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The ability of double-stranded DNA or RNA to locally melt and form kinks leads to strong non-linear elasticity effects that qualitatively affect their packing in confined spaces. Using analytical theory and numerical simulation we show that kink formation entails a mixed spool-nematic ordering of double-stranded DNA or RNA in spherical capsids, consisting of an outer spool domain and an inner, twisted nematic domain. These findings explain the experimentally observed nematic domains in viral capsids and imply that non-linear elasticity must be considered to predict the configurations and dynamics of double-stranded genomes in viruses, bacterial nucleoids or gene-delivery vehicles. The non-linear elastic theory suggests that spool-nematic ordering is a general feature of strongly confined kinkable polymers., Comment: 6 pages

We study the interaction between two charge regulating spherical macroions with dielectric interior and dissociable surface groups immersed in a monovalent electrolyte solution. The charge dissociation is modelled via the Frumkin-Fowler-Guggenheim isotherm, which allows for multiple adsorption equilibrium states. The interactions are derived from the solutions of the mean-field Poisson-Boltzmann type theory with charge regulation boundary conditions. For a range of conditions we find symmetry breaking transitions from symmetric to asymmetric charge distribution exhibiting annealed charge patchiness, which results in like-charge attraction even in a univalent electrolyte -- thus fundamentally modifying the nature of electrostatic interactions in charge-stabilized colloidal suspensions., Comment: 18 pages, 8 figures

We show that arbitrarily large polar flocks are susceptible to the presence of a single small obstacle. In a wide region of parameter space, the obstacle triggers counter-propagating dense bands leading to reversals of the flow. In very large systems, these bands interact yielding a never-ending chaotic dynamics that constitutes a new disordered phase of the system. While most of these results were obtained using simulations of aligning self-propelled particles, we find similar phenomena at the continuous level, not when considering the basic Toner-Tu hydrodynamic theory, but in simulations of truncations of the relevant Boltzmann equation., Comment: 5 pages, 4 figures, Supplementary information. Movies available from authors on request

Gradients in temperature, concentration or electrostatic potential cannot exert forces on a bulk fluid; they can, however, exert forces on a fluid in a microscopic boundary layer surrounding a (nano)colloidal solute, resulting in so-called phoretic flow. Here we present a simulation study of phoretic flow around a spherical colloid held fixed in a concentration gradient. We show that the resulting flow velocity depends non-monotonically on the strength of the colloid-fluid interaction. The reason for this non-monotonic dependence is that solute particles are effectively trapped in a shell around the colloid and cannot contribute to diffusio-phoresis. We also observe that the flow depends sensitively on the anisotropy of solute-colloid interaction.

The Lennard-Jones 12-6 potential (LJ) is arguably the most widely used pair potential in Molecular Simulations. In fact, it is so popular that the question is rarely asked whether it is fit for purpose. In this paper, we argue that, whilst the LJ potential was designed for noble gases such as argon, it is often used for systems where it is not expected to be particularly realistic. Under those circumstances, the disadvantages of the LJ potential become relevant: most important among these is that in simulations the LJ potential is always modified such that it has a finite range. More seriously, there is by now a whole family of different potentials that are all called Lennard-Jones 12-6, and that are all different - and that may have very different macroscopic properties. In this paper, we consider alternatives to the LJ 12-6 potential that could be employed under conditions where the LJ potential is only used as a typical short-ranged potential with attraction. We construct a class of potentials that are, in many respects LJ-like but that are by construction finite ranged, vanishing quadratically at the cut-off distance, and that are designed to be computationally cheap. Below, we present this potential and report numerical data for its thermodynamic and transport properties, for the most important cases: cut-off distance rc=2 (LJ-like) and rc=1.2 (a typical colloidal potential).

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 calculations 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., Comment: 5 pages

Biological membranes typically contain a large number of different components dispersed in small concentrations in the main membrane phase, including proteins, sugars, and lipids of varying geometrical properties. Most of these components do not bind the cargo. Here, we show that such `inert' components can be crucial for precise control of cross-membrane trafficking. Using a statistical mechanics model and molecular dynamics simulations, we demonstrate that the presence of inert membrane components of small isotropic curvatures dramatically influences cargo endocytosis, even if the total spontaneous curvature of such a membrane remains unchanged. Curved lipids, such as cholesterol, as well as asymmetrically included proteins and tethered sugars can hence all be actively participating in controlling membrane trafficking of nanoscopic cargo. We find that even a low-level expression of curved inert membrane components can determine the membrane selectivity towards the cargo size, and can be used to selectively target membranes of certain compositions. Our results suggest a robust and general way to control cargo trafficking by adjusting the membrane composition without needing to alter the concentration of receptors nor the average membrane curvature. This study indicates that cells can prepare for any trafficking event by incorporating curved inert components in either of the membrane leaflets.

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 formation 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., Comment: 18 pages, 4 figures

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 the 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., Comment: 30 pages 13 figures

Colloidal particles with DNA `legs' that can bind reversibly to receptors on a surface can be made to `walk' if there is a gradient in receptor concentration. We use a combination of theory and Monte Carlo simulations to explore how controllable parameters, e.g. coating density and binding strength, affect the dynamics of such colloids. We find that competition between thermodynamic and kinetic trends imply that there is an optimal value for both, the binding strength and the number of `legs' for which transport is fastest. Using available thermodynamic data on DNA binding, we indicate how directionally reversible, temperature-controlled transport of colloidal walkers can be achieved. In particular, the present results should make it possible to design a chromatographic technique that can be used to separate colloids with different DNA functionalization., Comment: to appear in Soft Matter

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 confining 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., Comment: 5 pages, 5 figures

We present Monte Carlo simulations of colloidal particles pulled into grafted polymer layers by external fields. The insertion free energy of a single colloid into the polymer layer is qualitatively different for surfaces with an ordered and a disordered distribution of grafting points. Moreover, the tendency of colloidal particles to traverse the grafting layer is strongly size dependent. In dense colloidal suspensions, under the influence of sufficiently strong external force, a collective instability allows the colloids to penetrate and form internally ordered, columnar structures spanning the polymer layer. Depending on the conditions, these colloidal clusters may be isolated or laterally percolating. The morphology of the observed patterns can be controlled by the external fields, which opens up new routes for the design of thin structured films., Comment: 5 pages, 4 figures

We investigate - with Monte Carlo computer simulations - the phase behaviour of dimeric colloidal molecules on periodic substrates with square symmetry. The molecules are formed in a two-dimensional suspension of like charged colloids subject to periodic external confinement, which can be experimentally realized by optical methods. We study the evolution of positional and orientational order by varying the temperature across the melting transition. We propose and evaluate appropriate order parameters as well as the specific heat capacity and show that the decay of positional correlations belongs to a class of crossover transitions while the orientational melting is a second-order phase transition., Comment: 13 pages, 9 figures, accepted in J. Phys.: Condens. Matter

We theoretically and numerically studied ordering of "colloidal ionic clusters" on periodic substrate potentials as those generated by optical trapping. Each cluster consists of three charged spherical colloids: two negatively and one positively charged. The substrate is a square or rectangular array of traps, each confining one such cluster. By varying the lattice constant from large to small, the observed clusters are first rod-like and form ferro- and antiferro-like phases, then they bend into a banana-like shape and finally condense into a percolated structure. Remarkably, in a broad parameter range between single-cluster and percolated structures, we have found stable supercomplexes composed of six colloids forming grape-like or rocket-like structures. We investigated the possibility of macroscopic pattern switching by applying external electrical fields., Comment: 14 pages, 13 figures

Digital video-microscopy measurements are reported of both elastic bandstructures and overdamped phonon decay times in two-dimensional colloidal crystals. Both quantities together allow to determine the friction coefficients along various high symmetry directions in q-space. These coefficients contain valuable information on the hydrodynamic forces acting between the colloidal particles. We find Stokes-like friction for phonons near the edge of the first Brillouin zone and vanishing friction coefficients for long wavelength phonons. The effect of this wavelength dependence in real-space is further investigated by simulating a crystal with constant friction (Langevin simulation) and comparing experimentally measured and simulated particle auto-correlation functions., Comment: 10 pages, 5 figures, 1 table, submitted to Soft Matter

Two dimensional suspensions of spherical colloids subject to periodic external fields exhibit a rich variety of molecular crystalline phases. We study in simulations the ground state configurations of dimeric and trimeric systems, that are realized on square and triangular lattices, when either two or three macroions are trapped in each external potential minimum. Bipartite orders of the checkerboard or stripe types are reported together with more complex quadripartite orderings, and the shortcomings of envisioning the colloids gathered in a single potential minimum as a composite rigid object are discussed. This work also sheds light on simplifying assumptions underlying previous theoretical treatments and that made possible the mapping onto spin models., Comment: 12 pages, 13 figures

We investigate the pseudo-Casimir force in a slab of material composed of nematically ordered long polymers. We write the total mesoscopic energy together with the constraint connecting the local density and director fluctuations and evaluate the corresponding fluctuation free energy by standard methods. It leads to a pseudo-Casimir force of a different type than in the case of standard, short molecule nematic. We investigate its separation dependence and its magnitude and explicitly derive the relevant limiting cases., Comment: 7 pages, 2 figures

Energy spectra of a particle with mass $m$ and charge $e$ in the cubic Aharonov-Bohm billiard containing around $10^4$ consecutive levels starting from the ground state have been analysed. The cubic Aharonov-Bohm billiard is a plane billiard defined by the cubic conformal mapping of the unit disc pervaded by a point magnetic flux through the origin perpendicular to the plane of the billiard. The magnetic flux does not influence the classical dynamics, but breaks the antiunitary symmetry in the system, which affects the statistics of energy levels. By varying the shape parameter $\lam$ the classical dynamics goes from integrable ($\lam =0$) to fully chaotic ($\lam = 0.2$; Africa billiard). The level spacing distribution $P(S)$ and the number variance $\Sigma^{2}(L)$ have been studied for 13 different shape parameters on the interval ($0\le\lam\le0.2$). GUE statistics has proven correct for completely chaotic case, while in the mixed regime the fractional power law level repulsion has been observed. The exponent of the level repulsion has been analysed and is found to change smoothly from 0 to 2 as the dynamics goes from integrable to ergodic. Further on, the semiclassical Berry-Robnik theory has been examined. We argue that the semiclassical regime has not been reached and give an estimate for the number of energy levels required for the Berry-Robnik statistics to apply., Comment: 6 pages in RevTex (5 figures in PostScript included) submitted to PRE

We study some new universal aspects of diffusion in chaotic systems, especially such having very large Lyapunov coefficients on the chaotic (indecomposable, topologically transitive) component. We do this by discretizing the chaotic component on the Surface-of-Section in a (large) number $N$ of simplectically equally big cells (in the sense of equal relative invariant ergodic measure, normalized so that the total measure of the chaotic component is unity). By iterating the transition of the chaotic orbit through SOS, where $j$ counts the number of iteration (discrete time), and assuming complete lack of correlations even between consecutive crossings (which can be justified due to the very large Lyapunov exponents), we show the universal approach of the relative measure of the occupied cells, denoted by $\rho(j)$, to the asymptotic value of unity, in the following way: $\rho(j) = 1 - (1-\frac{1}{N})^j$, so that in the limit of big $N$, $N\to \infty$, we have, for $j/N$ fixed, the exponential law $\rho(j) \approx 1 - \exp (-j/N)$. This analytic result is verified numerically in a variety of specific systems: For a plane billiard (Robnik 1983, $\lambda=0.375$), for a 3-D billiard (Prosen 1997, $a=-1/5, b=-12/5$), for ergodic logistic map (tent map), for standard map ($k=400$) and for hydrogen atom in strong magnetic field ($\epsilon=-0.05$) the agreement is almost perfect (except, in the latter two systems, for some long-time deviations on very small scale), but for H\'enon-Heiles system ($E=1/6$) and for the standard map ($k=3$) the deviations are noticed although they are not very big (only about 1%). We have tested the random number generators (Press et al 1986), and confirmed that some are almost perfect (ran0 and ran3), whilst two of them (ran1 and ran2) exhibit big deviations., Comment: 16 pages of LaTeX text, three figures (1(a-c), 2 and 3) available upon request; submitted to J. Phys. A: Math. Gen. (as a Letter)