Peter Spijker

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.

Coarse Grained Molecular Dynamics Simulations of Transmembrane Protein-Lipid Systems

Many biological cellular processes occur at the micro- or millisecond time scale. With traditional all-atom molecular modeling techniques it is difficult to investigate the dynamics of long time scales or large systems, such as protein aggregation or activation. Coarse graining (CG) can be used to reduce the number of degrees of freedom in such a system, and reduce the computational complexity. In this paper the first version of a coarse grained model for transmembrane proteins is presented. This model differs from other coarse grained protein models due to the introduction of a novel angle potential as well as a hydrogen bonding potential. These new potentials are used to stabilize the backbone. The model has been validated by investigating the adaptation of the hydrophobic mismatch induced by the insertion of WALP-peptides into a lipid membrane, showing that the first step in the adaptation is an increase in the membrane thickness, followed by a tilting of the peptide.

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.

Heat Transfer Predictions Using Accommodation Coefficients for a Dense Gas in a Micro/Nano-channel

The influence of gas-gas and gas-wall interactions on the heat flux predictions for a dense gas confined between two parallel walls of a micro/nano-channel is realized using combined Monte Carlo (MC) and Molecular Dynamics (MD) techniques. The accommodation coefficients are computed from explicit MD simulations. These MD coefficients are then used as effective accommodation coefficients in Maxwell-like boundary conditions in MC simulations. We find that heat flux predictions from MC based on these coefficients compare good with the results of explicit simulations except the case when there are hydrophobic gas-wall/gas-gas interactions. For this case an artificial wall was introduced in order to measure these MD accommodation coefficients at this artificial border. Good agreement is found then for both hydrophilic and hydrophobic gas-wall interactions and we show this by confronting the heat fluxes from explicit MD simulations with the the MC heat flux predictions for all the generic accommodation coefficients.Copyright

Comparison of molecular dynamics and kinetic modeling of gas-surface interaction

The interaction of a dilute monatomic gas with a solid surface is studied by Molecular Dynamics (MD) simulations and by numerical solutions of a recently proposed kinetic model. Following previous investigations, the heat transport between parallel walls and Couette flow have been adopted as test problems. The distribution functions of re‐emitted atoms and the accommodation coefficients obtained from the two techniques are compared in different flow conditions. It is shown that the kinetic model predictions are close to MD results.

Velocity correlations and accommodation coefficients for gas-wall interactions in nanochannels

In order to understand the behavior of a gas close to a channel wall, it is important to model the gas‐wall interactions correctly. When using Molecular Dynamics (MD) simulations these interactions are modeled explicitly, but the computations are time consuming. Replacing the explicit wall with an appropriate wall model reduces the computational time, but should still remain the same characteristics. In this paper the focus lies with an argon gas confined between two platinum walls at different temperature. Several wall models are investigated for their feasibility as a replacement of the MD simulations and are mainly compared using the velocity correlations between impinging and reflecting particles. Moreover, a new method to compute the accommodation coefficient using the velocity correlations is demonstrated.

Velocity Correlations Between Impinging and Reflecting Particles Using MD Simulations and Different Wall Models

The replacement of the the explicit wall in Molecular Dynamics (MD) simulations of nanochannels with an appropriate wall model is important to model the behavior of the gas close to the channel wall correctly. In this paper a comparison of four different wall models with explicit wall MD simulations is reported in the case of a gas confined between two plates of different temperature. Accommodation coefficients are computed from the explicit wall MD simulations using different techniques. Examples are given that for the same system different methods may produce different accommodation coefficients. The computed accommodation coefficients are subsequently used as input to some of the wall models. From comparison of simulations with explicitly modelled walls or using wall models it is shown that not only is it important to look at the distribution of outgoing velocities, but also at the correlation of incoming and outgoing velocities.Copyright

New Derivation of a Particle Wall Boundary Condition in Molecular Dynamics

In this paper a new particle wall boundary condition to replace explicit solid walls in molecular dynamics (MD) simulations is proposed. This new wall potential reduces the computational complexity considerably and allows the investigation of larger channels without compromising macroscopic quantities, such as density, temperature, pressure and heat flux. Since it is common practice in MD to truncate pair interaction potentials, an alternative and explicit derivation of the wall potential is possible, which is in contrast to previous work. Moreover, different types of crystal lattices can be included in the new potential. To demonstrate the applicablity of the method, MD simulations of a gas between two parallel plates at different temperatures and densities have been performed. The results of these simulations are compared to explicit wall simulations and previously proposed wall potentials. Although differences with other wall potentials are minor, some superior aspects of the new potential are addressed.Copyright