Rigorous embedding of cell dynamics simulations in the Cahn-Hilliard-Cook framework: imposing stability and isotropy

Solid state NMR/Biophysical Organic Chemistr

Stochastic quasi-Newton molecular simulations

Article / Letter to editorLeiden Institute of Chemistr

Comment on "Microscopic mechanisms of electric-field-induced alignment of block copolymer microdomains"

Sterrewacht Leiden - OU

Kinetic pathways of sheared block copolymer systems derived from Minkowski functionals

We employ Minkowski functionals to analyze the kinetics of pattern formation under an applied external shear flow. The considered pattern formation model describes the dynamics of phase separating block copolymer systems. For our purpose, we have chosen two block copolymer systems (a melt and a solution) that exhibit a hexagonal cylindrical morphology as an equilibrium structure. Our main objective is the determination of efficient choices for the treshold values that are required for the calculation of the Minkowski functionals. We find that a minimal set of two treshold values (one from which should be equal to an average density value and another to a higher density value) is sufficient to unraffle the phase separation kinetics. Given these choices, we focus on the influence of the degree of phase separation, and the instance at which the shear is applied, on the kinetic pathways. We also found a remarkable similarity of the time evolution of Euler characteristic and the segregation parameter for the average density choice.Soft Matter Chemistr

The role of size and nature in nanoparticle binding to a model lung membrane: an atomistic study

Understanding the uptake of nanoparticles (NPs) by different types of cellular membranes plays a pivotal role in the design of NPs for medical applications and in avoiding adverse effects that result in nanotoxicity. Yet, the role of key design parameters, such as the bare NP material, NP size and surface reactivity, and the nature of NP coatings, in membrane remodelling and uptake mechanisms is still very poorly understood, particularly towards the lower range of NP dimensions that are beyond the experimental imaging resolution. The same can be said about the role of a particular membrane composition. Here, we systematically employ biased and unbiased molecular dynamics simulations to calculate the binding energy for three bare materials (Ag/SiO2/TiO2) and three NP sizes (1/3/5 nm diameter) with a representative lung surfactant membrane, and to study their binding kinetics. The calculated binding energies show that irrespective of size, Ag nanoparticles bind very strongly to the bilayer, while the NPs made of SiO2 or TiO2 experience very low to no binding. The unbiased simulations provide insight into how the NPs and membrane affect each other in terms of the solvent-accessible surface area (SASA) of the NPs and the defect types and fluidity of the membrane. Using these systematic fine-grained results in coarsening procedures will pave the way for simulations considering NP sizes that are well beyond the membrane thickness, i.e. closer to experimental dimensions, for which different binding characteristics and more significant membrane remodelling are expected.Horizon 2020(H2020)814426Solid state NMR/Biophysical Organic Chemistr

A core-shell approach for systematically coarsening nanoparticle–membrane interactions: application to silver nanoparticles

Horizon 2020(H2020)814426Solid state NMR/Biophysical Organic Chemistr

Computational insight in the role of fusogenic lipopeptides at the onset of liposome fusion

Solid state NMR/Biophysical Organic Chemistr

Stochastic quasi-Newton molecular simulations

Soft Matter Chemistr

Self-Assembly of Polymeric Particles in Poiseuille Flow: A Hybrid Lattice Boltzmann/External Potential Dynamics Simulation Study

We present a hybrid simulation method which allows one to study the dynamical evolution of self-assembling (co)polymer solutions in the presence of hydrodynamic interactions. The method combines an established dynamic density functional theory for polymers that accounts for the nonlocal character of chain dynamics at the level of the Rouse model, the external potential dynamics (EPD) model, with an established Navier–Stokes solver, the Lattice Boltzmann (LB) method. We apply the method to study the self-assembly of nanoparticles and vesicles in two-dimensional copolymer solutions in a typical microchannel Poiseuille flow profile. The simulations start from fully mixed systems which are suddenly quenched below the spinodal line. In order to isolate effects caused by walls, we use a reverse Poiseuille flow geometry with periodic boundary conditions. We identify three stages of self-assembly, i.e., initial spinodal decomposition, particle nucleation, and particle growth (ripening). We find that (i) in the presence of shear the nucleation of droplets is delayed by an amount roughly proportional to the shear rate, (ii) shear flow greatly increases the rates of particle fusions, and (iii) in later stages of self-assembly stronger shear flows may induce irreversible shape transformation via finger formation, in particular in vesicle systems. The combination of these effects leads to an accumulation of particles close to the center of the Poiseuille flow profile, and the polymeric matter has a double peak distribution centered around the flow maximum.Solid state NMR/Biophysical Organic Chemistr