Native geometry and the dynamics of protein folding

In this paper we investigate the role of native geometry on the kinetics of protein folding based on simple lattice models and Monte Carlo simulations. Results obtained within the scope of the Miyazawa-Jernigan indicate the existence of two dynamical folding regimes depending on the protein chain length. For chains larger than 80 amino acids the folding performance is sensitive to the native state's conformation. Smaller chains, with less than 80 amino acids, fold via two-state kinetics and exhibit a significant correlation between the contact order parameter and the logarithmic folding times. In particular, chains with N=48 amino acids were found to belong to two broad classes of folding, characterized by different cooperativity, depending on the contact order parameter. Preliminary results based on the G\={o} model show that the effect of long range contact interaction strength in the folding kinetics is largely dependent on the native state's geometry.Comment: Proceedings of the BIFI 2004 - I International Conference, Zaragoza (Spain) Biology after the genome: a physical view. To appear in Biophysical Chemistr

Orientational transitions in a nematic confined by competing surfaces

The effect of confinement on the orientational structure of a nematic liquid crystal model has been investigated by using a version of density-functional theory (DFT). We have focused on the case of a nematic confined by opposing flat surfaces, in slab geometry (slit pore), which favor planar molecular alignment (parallel to the surface) and homeotropic alignment (perpendicular to the surface), respectively. The spatial dependence of the tilt angle of the director with respect to the surface normal has been studied, as well as the tensorial order parameter describing the molecular order around the director. For a pore of given width, we find that, for weak surface fields, the alignment of the nematic director is perpendicular to the surface in a region next to the surface favoring homeotropic alignment, and parallel along the rest of the pore, with a interface separating these regions (S phase). For strong surface fields, the director is distorted uniformly, the tilt angle exhibiting a linear dependence with the distance normal to the surface (L phase). Our calculations reveal the existence of a first-order transition between the two director configurations, which is driven by changes in the surface field strength, and also by changes in the pore width. In the latter case the transition occurs, for a given surface field, between the S phase for narrow pores and the L phase for wider pores. A link between the L-S transition and the anchoring transition observed for the semi-infinite case is proposed. We also provide calculations with a phenomenological approach that yields the same main result that DFT in the scale length where this is valid.Comment: submitted to PR

Computer simulation study of the nematic–vapour interface in the Gay–Berne model

We present computer simulations of the vapour–nematic interface of the Gay–Berne model. We considered situations which correspond to either prolate or oblate molecules. We determine the anchoring of the nematic phase and correlate it with the intermolecular potential parameters. On the other hand, we evaluate the surface tension associated to this interface. We find a corresponding states law for the surface tension dependence on the temperature, valid for both prolate and oblate molecules.Fundación Portuguesa para la Ciencia y la Tecnología EXCL / FIS-NAN / 0083/2012Ministerio de Economía y Competitividad FIS2012-32455Junta de Andalucía P09-FQM-493

The liquid-vapor interface of an ionic fluid

We investigate the liquid-vapor interface of the restricted primitive model (RPM) for an ionic fluid using a density-functional approximation based on correlation functions of the homogeneous fluid as obtained from the mean-spherical approximation (MSA). In the limit of a homogeneous fluid our approach yields the well-known MSA (energy) equation of state. The ionic interfacial density profiles, which for the RPM are identical for both species, have a shape similar to those of simple atomic fluids in that the decay towards the bulk values is more rapid on the vapor side than on the liquid side. This is the opposite asymmetry of the decay to that found in earlier calculations for the RPM based on a square-gradient theory. The width of the interface is, for a wide range of temperatures, approximately four times the second moment correlation length of the liquid phase. We discuss the magnitude and temperature dependence of the surface tension, and argue that for temperatures near the triple point the ratio of the dimensionless surface tension and critical temperature is much smaller for the RPM than for simple atomic fluids.Comment: 6 postscript figures, submitted to Phys. Rev.

Stochastic fluctuations in epidemics on networks

The effects of demographic stochasticity on the long-term behaviour of endemic infectious diseases have been considered for long as a necessary addition to an underlying deterministic theory. The latter would explain the regular behaviour of recurrent epidemics and the former the superimposed noise of observed incidence patterns. Recently, a stochastic theory based on a mechanism of resonance with internal noise has shifted the role of stochasticity closer to the centre stage, by showing that the major dynamic patterns found in the incidence data can be explained as resonant fluctuations, whose behaviour is largely independent of the amplitude of seasonal forcing, and by contrast very sensitive to the basic epidemiological parameters. Here we elaborate on that approach, by adding an ingredient which is missing in standard epidemic models, the ‘mixing network’ through which infection may propagate. We find that spatial correlations have a major effect on the enhancement of the amplitude and the coherence of the resonant stochastic fluctuations, providing the ordered patterns of recurrent epidemics, whose period may differ significantly from that of the small oscillations around the deterministic equilibrium. We also show that the inclusion of a more realistic, time-correlated recovery profile instead of exponentially distributed infectious periods may, even in the random-mixing limit, contribute to the same effect

Epidemics in small world networks

For many infectious diseases, a small-world network on an underlying regular lattice is a suitable simplified model for the contact structure of the host population. It is well known that the contact network, described in this setting by a single parameter, the small-world parameter p, plays an important role both in the short term and in the long term dynamics of epidemic spread. We have studied the effect of the network structure on models of immune for life diseases and found that in addition to the reduction of the effective transmission rate, through the screening of infectives, spatial correlations may strongly enhance the stochastic fluctuations. As a consequence, time series of unforced Susceptible-Exposed-Infected-Recovered (SEIR) models provide patterns of recurrent epidemics with realistic amplitudes, suggesting that these models together with complex networks of contacts are the key ingredients to describe the prevaccination dynamical patterns of diseases such as measles and pertussis. We have also studied the role of the host contact strucuture in pathogen antigenic variation, through its effect on the final outcome of an invasion by a viral strain of a population where a very similar virus is endemic. Similar viral strains are modelled by the same infection and reinfection parameters, and by a given degree of cross immunity that represents the antigenic distance between the competing strains. We have found, somewhat surprisingly, that clustering on the network decreases the potential to sustain pathogen diversity. Copyright EDP Sciences/Società Italiana di Fisica/Springer-Verlag 200689.75.-k Complex systems, 87.10.+e General theory and mathematical aspects, 87.23.-n Ecology and evolution,

Colloidal dipolar interactions in 2D smectic-C films

We use a two-dimensional (2D) elastic free energy to calculate the effective interaction between two circular disks immersed in smectic-C films. For strong homeotropic anchoring, the distortion of the director field caused by the disks generates topological defects that induce an effective interaction between the disks. We use finite elements, with adaptive meshing, to minimize the 2D elastic free energy. The method is shown to be accurate and efficient for inhomogeneities on the length scales set by the disks and the defects, that differ by up to 3 orders of magnitude. We compute the effective interaction between two disk-defect pairs in a simple (linear) configuration. For large disk separations, $D$, the elastic free energy scales as $\sim D^{-2}$, confirming the dipolar character of the long-range effective interaction. For small $D$ the energy exhibits a pronounced minimum. The lowest energy corresponds to a symmetrical configuration of the disk-defect pairs, with the inner defect at the mid-point between the disks. The disks are separated by a distance that is twice the distance of the outer defect from the nearest disk. The latter is identical to the equilibrium distance of a defect nucleated by an isolated disk

A MODEL FOR THE STRUCTURE OF SOME SEMICONDUCTING LIQUID ALLOYS : EVIDENCE FOR IONIC BONDING

Several liquid metallic alloys exhibit a transition from a metallic to a "semiconducting" state as a function of concentration. At the particular stoichiometric composition where the transition occurs the electronic structure of the alloy is very different in character from that of the pure metallic constituents. For example in CsAu there is much evidence to suggest that this is a fully ionized melt consisting of Cs+ and Au- ions while for other alloys such as Mg3Bi2, Cs3Sb and Li4Pb the situation is more uncertain and it has been suggested that these alloys may form covalently bonded "molecules" or complexes. Diffraction experiments can play a useful role in the elucidation of the bonding in such alloys. The partial structure factors of a covalently bonded system will exhibit features which are not observed for ionic systems and vice versa. In order to interpret neutron and X-ray diffraction data on these liquid semiconductors we have calculated the partial structure factors assuming an ionic model applies. More specifically, we have modelled the interatomic potentials by charged hard-spheres and computed the structure factors within the mean-spherical-approximation. The amount of charge transfer from one species to another and the diameters of the spheres can be varied. By comparing our calculated total neutron and X-ray scattered intensities with the experimental data we can examine the validity of the ionic picture. We find strong evidence for fully ionic bonding in CsAu and for pronounced charge transfer in Li4Pb and Mg3Bi2. We argue that the large low-angle peak which is observed in both the neutron and X-ray data in Li4Pb arises from molten salt-like charge ordering. A similar charge-ordering effect gives a good account of the structure observed in Mg3Bi2. For Cs3Sb the ionic model may be less realistic. A preliminary account of the calculations and comparison with experiment for CsAu has been published. A more detailed paper is in preparation

Reentrant Phase Diagram of Network Fluids

We introduce a microscopic model for particles with dissimilar patches which displays an unconventional "pinched" phase diagram, similar to the one predicted by Tlusty and Safran in the context of dipolar fluids [Science 290, 1328 (2000)]. The model-based on two types of patch interactions, which account, respectively, for chaining and branching of the self-assembled networks-is studied both numerically via Monte Carlo simulations and theoretically via first-order perturbation theory. The dense phase is rich in junctions, while the less-dense phase is rich in chain ends. The model provides a reference system for a deep understanding of the competition between condensation and self-assembly into equilibrium-polymer chains