P.A.J. Hilbers

Theoretical models of nonlinear effects in two-component cooperative supramolecular copolymerizations

The understanding of multi-component mixtures of self-assembling molecules under thermodynamic equilibrium can only be advanced by a combined experimental and theoretical approach. In such systems, small differences in association energy between the various components can be significantly amplified at the supramolecular level via intricate nonlinear effects. Here we report a theoretical investigation of two-component, self-assembling systems in order to rationalize chiral amplification in cooperative supramolecular copolymerizations. Unlike previous models based on theories developed for covalent polymers, the models presented here take into account the equilibrium between the monomer pool and supramolecular polymers, and the cooperative growth of the latter. Using two distinct methodologies, that is, solving mass-balance equations and stochastic simulation, we show that monomer exchange accounts for numerous unexplained observations in chiral amplification in supramolecular copolymerization. In analogy with asymmetric catalysis, amplification of chirality in supramolecular polymers results in an asymmetric depletion of the enantiomerically related monomer pool.

Vesicle deformation by draining : geometrical and topological shape changes

A variety of factors, including changes in temperature or osmotic pressure, can trigger morphological transitions of vesicles. Upon osmotic upshift, water diffuses across the membrane in response to the osmotic difference, resulting in a decreased vesicle volume to membrane area ratio and, consequently, a different shape. In this paper, we study the vesicle deformations on osmotic deflation using coarse grained molecular dynamics simulations. Simple deflation of a spontaneously formed spherical vesicle results in oblate ellipsoid and discous vesicles. However, when the hydration of the lipids in the outer membrane leaflet is increased, which can be the result of a changed pH or ion concentration, prolate ellipsoid, pear-shaped and budded vesicles are formed. Under certain conditions the deflation even results in vesicle fission. The simulations also show that vesicles formed by a bilayer to vesicle transition are, although spontaneously formed, not immediately stress-free. Instead, the membrane is stretched during the final stage of the transition and only reaches equilibrium once the excess interior water has diffused across the membrane. This suggests the presence of residual membrane stress immediately after vesicle closure in experimental vesicle formation and is especially important for MD simulations of vesicles where the time scale to reach equilibrium is out of reach.

Heat transfer predictions for micro-/nanochannels at the atomistic level using combined molecular dynamics and Monte Carlo techniques

The thermal behavior of a gas confined between two parallel walls is investigated. Wall effects such as hydrophobic or hydrophilic wall interactions are studied, and the effect on the heat flux and other characteristic parameters such as density and temperature is shown. For a dilute gas, the dependence on gas-wall interactions of the temperature profile between the walls for the incident and reflected molecules is obtained using molecular dynamics (MD). From these profiles, the effective accommodation coefficients for different interactions and different mass fluid/wall ratio are derived. We show that Monte Carlo (MC) with Maxwell boundary conditions based on the accommodation coefficient gives good results for heat flux predictions when compared with pure molecular dynamics simulations. We use these effective coefficients to compute the heat flux predictions for a dense gas using MD and MC with Maxwell-like boundary conditions.

The CUMULUS coarse graining method: transferable potentials for water and solutes

Molecular dynamics (MD) simulations are an important tool for studying various interesting phenomena in nature at the molecular level. To allow molecular simulation methods to be applied to larger systems and for longer time scales, coarse grained (CG) models have been developed in which groups of atoms are represented by a single coarse grained particle. In so-called multiscale CG models, an atomistic simulation is coarse grained and subsequently used to derive a CG force field. Existing multiscale methods represent either (parts of) molecules as a single CG particle, or groups of molecules of fluctuating size as a single CG particle. Here, a novel method is introduced to coarse grain an atomistic simulation, the CUMULUS coarse graining method. In this method, CG particles have a unique, fixed composition. This important feature of our coarse graining method, which is not available in the current methods, provides a systematic method to include CG solute particles in solutions of salts in water. Combined with the iterative Boltzmann inversion procedure, our coarse graining method is employed to derive CG force fields for systems containing pure water, sodium chloride solutions, and water-octanol mixtures. It is found that the obtained force fields accurately reproduce the structural information from the atomistic simulations, as measured by the radial distribution functions. Furthermore, we conclude that the obtained CG force fields are transferable to systems of different composition for the systems studied here.

Role of surface diffusion in the ordering of adsorbed molecules: dynamic Monte Carlo simulations of NO on Rh(111)

The saturation coverage of molecules adsorbed on metal surfaces is often seen to increase with temperature of adsorption, and may be accompanied by the ordering of the molecules into periodic structures at higher temperatures. The case of NO on Rh(111) presents a specific example of this behavior. Modelling the adsorption process by means of Monte Carlo simulations in which diffusion and lateral interaction are considered indicates that both the increase of the saturation coverage and the ordering with increasing adsorption temperature are in agreement with an enhanced mobility of the adsorbed molecules.

On protein crowding and bilayer bulging in spontaneous vesicle formation

Spontaneous aggregation of lipids into bilayers and vesicles is a key property for the formation of biological membranes. Understanding the compartmentalization achieved by vesicle formation is an important step toward understanding the origin of life, and is crucial in current efforts to develop artificial life. Spontaneously formed vesicles may be applied as artificial cells if they can efficiently encapsulate biomacromolecules. Recent studies report an enhanced concentration of encapsulated proteins during vesicle formation. In order to obtain more insight into this encapsulation process, here we simulate the spontaneous transition of flat bilayers to vesicles in the presence of solvated model proteins using molecular dynamics simulations. In the bilayer-vesicle transition, which is found to be unaffected by the presence of the solvated proteins, the bilayer edge remains at almost the same height, while the center of the membrane bulges out, a molecular pathway we denominate bilayer bulging. This bulging results in an interior protein concentration that is significantly lower than that of the solution. By means of an increased protein-membrane interaction, enhanced encapsulation of proteins inside the vesicles could be achieved in our simulations.

Implicit particle wall boundary condition in molecular dynamics

Thin film and nano-tube manufacturing, micro-channel cooling, and many other similar interesting techniques demand the prediction of heat transfer characteristics at the nanometre scale. In this respect, the transport properties at gas—solid and liquid—solid interfaces are very important. The processes at these interfaces can be studied in detail with molecular dynamics (MD) simulations. However, the computational cost involved in simulating the solid wall currently restrains the size of channels, which can be simulated. Therefore, the solid wall is sometimes replaced by boundary conditions, which often compromise on macroscopic quantities, such as density, temperature, pressure, and heat flux. In the current paper, a new particle wall boundary condition is presented, which is in good agreement with existing boundary conditions, but allows for the pressure calculation. This new boundary condition is based on averaging the contributions of an explicit solid wall and is derived using knowledge on common practices in MD algorithms, such as truncation and shifting. Moreover, it allows for different crystal lattices to be included in the new potential. The applicability of the new method is demonstrated by MD simulations of a gas between two parallel plates at different temperatures and densities. Furthermore, these simulations are compared with explicit wall simulations and existing boundary conditions.

Coarse-grained simulations of poly(propylene imine) dendrimers in solution

The behavior of poly(propylene imine) (PPI) dendrimers in concentrated solutions has been investigated using molecular dynamics simulations containing up to a thousand PPI dendrimers of generation 4 or 5 in explicit water. To deal with large system sizes and time scales required to study the solutions over a wide range of dendrimer concentrations, a previously published coarse-grained model was applied. Simulation results on the radius of gyration, structure factor, intermolecular spacing, dendrimer interpenetration, and water penetration are compared with available experimental data, providing a clear concentration dependent molecular picture of PPI dendrimers. It is shown that with increasing concentration the dendrimer volume diminishes accompanied by a reduction of internalized water, ultimately resulting in solvent filled cavities between stacked dendrimers. Concurrently dendrimer interpenetration increases only slightly, leaving each dendrimer a separate entity also at high concentrations. Moreover, we compare apparent structure factors, as calculated in experimental studies relying on the decoupling approximation and the constant atomic form factor assumption, with directly computed structure factors. We demonstrate that these already diverge at rather low concentrations, not because of small changes in form factor, but rather because the decoupling approximation fails as monomer positions of separate dendrimers become correlated at concentrations well below the overlap concentration.

Coarse-grained modelling of urea-adamantyl functionalized poly(propylene imine) dendrimers

To investigate the behaviour of poly(propylene imine) dendrimers – and urea–adamantyl functionalised ones – in solution using molecular dynamics simulations, we developed a coarse-grained model to tackle the relatively large system sizes and time scales needed. Harmonic bond and angle potentials were derived from atomistic simulations using an iterative Boltzmann inversion scheme, modified to incorporate Gaussian fits of the bond and angle distributions. With the coarse-grained model and accompanying force field simulations of generations 1–7 of both dendrimer types in water were performed. They compare favourably with atomistic simulations and experimental results on the basis of size, shape, monomer density, spacer back-folding and atomic form factor measurements. These results show that the structural dynamics of these dendrimers originate from flexible chains constrained by configurational and spatial requirements. Large dendrimers are more rigid and spherical, while small ones are flexible, alternatively rod-like and globular.

Heat Transfer Predictions for Micro/Nano-Channels at Atomistic Level Using Combined Molecular Dynamics and Monte Carlo Techniques

The thermal behavior of a gas confined between two parallel walls is investigated. Wall effects like hydrophobic or hydrophilic wall interactions are studied, and the effect on the heat flux and other characteristic parameters like density and temperature is shown. For a dilute gas, the dependence on gas-wall interactions of the temperature profile between the walls for the incident and reflected molecules is obtained using Molecular Dynamics. From these profiles, the effective accomodation coefficients for different interactions and different mass fluid/wall ratio are derived. We show that MC with Maxwell boundary conditions based on the accomodation coefficient gives good results for heat flux predictions when compared to pure Molecular Dynamics simulations. We use these effective coefficients to compute the heat flux predictions for a dense gas using MD and MC with Maxwell-like boundary conditions.