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

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

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

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

Interfacial tension and nucleation in mixtures of colloids and long ideal polymer coils

Mixtures of ideal polymers with hard spheres whose diameters are smaller than the radius of gyration of the polymer, exhibit extensive immiscibility. The interfacial tension between demixed phases of these mixtures is estimated, as is the barrier to nucleation. The barrier is found to scale linearly with the radius of the polymer, causing it to become large for large polymers. Thus for large polymers nucleation is suppressed and phase separation proceeds via spinodal decomposition, as it does in polymer blends.Comment: 4 pages (v2 includes discussion of the scaling of the interfacial tension along the coexistence curve and its relation to the Ginzburg criterion

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

Forward Flux Sampling for rare event simulations

Rare events are ubiquitous in many different fields, yet they are notoriously difficult to simulate because few, if any, events are observed in a conventiona l simulation run. Over the past several decades, specialised simulation methods have been developed to overcome this problem. We review one recently-developed class of such methods, known as Forward Flux Sampling. Forward Flux Sampling uses a series of interfaces between the initial and final states to calculate rate constants and generate transition paths, for rare events in equilibrium or nonequilibrium systems with stochastic dynamics. This review draws together a number of recent advances, summarizes several applications of the method and highlights challenges that remain to be overcome.Comment: minor typos in the manuscript. J.Phys.:Condensed Matter (accepted for publication

Long Cycles in a Perturbed Mean Field Model of a Boson Gas

In this paper we give a precise mathematical formulation of the relation between Bose condensation and long cycles and prove its validity for the perturbed mean field model of a Bose gas. We decompose the total density $\rho=\rho_{{\rm short}}+\rho_{{\rm long}}$ into the number density of particles belonging to cycles of finite length ($\rho_{{\rm short}}$) and to infinitely long cycles ($\rho_{{\rm long}}$) in the thermodynamic limit. For this model we prove that when there is Bose condensation, $\rho_{{\rm long}}$ is different from zero and identical to the condensate density. This is achieved through an application of the theory of large deviations. We discuss the possible equivalence of $\rho_{{\rm long}}\neq 0$ with off-diagonal long range order and winding paths that occur in the path integral representation of the Bose gas.Comment: 10 page

Interactions between proteins bound to biomembranes

We study a physical model for the interaction between general inclusions bound to fluid membranes that possess finite tension, as well as the usual bending rigidity. We are motivated by an interest in proteins bound to cell membranes that apply forces to these membranes, due to either entropic or direct chemical interactions. We find an exact analytic solution for the repulsive interaction between two similar circularly symmetric inclusions. This repulsion extends over length scales of order tens of nanometers, and contrasts with the membrane-mediated contact attraction for similar inclusions on tensionless membranes. For non circularly symmetric inclusions we study the small, algebraically long-ranged, attractive contribution to the force that arises. We discuss the relevance of our results to biological phenomena, such as the budding of caveolae from cell membranes and the striations that are observed on their coats.Comment: 22 pages, 2 figure