arXiv subjects

M. M. Telo da Gama

Publications and source records attributed to M. M. Telo da Gama.

At least 55 records · Page 3Linked to original sources

arXiv2007

Stochastic Fluctuations in Epidemics on Networks

The effects of demographic stochasticity in 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 center 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 in 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.

q-bio.PE↗

arXiv2007

Pathways to folding, nucleation events and native geometry

We perform extensive Monte Carlo simulations of a lattice model and the Go potential to investigate the existence of folding pathways at the level of contact cluster formation for two native structures with markedly different geometries. Our analysis of folding pathways revealed a common underlying folding mechanism, based on nucleation phenomena, for both protein models. However, folding to the more complex geometry (i.e. that with more non-local contacts) is driven by a folding nucleus whose geometric traits more closely resemble those of the native fold. For this geometry folding is clearly a more cooperative process.

q-bio.BM↗

arXiv2006

Nucleation phenomena in protein folding: The modulating role of protein sequence

For the vast majority of naturally occurring, small, single domain proteins folding is often described as a two-state process that lacks detectable intermediates. This observation has often been rationalized on the basis of a nucleation mechanism for protein folding whose basic premise is the idea that after completion of a specific set of contacts forming the so-called folding nucleus the native state is achieved promptly. Here we propose a methodology to identify folding nuclei in small lattice polymers and apply it to the study of protein molecules with chain length N=48. To investigate the extent to which protein topology is a robust determinant of the nucleation mechanism we compare the nucleation scenario of a native-centric model with that of a sequence specific model sharing the same native fold. To evaluate the impact of the sequence's finner details in the nucleation mechanism we consider the folding of two non- homologous sequences. We conclude that in a sequence-specific model the folding nucleus is, to some extent, formed by the most stable contacts in the protein and that the less stable linkages in the folding nucleus are solely determined by the fold's topology. We have also found that independently of protein sequence the folding nucleus performs the same `topological' function. This unifying feature of the nucleation mechanism results from the residues forming the folding nucleus being distributed along the protein chain in a similar and well-defined manner that is determined by the fold's topological features.

q-bio.BM↗

arXiv2006

On elliptical soft colloids in smectic-C films

We investigate theoretically the elliptical shapes of soft colloids in freely standing smectic C films, that have been reported recently. The colloids favour parallel alignment of the liquid crystal molecules at their surfaces and, for sufficiently strong anchoring, will generate a pair of defects at the poles of the colloidal particles. The elastic free energy of the liquid crystal matrix will, in turn, affect the shape of the colloids. In this study we will focus on elliptical soft colloids and determine how their equilibrium shapes depend on the elastic constants of the liquid crystal, the anchoring strength, the surface tension and the size of the colloids. A shape diagram is obtained analytically, by minimizing the Frank elastic free energy, in the limit of small eccentricities. The analytical results are verified, and generalized to arbitrary eccentricities, by numerical minimization of an appropriate Landau free energy. The latter is required for an adequate description of the topological defects when the liquid crystal correlation length is comparable to the size of the colloidal particles.

cond-mat.soft↗

arXiv2005

Nonequilibrium Bound Interfaces

An overview of recent studies of nonequilibrium bound interfaces is given. Attention is focused on Kardar-Parisi-Zhang interfaces in the presence of upper and lower walls, interacting via short-- and long--ranged potentials. A comparison with equilibrium interfaces is carried out, and connections with other nonequilbrium systems are illustrated. Experimental realizations of the phenomenology described in this article are briefly discussed.

cond-mat.stat-mech↗

arXiv2005

Does host contact structure reduce pathogen diversity?

We investigate the dynamics of a simple epidemiological model for the invasion by a pathogen strain of a population where another strain circulates. We assume that reinfection by the same strain is possible but occurs at a reduced rate due to acquired immunity. The rate of reinfection by a distinct strain is also reduced due to cross-immunity. Individual based simulations of this model on a `small-world' network show that the host contact network structure significantly affects the outcome of such an invasion, and as a consequence will affect the patterns of pathogen evolution. In particular, host populations interacting through a 'small-world' network of contacts support lower prevalence of infection than well-mixed populations, and the region in parameter space for which an invading strain can become endemic and coexist with the circulating strain is smaller, reducing the potential to accommodate pathogen diversity. We discuss the underlying mechanisms for the reported effects, and we propose an effective mean-field model to account for the contact structure of the host population in 'small-world' networks.

q-bio.PE↗

arXiv2005

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.

q-bio.PE↗

arXiv2005

Folding of small proteins: A matter of geometry?

We review some of our recent results obtained within the scope of simple lattice models and Monte Carlo simulations that illustrate the role of native geometry in the folding kinetics of two state folders.

q-bio.BM↗

arXiv2005

The nature of the phase transition in dipolar fluids

Monte Carlo computer simulations of a quasi two dimensional (2D) dipolar fluid at low and intermediate densities indicate that the structure of the fluid is well described by an ideal mixture of self-assembling clusters. A detailed analysis of the topology of the clusters, of their internal energy and of their size (or mass) distributions further suggests that the system undergoes a phase transition from a dilute phase characterized by a number of disconnected clusters to a condensed phase characterized by a network or spanning (macroscopic) cluster that includes most of the particles in the system.

cond-mat.soft↗

arXiv2005

The Go model revisited: Native structure and the geometric coupling between local and long-range contacts

Monte Carlo simulations show that long-range interactions play a major role in determining the folding rates of 48-mer three-dimensional lattice polymers modelled by the Go potential. For three target structures with different native geometries we found a sharp increase in the folding time when the relative contribution of the long-range interactions to the native state's energy is decreased from ~50% towards zero. However, the dispersion of the simulated folding times depends strongly on the native geometry and Go polymers folding to one of the target structures exhibit folding times spanning three orders of magnitude. We have also found that, depending on the target geometry, a strong geometric coupling may exist between local and long-range contacts meaning that, when this coupling exists, the formation of long-range contacts is forced by the previous formation of local contacts. The absence of a strong geometric coupling leads to kinetics that are more sensitive to the interaction energy parameters; in this case the formation of local contacts is not sufficient to promote the establishment of long-range ones when these are strongly penalized energetically, leading to longer folding times.

q-bio.BM↗

arXiv2004

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 Gō model show that the effect of long range contact interaction strength in the folding kinetics is largely dependent on the native state's geometry.

q-bio.BM↗

arXiv2004

Generic two-phase coexistence in nonequilibrium systems

Gibbs' phase rule states that two-phase coexistence of a single-component system, characterized by an n-dimensional parameter-space, may occur in an n-1-dimensional region. For example, the two equilibrium phases of the Ising model coexist on a line in the temperature-magnetic-field phase diagram. Nonequilibrium systems may violate this rule and several models, where phase coexistence occurs over a finite (n-dimensional) region of the parameter space, have been reported. The first example of this behaviour was found in Toom's model [Toom,Geoff,GG], that exhibits generic bistability, i.e. two-phase coexistence over a finite region of its two-dimensional parameter space (see Section 1). In addition to its interest as a genuine nonequilibrium property, generic multistability, defined as a generalization of bistability, is both of practical and theoretical relevance. In particular, it has been used recently to argue that some complex structures appearing in nature could be truly stable rather than metastable (with important applications in theoretical biology), and as the theoretical basis for an error-correction method in computer science (see [GG,Gacs] for an illuminating and pedagogical discussion of these ideas).

cond-mat.stat-mech↗

arXiv2004

Recurrent epidemics in small world networks

The effect of spatial correlations on the spread of infectious diseases was investigated using a stochastic SIR (Susceptible-Infective-Recovered) model on complex networks. It was found that in addition to the reduction of the effective transmission rate, through the screening of infectives, spatial correlations may have another major effect through the enhancement of stochastic fluctuations. As a consequence large populations will have to become even larger to 'average out' significant differences from the solution of deterministic models. Furthermore, time series of the (unforced) model provide patterns of recurrent epidemics with slightly irregular periods and realistic amplitudes, suggesting that stochastic models together with complex networks of contacts may be sufficient to describe the long term dynamics of some diseases. The spatial effects were analysed quantitatively by modelling measles and pertussis, using a SEIR (Susceptible-Exposed-Infective-Recovered) model. Both the period and the spatial coherence of the epidemic peaks of pertussis are well described by the unforced model for realistic values of the parameters.

q-bio.PE↗

arXiv2004

Diffusion-limited deposition of dipolar particles

Deposits of dipolar particles are investigated by means of extensive Monte Carlo simulations. We found that the effect of the interactions is described by an initial, non-universal, scaling regime characterized by orientationally ordered deposits. In the dipolar regime, the order and geometry of the clusters depend on the strength of the interactions and the magnetic properties are tunable by controlling the growth conditions. At later stages, the growth is dominated by thermal effects and the diffusion-limited universal regime obtains, at finite temperatures. At low temperatures the crossover size increases exponentially as T decreases and at T=0 only the dipolar regime is observed.

cond-mat.stat-mech↗

arXiv2004

The key-lock mechanism in nematic colloidal dispersions

We consider the interaction of two-dimensional colloids, in nematic liquid crystals, with walls or geometrical boundaries. The interactions between colloidal disks and flat walls, with homeotropic boundary conditions, are always repulsive. The repulsions may be turned into strong attractions at structured or sculpted walls with cavities, matching closely the shape and size of the colloids. This key-lock type of interaction is analyzed in detail for spherocylindrical cavities of various length to breath ratios, by minimizing the Landau-de Gennes free energy functional of the orientational order parameter. We find that the attractions occur only for walls with cavities within a small range of the colloidal size and for a narrow range of orientations around the wall's symmetry axis.

cond-mat.soft↗

arXiv2004

Folding and form: Insights from lattice simulations

Monte Carlo simulations of a Miyazawa-Jernigan lattice-polymer model indicate that, depending on the native's structure geometry, the model exhibits two broad classes of folding mechanisms for two-state folders. Folding to native structures of low contact order is driven by contact range and is characterised by progressive accumulation of structure towards the native fold. By contrast, folding to high contact order targets is largely dominated by intermediate stage contacts which are not present in the native fold, yielding a more cooperative folding process.

cond-mat.soft↗

arXiv2003

Interaction of colloids with a nematic-isotropic interface

The Landau-de Gennes free energy is used to calculate the interaction between long cylindrical colloids and the nematic-isotropic (NI) interface. This interaction has two contributions: one is specific of liquid crystals and results from the deformation of the director field close to the particles or to the interface, while the other is generic and results from wetting and surface tension effects. Deep in the nematic phase the director field of long cylindrical colloids, with strong homeotropic anchoring, exhibits two half-integer defect lines. As the colloid moves towards the interface, the director configuration changes through a series of discontinuous transitions, where one or two of the defects are annihilated. In addition, the NI interface bends towards the colloid in order to minimize the elastic free energy in the nematic. In the isotropic phase, the colloid is surrounded by a thin nematic layer that reduces the surface free energy under favorable wetting conditions. The interaction has a well-defined minimum near the interface. In this region the director and interfacial structures are complex and cannot be described analytically. Using the numerical results for the Landau-de Gennes free energy in the harmonic region, we obtained simple scaling laws for the (linear) force on the colloid.

cond-mat.soft↗

arXiv2003

Forces between elongated particles in a nematic colloid

Using molecular dynamics (MD) simulations we study the interactions between elongated colloidal particles (length to breath ratio > 1) in a nematic host. The simulation results are compared to the results of a Landau-de Gennes elastic free energy. We find that depletion forces dominate for the sizes of the colloidal particles studied. The tangential component of the force, however, allows us to resolve the elastic contribution to the total interaction. We find that this contribution differs from the quadrupolar interaction predicted at large separations. The difference is due to the presence of nonlinear effects, namely th e change in the positions and structure of the defects and their annihilation at small separations.

cond-mat.soft↗