdok PBC theory. From attachment energy and critical Ising temperature calculations, theoretical growth forms were constructed using different atom-atom potential models. These were compared to the Donnay-Harker model, equilibrium form and experimental growth forms. In the case of alpha-glycine, the theoretical growth forms are in good agreement with crystals grown from aqueous solution. Crystals obtained by sublimation seem to show some faces which are not F-faces sensu stricto

Simulations of elementary processes in entangle wormlike micelles under tension : a kinetic pathway to Y-junctions and shear induced structures

The merging process of two amphiphilic cylindrical micelles has been simulated using a coarse grained model in which amphiphiles are represented as chains of one head particle and four tail particles. In our set-up with twisted boundary conditions, a ring-shaped worm is effectively entangled with itself. Upon stretching the box, putting the worms under tension, a fusion into an H-like structure is observed, which eventually transforms into an almost tensionless structure with two freely gliding Y-junctions. The tensions on the worms never reach the point where scission becomes an alternative to fusion. We end with a short discussion of the possible implications of these observations

Shear viscosities and normal stress differences of rigid liquid-crystalline polymers

Shear viscosities as well as first and second normal stress differences of solutions of rigid spherocylindrical colloids are investigated by Brownian dynamics simulations for aspect ratios L/D in a range from 25 to 60 and scaled volume fractions L/D from 0.5 to 4.5. Shear thinning behavior is observed in all cases. In the isotropic phase, the calculated viscosities at low volume fractions are in agreement with predictions by Dhont and Briels, while over a larger range of shear rates they are described by the Hess equation. The self-rotational diffusion coefficients obtained from the flow curves agree very well with those calculated by traditional methods. In the nematic phase, the inflection point of the flow curve is associated with the critical shear rate at which the orientational director changes its motion from kayaking to wagging. The first normal stress difference N1 in the nematic solution is positive at low and high shear rates but negative at moderate rates, which is rather distinct from the monotone behavior shown by isotropic solutions. The simulated second normal stress difference N2 is found much smaller in amplitude than N1 and always opposite in sign. Our findings qualitatively confirm existing theoretical predictions and experimental measurements. A newly developed event-driven Brownian dynamics algorithm, in which the excluded-volume interactions between particles are incorporated as collisions instead of as repulsive potentials, has made these simulations feasible