Pieter J. in 't Veld

Simulation of the Mechanical Strength of a Single Collagen Molecule

We perform atomistic simulations on a single collagen molecule to determine its intrinsic molecular strength. A tensile pull simulation to determine the tensile strength and Youngs modulus is performed, and a simulation that separates two of the three helices of collagen examines the internal strength of the molecule. The magnitude of the calculated tensile forces is consistent with the strong forces of bond stretching and angle bending that are involved in the tensile deformation. The triple helix unwinds with increasing tensile force. Pulling apart the triple helix has a smaller, oscillatory force. The oscillations are due to the sequential separation of the hydrogen-bonded helices. The force rises due to reorienting the residues in the direction of the separation force. The force drop occurs once the hydrogen bond between residues on different helices break and the residues separate.

Accurate and efficient methods for modeling colloidal mixtures in an explicit solvent using molecular dynamics

Most simulations of colloidal suspensions treat the solvent implicitly or as a continuum. However as particle size decreases to the nanometer scale, this approximation fails and one needs to treat the solvent explicitly. Due to the large number of smaller solvent particles, such simulations are computationally challenging. Additionally, as the ratio of nanoparticle size to solvent size increases, commonly-used molecular dynamics algorithms for neighbor finding and parallel communication become inefficient. Here we present modified algorithms that enable fast single processor performance and reasonable parallel scalability for mixtures with a wide range of particle size ratios. The methods developed are applicable for any system with widely varying force distance cutoffs, independent of particle sizes and independent of the interaction potential. As a demonstration of the new algorithms effectiveness, we present results for the pair correlation function and diffusion constant for mixtures where colloidal particles interact via integrated potentials. In these systems, with nanoparticles 20 times larger than the surrounding solvent particles, our parallel molecular dynamics code runs more than 100 times faster using the new algorithms.

Mesoscale hydrodynamics via stochastic rotation dynamics: Comparison with Lennard-Jones fluid

Stochastic rotation dynamics (SRD) is a relatively recent technique, closely related to lattice Boltzmann, for capturing hydrodynamic fluid flow at the mesoscale. The SRD method is based on simple constituent fluid particle interactions and dynamics. Here we parametrize the SRD fluid to provide a one to one match in the shear viscosity of a Lennard-Jones fluid and present viscosity measurements for a range of such parameters. We demonstrate how to apply the Müller-Plathe reverse perturbation method for determining the shear viscosity of the SRD fluid and discuss how finite system size and momentum exchange rates effect the measured viscosity. The implementation and performance of SRD in a parallel molecular dynamics code is also described.

Hydrophobic/hydrophilic solvation: inferences from Monte Carlo simulations and experiments

In this study Monte Carlo simulations are used to determine the solvation properties of model hydrophobic (xenon and hard sphere) and hydrophilic (dimethyl ether) solutes in SPC/E water. Various contributions to the experimental solvation entropy, including the solvent reorganization entropy, have been determined. The main conclusion drawn, which is in accord with solubility data, is that poor solubility correlates with poor solute-water interaction. At room temperature, energy dominates the aqueous solubility of both hydrophobic and hydrophilic solutes, rather than entropy. However, at higher temperatures the solubility can pass through a minimum, and then entropy becomes dominant. Another interesting finding is the presence of larger than expected cavities in water. Two different simulation results support this finding. This unexpected hollow structure in water explains why a hard sphere solute is more soluble in water than in a comparable hard sphere or Lennard-Jones solvent. Hydrogen bonding causes water to aggregate into clusters that produce a few large cavities rather than many smaller cavities. The propensity for clustering also explains why water gives the illusion of being a low density liquid. Sufficient theoretical apparatus is developed to connect theoretical solvation properties to those measured by simulation and experiment. Finally, based on gas solubility, an intuitive hydrophobic/hydrophilic scale is developed.

Liquid-vapor coexistence for nanoparticles of various size.

We present molecular dynamics simulations of the liquid-vapor phase coexistence of pure nanoparticle systems with three different model nanoparticle interactions. Our simulations show that the form of the interaction potential between nanoparticles strongly influences their coexistence behavior. For nanoparticles interacting with an integrated Lennard-Jones potential, the critical temperature and critical density increase with increasing particle size. In contrast, nanoparticles interacting via a Lennard-Jones potential shifted to the surface of the nanoparticle do not exhibit the expected size dependence of the phase diagram. For this model, the critical temperature decreases with increasing nanoparticle size. Similar results were observed for composite nanoparticles, with the interactions truncated at a finite distance.

Quasiperiodicity and the nanoscopic morphology of some polyurethanes

When straining polyurethane elastomers (PUEs), it is often observed that the long-period peak of the small-angle X-ray scattering (SAXS) does not shift normally. An explanation is indicated for some PUEs in the real-space chord distribution. It exhibits a sequence of constant long-period bands. The band positions form a Fibonacci sequence. This relates to the underlying chemical synthesis by polyaddition of hard and soft modules, indicating a nearly quasiperiodic setup in sequences of stringed hard domains. These sequences appear to be the probes provided by SAXS for the study of morphology evolution in such PUEs. Should a regular-as-possible arrangement of physical crosslinks optimize a property of the material, then in the synthesis the mole fraction nH of hard modules should be chosen to be nH = τ/(1 + τ) ≃ 0.62, where τ is the golden ratio.

Molecular Simulations of Nanoparticles in an Explicit Solvent

Results of large scale equilibrium and non‐equilibrium molecular dynamics (NEMD) simulations are presented for nanoparticles in an explicit solvent. The nanoparticles are modeled as a uniform distribution of Lennard‐Jones particles, while the solvent is represented by standard Lennard‐Jones particles. Unlike hard sphere models, the nanoparticles and solvent do not phase separate for disparate sizes of nanoparticles and solvent, which allows us to study the static and dynamic properties of nanoparticle suspensions with an explicit solvent. Here we present results for nanoparticles of size 5 to 20 times that of the solvent for a range of concentrations from 7 to 40% volume fraction. The nanoparticles are found to segregate to the liquid/vapor interface or repel the interface depending on the relative strength of the nanoparticle/nanoparticle and nanoparticle/solvent interactions. Results from NEMD simulations suggest that the shear rheology of the suspension depends only on the nanoparticle concentration no...