The study of protein mass transport via atomistic simulation requires time and length scales beyond the computational capabilities of modern computer systems. The raspberry model for colloidal particles in combination with the mesoscopic hydrodynamic method of lattice Boltzmann facilitates coarse-grained simulations that are on the order of microseconds and hundreds of nanometers for the study of diffusive transport of protein-like colloid particles. The raspberry model reproduces linearity in resistance to motion versus particle size and correct enhanced drag within cylindrical pores at off-center coordinates for spherical particles. Owing to the high aspect ratio of many proteins, ellipsoidal raspberry colloid particles were constructed and reproduced the geometric resistance factors of Perrin and of Happel and Brenner in the laboratory-frame and in the moving body-frame. Accurate body-frame rotations during diffusive motion have been captured for the first time using projections of displacements. The spatial discretization of the fluid leads to a renormalization of the hydrodynamic radius, however, the data describes a self-consistent hydrodynamic frame within this renormalized system.

The supplementary material, in the form of one pdf file, is available from the journal web page at http://dx.doi.org/10.1140/epjst/e2016-02676-9 The Publishers regret this mistake and apologize for any inconvenience caused.

NIPAM (N-isopropylacrylamide)-based polymers in water show many interesting properties in experiments, including a lower critical solution temperature (LCST) at 305 K and a conformational transition of single chains at the same temperature. The results of many simulation studies suggest that standard force fields are able to describe the conformational transition and the phase equilibrium well. We show by performing long molecular dynamics simulations of the direct liquid-liquid phase equilibrium of NIPAM trimers in water that there is no LCST in the expected temperature range for any of the force fields under study. The results show further that the relaxation times of single-chain simulations are considerably longer than anticipated. Conformational transitions of single polymers can therefore not necessarily be used as surrogates for a real phase transition.

The polymer poly(N-isopropylacrylamide) (PNIPAM) is studied using a novel combination of multiscale modeling methodologies. We develop an iterative Boltzmann inversion potential of concentrated PNIPAM solutions and combine it with lattice Boltzmann as a Navier-Stokes equation solver for the solvent. We study in detail the influence of the methodology on statics and dynamics of the system. The combination is successful and significantly simpler and faster than other mapping techniques for polymer solution while keeping the correct hydrodynamics. The model can semiquantitatively describe the correct phase behavior and polymer dynamics.

Using dissipative particle dynamics simulation, we probe the tunable permeability of cross-linked microcapsules made from pH-sensitive diblock copolymers poly(ethylene oxide)-b-poly(N,N-diethylamino-2-ethyl methacrylate) (PEO-b-PDEAEMA). We first examine the self-assembly of non-cross-linked microcapsules and their pH-responsive collapse and then explore the effects of cross-linking and block interaction on the swelling or deswelling of cross-linked microcapsules. Our results reveal a preferential loading of hydrophobic dicyclopentadiene (DCPD) molecules in PEO-b-PDEAEMA copolymers. Upon reduction of pH, non-cross-linked microcapsules fully decompose into small wormlike clusters as a result of large self-repulsions of protonated copolymers. With increasing degree of cross-linking, the morphology of the microcapsule becomes more stable to pH change. The highly cross-linked microcapsule shell undergoes significant local polymer rearrangement in acidic solution, which eliminates the amphiphilicility and therefore enlarges the permeability of the shell. The responsive cross-linked shell experiences a disperse-to-buckle configurational transition upon reduction of pH, which is effective for the steady or pulsatile regulation of shell permeability. The swelling rate of the cross-linked shell is dependent on both electrostatic and nonelectrostatic interactions between the pH-sensitive groups as well as the other groups. Our study highlights the combination of cross-linking structure and block interactions in stabilizing microcapsules and tuning their selective permeability.