Systematic characterization of thermodynamic and dynamical phase behavior in systems with short-ranged attraction

In this paper we demonstrate the feasibility and utility of an augmented version of the Gibbs ensemble Monte Carlo method for computing the phase behavior of systems with strong, extremely short-ranged attractions. For generic potential shapes, this approach allows for the investigation of narrower attractive widths than those previously reported. Direct comparison to previous self-consistent Ornstein-Zernike approximation calculations are made. A preliminary investigation of out-of-equilibrium behavior is also performed. Our results suggest that the recent observations of stable cluster phases in systems without long-ranged repulsions are intimately related to gas-crystal and metastable gas-liquid phase separation.Comment: 10 pages, 8 figure

Crystallization and gelation in colloidal systems with short-ranged attractive interactions

We systematically study the relationship between equilibrium and non-equilibrium phase diagrams of a system of short-ranged attractive colloids. Using Monte Carlo and Brownian dynamics simulations we find a window of enhanced crystallization that is limited at high interaction strength by a slowing down of the dynamics and at low interaction strength by the high nucleation barrier. We find that the crystallization is enhanced by the metastable gas-liquid binodal by means of a two-stage crystallization process. First, the formation of a dense liquid is observed and second the crystal nucleates within the dense fluid. In addition, we find at low colloid packing fractions a fluid of clusters, and at higher colloid packing fractions a percolating network due to an arrested gas-liquid phase separation that we identify with gelation. We find that this arrest is due to crystallization at low interaction energy and it is caused by a slowing down of the dynamics at high interaction strength. Likewise, we observe that the clusters which are formed at low colloid packing fractions are crystalline at low interaction energy, but glassy at high interaction energy. The clusters coalesce upon encounter.Comment: 8 pages, 8 figure

Reverse-selective diffusion in nanocomposite membranes

The permeability of certain polymer membranes with impenetrable nanoinclusions increases with the particle volume fraction (Merkel et al., Science, 296, 2002). This intriguing observation contradicts even qualitative expectations based on Maxwell's classical theory of conduction/diffusion in composites with homogeneous phases. This letter presents a simple theoretical interpretation based on classical models of diffusion and polymer physics. An essential feature of the theory is a polymer-segment depletion layer at the inclusion-polymer interface. The accompanying increase in free volume leads to a significant increase in the local penetrant diffusivity, which, in turn, increases the bulk permeability while exhibiting reverse selectivity. This model captures the observed dependence of the bulk permeability on the inclusion size and volume fraction, providing a straightforward connection between membrane microstructure and performance

Quantitation of intracellular NAD(P)H can monitor an imbalance of DNA single strand break repair in base excision repair deficient cells in real time

DNA single strand breaks (SSBs) are one of the most frequent DNA lesions in genomic DNA generated either by oxidative stress or during the base excision repair pathways. Here we established a new real-time assay to assess an imbalance of DNA SSB repair by indirectly measuring PARP-1 activation through the depletion of intracellular NAD(P)H. A water-soluble tetrazolium salt is used to monitor the amount of NAD(P)H in living cells through its reduction to a yellow colored water-soluble formazan dye. While this assay is not a direct method, it does not require DNA extraction or alkaline treatment, both of which could potentially cause an artifactual induction of SSBs. In addition, it takes only 4 h and requires less than a half million cells to perform this measurement. Using this assay, we demonstrated that the dose- and time-dependent depletion of NAD(P)H in XRCC1-deficient CHO cells exposed to methyl methanesulfonate. This decrease was almost completely blocked by a PARP inhibitor. Furthermore, methyl methanesulfonate reduced NAD(P)H in PARP-1+/+cells, whereas PARP-1¿/¿ cells were more resistant to the decrease in NAD(P)H. These results indicate that the analysis of intracellular NAD(P)H level using water-soluble tetrazolium salt can assess an imbalance of SSB repair in living cells in real time

Structure and thermodynamics of colloid-polymer mixtures: a macromolecular approach

The change of the structure of concentrated colloidal suspensions upon addition of non-adsorbing polymer is studied within a two-component, Ornstein-Zernicke based liquid state approach. The polymers' conformational degrees of freedom are considered and excluded volume is enforced at the segment level. The polymer correlation hole, depletion layer, and excess chemical potentials are described in agreement with polymer physics theory in contrast to models treating the macromolecules as effective spheres. Known depletion attraction effects are recovered for low particle density, while at higher densities novel many-body effects emerge which become dominant for large polymers.Comment: 7 pages, 4 figures; to be published in Europhys. Let

Entropic torque

Quantitative predictions are presented of a depletion-induced torque and force acting on a single colloidal hard rod immersed in a solvent of hard spheres close to a planar hard wall. This torque and force, which are entirely of entropic origin, may play an important role for the key-lock principle, where a biological macromolecule (the key) is only functional in a particular orientation with respect to a cavity (the lock)

Helical Tubes in Crowded Environments

When placed in a crowded environment, a semi-flexible tube is forced to fold so as to make a more compact shape. One compact shape that often arises in nature is the tight helix, especially when the tube thickness is of comparable size to the tube length. In this paper we use an excluded volume effect to model the effects of crowding. This gives us a measure of compactness for configurations of the tube, which we use to look at structures of the semi-flexible tube that minimize the excluded volume. We focus most of our attention on the helix and which helical geometries are most compact. We found that helices of specific pitch to radius ratio 2.512 to be optimally compact. This is the same geometry that minimizes the global curvature of the curve defining the tube. We further investigate the effects of adding a bending energy or multiple tubes to begin to explore the more complete space of possible geometries a tube could form.Comment: 10 page

Monte Carlo simulations of the solid-liquid transition in hard spheres and colloid-polymer mixtures

Monte Carlo simulations at constant pressure are performed to study coexistence and interfacial properties of the liquid-solid transition in hard spheres and in colloid-polymer mixtures. The latter system is described as a one-component Asakura-Oosawa (AO) model where the polymer's degrees of freedom are incorporated via an attractive part in the effective potential for the colloid-colloid interactions. For the considered AO model, the polymer reservoir packing fraction is eta_p^r=0.1 and the colloid-polymer size ratio is q=sigma_p/\sigma=0.15 (with sigma_p and sigma the diameter of polymers and colloids, respectively). Inhomogeneous solid-liquid systems are prepared by placing the solid fcc phase in the middle of a rectangular simulation box creating two interfaces with the adjoined bulk liquid. By analyzing the growth of the crystalline region at various pressures and for different system sizes, the coexistence pressure p_co is obtained, yielding p_co=11.576 k_BT/sigma^3 for the hard sphere system and p_co=8.0 k_BT/sigma^3 for the AO model (with k_B the Boltzmann constant and T the temperature). Several order parameters are introduced to distinguish between solid and liquid phases and to describe the interfacial properties. From the capillary-wave broadening of the solid-liquid interface, the interfacial stiffness is obtained for the (100) crystalline plane, giving the values gamma=0.49 k_BT/sigma^2 for the hard-sphere system and gamma=0.95 k_BT/sigma^2 for the AO model.Comment: 11 pages, 13 figure

Description of the fluctuating colloid-polymer interface

To describe the full spectrum of surface fluctuations of the interface between phase-separated colloid-polymer mixtures from low scattering vector q (classical capillary wave theory) to high q (bulk-like fluctuations), one must take account of the interface's bending rigidity. We find that the bending rigidity is negative and that on approach to the critical point it vanishes proportionally to the interfacial tension. Both features are in agreement with Monte Carlo simulations.Comment: 5 pages, 3 figures, 1 table. Accepted for publication in Phys. Rev. Let

Generalized Geometric Cluster Algorithm for Fluid Simulation

We present a detailed description of the generalized geometric cluster algorithm for the efficient simulation of continuum fluids. The connection with well-known cluster algorithms for lattice spin models is discussed, and an explicit full cluster decomposition is derived for a particle configuration in a fluid. We investigate a number of basic properties of the geometric cluster algorithm, including the dependence of the cluster-size distribution on density and temperature. Practical aspects of its implementation and possible extensions are discussed. The capabilities and efficiency of our approach are illustrated by means of two example studies.Comment: Accepted for publication in Phys. Rev. E. Follow-up to cond-mat/041274