The net charge of solvated entities, ranging from polyelectrolytes and biomolecules to charged nanoparticles and membranes, depends on the local dissociation equilibrium of individual ionizable groups. Incorporation of this phenomenon, emph{charge re
gulation}, in theoretical and computational models requires dynamic, configuration-dependent recalculation of surface charges and is therefore typically approximated by assuming constant net charge on particles. Various computational methods exist that address this. We present an alternative, particularly efficient charge regulation Monte Carlo method (CR-MC), which explicitly models the redistribution of individual charges and accurately samples the correct grand-canonical charge distribution. In addition, we provide an open-source implementation in the LAMMPS molecular dynamics (MD) simulation package, resulting in a hybrid MD/CR-MC simulation method. This implementation is designed to handle a wide range of implicit-solvent systems that model discreet ionizable groups or surface sites. The computational cost of the method scales linearly with the number of ionizable groups, thereby allowing accurate simulations of systems containing thousands of individual ionizable sites. By matter of illustration, we use the CR-MC method to quantify the effects of charge regulation on the nature of the polyelectrolyte coil--globule transition and on the effective interaction between oppositely charged nanoparticles.
Nanoparticles in solution acquire charge through dissociation or association of surface groups. Thus, a proper description of their electrostatic interactions requires the use of charge-regulating boundary conditions rather than the commonly employed
constant-charge approximation. We implement a hybrid Monte Carlo/Molecular Dynamics scheme that dynamically adjusts the charges of individual surface groups of objects while evolving their trajectories. Charge-regulation effects are shown to qualitatively change self-assembled structures due to global charge redistribution, stabilizing asymmetric constructs. We delineate under which conditions the conventional constant-charge approximation may be employed and clarify the interplay between charge regulation and dielectric polarization.
Although the free energy of a genome packing into a virus is dominated by DNA-DNA interactions, ordering of the DNA inside the capsid is elasticity-driven, suggesting general solutions with DNA organized into spool-like domains. Using analytical calc
ulations and computer simulations of a long elastic filament confined to a spherical container, we show that the ground state is not a single spool as assumed hitherto, but an ordering mosaic of multiple homogeneously-ordered domains. At low densities, we observe concentric spools, while at higher densities, other morphologies emerge, which resemble topological links. We discuss our results in the context of metallic wires, viral DNA, and flexible polymers.
The organization of nano-particles inside grafted polymer layers is governed by the interplay of polymer-induced entropic interactions and the action of externally applied fields. Earlier work had shown that strong external forces can drive the forma
tion of colloidal structures in polymer brushes. Here we show that external fields are not essential to obtain such colloidal patterns: we report Monte Carlo and Molecular dynamics simulations that demonstrate that ordered structures can be achieved by compressing a `sandwich of two grafted polymer layers, or by squeezing a coated nanotube, with nano-particles in between. We show that the pattern formation can be efficiently controlled by the applied pressure, while the characteristic length--scale, i.e. the typical width of the patterns, is sensitive to the length of the polymers. Based on the results of the simulations, we derive an approximate equation of state for nano-sandwiches.
Multivalent particles have the ability to form multiple bonds to a substrate. Hence, a multivalent interaction can be strong, even if the individual bonds are weak. However, much more interestingly, multivalency greatly increases the sensitivity of t
he particle-substrate interaction to external conditions, resulting in an ultra-sensitive and highly non-linear dependence of the binding strength on parameters such as temperature, pH or receptor concentration. In this chapter we focus on super-selectivity: the high sensitivity of the strength of multivalent binding to the number of accessible binding sites on the target surface. For example, the docking of a multivalent particle on a cell-surface can be very sensitive (super-selective) to the concentration of the receptors to which the multiple ligands can bind. We present a theoretical analysis of systems of multivalent particles and describe the mechanism by which multivalency leads to super-selectivity. We introduce a simple analytical model that allows us to predict the overall strength of interactions based on physiochemical characteristics of multivalent binders. Finally, we formulate a set of simple design rules for multivalent interactions that yield optimal selectivity.
Confinement can have a dramatic effect on the behavior of all sorts of particulate systems and it therefore is an important phenomenon in many different areas of physics and technology. Here, we investigate the role played by the softness of the conf
ining potential. Using grand canonical Monte Carlo simulations, we determine the phase diagram of three-dimensional hard spheres that in one dimension are constrained to a plane by a harmonic potential. The phase behavior depends strongly on the density and on the stiffness of the harmonic confinement. Whilst we find the familiar sequence of confined hexagonal and square-symmetric packings, we do not observe any of the usual intervening ordered phases. Instead, the system phase separates under strong confinement, or forms a layered re-entrant liquid phase under weaker confinement. It is plausible that this behavior is due to the larger positional freedom in a soft confining potential and to the contribution that the confinement energy makes to the total free energy. The fact that specific structures can be induced or suppressed by simply changing the confinement conditions (e.g. in a dielectrophoretic trap) is important for applications that involve self-assembled structures of colloidal particles.
