Specific protein-protein binding in many-component mixtures of proteins

Proteins must bind to specific other proteins in vivo in order to function. The proteins must bind only to one or a few other proteins of the of order a thousand proteins typically present in vivo. Using a simple model of a protein, specific binding in many component mixtures is studied. It is found to be a demanding function in the sense that it demands that the binding sites of the proteins be encoded by long sequences of bits, and the requirement for specific binding then strongly constrains these sequences. This is quantified by the capacity of proteins of a given size (sequence length), which is the maximum number of specific-binding interactions possible in a mixture. This calculation of the maximum number possible is in the same spirit as the work of Shannon and others on the maximum rate of communication through noisy channels.Comment: 13 pages, 3 figures (changes for v2 mainly notational - to be more in line with notation in information theory literature

A model for the accidental catalysis of protein unfolding in vivo

Activated processes such as protein unfolding are highly sensitive to heterogeneity in the environment. We study a highly simplified model of a protein in a random heterogeneous environment, a model of the in vivo environment. It is found that if the heterogeneity is sufficiently large the total rate of the process is essentially a random variable; this may be the cause of the species-to-species variability in the rate of prion protein conversion found by Deleault et al. [Nature, 425 (2003) 717].Comment: 5 pages, 2 figure

Flory-Huggins theory for athermal mixtures of hard spheres and larger flexible polymers

A simple analytic theory for mixtures of hard spheres and larger polymers with excluded volume interactions is developed. The mixture is shown to exhibit extensive immiscibility. For large polymers with strong excluded volume interactions, the density of monomers at the critical point for demixing decreases as one over the square root of the length of the polymer, while the density of spheres tends to a constant. This is very different to the behaviour of mixtures of hard spheres and ideal polymers, these mixtures although even less miscible than those with polymers with excluded volume interactions, have a much higher polymer density at the critical point of demixing. The theory applies to the complete range of mixtures of spheres with flexible polymers, from those with strong excluded volume interactions to ideal polymers.Comment: 9 pages, 4 figure

Phase separation in mixtures of colloids and long ideal polymer coils

Colloidal suspensions with free polymer coils which are larger than the colloidal particles are considered. The polymer-colloid interaction is modeled by an extension of the Asakura-Oosawa model. Phase separation occurs into dilute and dense fluid phases of colloidal particles when polymer is added. The critical density of this transition tends to zero as the size of the polymer coils diverges.Comment: 5 pages, 3 figure

Homogeneous nucleation of a non-critical phase near a continuous phase transition

Homogeneous nucleation of a new phase near a second, continuous, transition, is considered. The continuous transition is in the metastable region associated with the first-order phase transition, one of whose coexisting phases is nucleating. Mean-field calculations show that as the continuous transition is approached, the size of the nucleus varies as the response function of the order parameter of the continuous transition. This response function diverges at the continuous transition, as does the temperature derivative of the free energy barrier to nucleation. This rapid drop of the barrier as the continuous transition is approached means that the continuous transition acts to reduce the barrier to nucleation at the first-order transition. This may be useful in the crystallisation of globular proteins.Comment: 6 pages, 1 figur

A coil-globule transition of a semiflexible polymer driven by the addition of spherical particles

The phase behaviour of a single large semiflexible polymer immersed in a suspension of spherical particles is studied. All interactions are simple excluded volume interactions and the diameter of the spherical particles is an order of magnitude larger than the diameter of the polymer. The spherical particles induce a quite long ranged depletion attraction between the segments of the polymer and this induces a continuous coil-globule transition in the polymer. This behaviour gives an indication of the condensing effect of macromolecular crowding on DNA.Comment: 12 pages, 4 figure

Heterogeneous nucleation near a metastable vapour-liquid transition: the effect of wetting transitions

Phase transformations such as freezing typically start with heterogeneous nucleation. Heterogeneous nucleation near a wetting transition, of a crystalline phase is studied. The wetting transition occurs at or near a vapour-liquid transition which occurs in a metastable fluid. The fluid is metastable with respect to crystallisation, and it is the crystallisation of this fluid phase that we are interested in. At a wetting transition a thick layer of a liquid phase forms at a surface in contact with the vapour phase. The crystalline nucleus is then immersed in this liquid layer, which reduces the free energy barrier to nucleation and so dramatically increases the nucleation rate. The variation in the rate of heterogeneous nucleation close to wetting transitions is calculated for systems in which the longest-range forces are dispersion forces.Comment: 11 pages including 3 figure

Microphase morphology in two dimensional fluids under lateral confinement

We study the effects of confinement between two parallel walls on a two dimensional fluid with competing interactions which lead to the formation of particle micro-domains at the thermodynamic equilibrium (microphases or microseparation). The possibility to induce structural changes of the morphology of the micro-domains is explored, under different confinement conditions and temperatures. In presence of neutral walls, a switch from stripes of particles to circular clusters (droplets) occurs as the temperature decreases, which does not happen in bulk. While the passage from droplets to stripes, as the density increases, is a well known phenomenon, the change of the stripes into droplets as an effect of temperature is rather unexpected. Depending on the wall separation and on the wall-fluid interaction parameters, the stripes can switch from parallel to perpendicular to the walls and also a mixed morphology can be stable.Comment: accepted by Physical Review E (rapid communications

The sedimentology of gravel beds in groundwater-dominated chalk streams: Implications for sediment modelling and management

Elevated fine sediment accumulation in a river system's gravel bed is known to cause detrimental ecological impacts. Current sediment targets and approaches to mitigation have failed due to the oversimplification of geomorphological processes controlling fine sediment accumulation and the lack of relevant scientific knowledge underpinning them. This is particularly apparent in chalk streams (groundwater-dominated systems) which regularly exhibit high rates of sediment accumulation despite low suspended sediment yields. A necessary first step is to better characterise their sedimentology; thus, the novelty of this study was to determine the sedimentological characteristics of chalk stream gravel beds, specifically the quantity and distribution of fine sediment with depth. We collated published and unpublished freeze-core data, encompassing 90 sites across 11 UK chalk streams. Results showed average quantities of fine sediment (75% of beds exceeding thresholds for ecological degradation. Quantities of fine sediment increased with increasing depth into the bed, with an average increase between surface and subsurface layers of 54%, and 89% of the gravel bed over-saturated with fine sediment. Regional differences were attributed to differences in stream power and local sediment sources, including surficial geology and catchment land use. Additionally, a major contrast was identified between experimental conditions in flume studies used to establish models describing interactions/mechanisms of fine sediment infiltration into immobile gravel beds and the natural conditions observed in chalk streams. As such, the use of such models as a basis to explore sediment management scenarios is unlikely to predict the outcome of such management techniques correctly in a real-world situation

Phase behaviour of a model of colloidal particles with a fluctuating internal state

Colloidal particles are not simple rigid particles, in general an isolated particle is a system with many degrees of freedom in its own right, e.g., the counterions around a charged colloidal particle.The behaviour of model colloidal particles, with a simple phenomenological model to account for these degrees of freedom, is studied. It is found that the interaction between the particles is not pairwise additive. It is even possible that the interaction between a triplet of particles is attractive while the pair interaction is repulsive. When this is so the liquid phase is either stable only in a small region of the phase diagram or absent altogether.Comment: 12 pages including 4 figure