Network-based vaccination improves prospects for disease control in wild chimpanzees

Many endangered wildlife populations are vulnerable to infectious diseases for which vaccines exist; yet, pragmatic considerations often preclude large-scale vaccination efforts. These barriers could be reduced by focusing on individuals with the highest contact rates. However, the question then becomes whether targeted vaccination is sufficient to prevent large outbreaks. To evaluate the efficacy of targeted wildlife vaccinations, we simulate pathogen transmission and control on monthly association networks informed by behavioural data from a wild chimpanzee community (Kanyawara N = 37, Kibale National Park, Uganda). Despite considerable variation across monthly networks, our simulations indicate that targeting the most connected individuals can prevent large outbreaks with up to 35% fewer vaccines than random vaccination. Transmission heterogeneities might be attributed to biological differences among individuals (e.g. sex, age, dominance and family size). Thus, we also evaluate the effectiveness of a trait-based vaccination strategy, as trait data are often easier to collect than interaction data. Our simulations indicate that a trait-based strategy can prevent large outbreaks with up to 18% fewer vaccines than random vaccination, demonstrating that individual traits can serve as effective estimates of connectivity. Overall, these results suggest that fine-scale behavioural data can help optimize pathogen control efforts for endangered wildlife.     

Beyond contact-based transmission networks: the role of spatial coincidence

Animal societies rely on interactions between group members to effectively communicate and coordinate their actions. To date, the transmission properties of interaction networks formed by direct physical contacts have been extensively studied for many animal societies and in all cases found to inhibit spreading. Such direct interactions do not, however, represent the only viable pathways. When spreading agents can persist in the environment, indirect transmission via ‘same-place, different-time’ spatial coincidences becomes possible. Previous studies have neglected these indirect pathways and their role in transmission. Here, we use rock ant colonies, a model social species whose flat nest geometry, coupled with individually tagged workers, allowed us to build temporally and spatially explicit interaction networks in which edges represent either direct physical contacts or indirect spatial coincidences. We show how the addition of indirect pathways allows the network to enhance or inhibit the spreading of different types of agent. This dual-functionality arises from an interplay between the interaction-strength distribution generated by the ants'' movement and environmental decay characteristics of the spreading agent. These findings offer a general mechanism for understanding how interaction patterns might be tuned in animal societies to control the simultaneous transmission of harmful and beneficial agents.     

Stochastic extinction and the selection of the transmission mode in microparasites.

Stochastic fluctuations in the transmission process of microparasites generate a risk of parasite extinction that cannot be assessed by deterministic models, especially in host populations of small size. While this risk of extinction represents a strong selection pressure for microparasites, it is usually not clearly separated from the deterministic ones. We suggest here that this stochastic selection pressure can affect the selection of the transmission mode of microparasites. To avoid extinction, parasites should maximize their inter-population transmission to ensure frequent reintroductions. Since the types of contacts may differ if congeners belong to the same or distinct populations, strains that are mainly transmitted through inter-population contacts might be selected. To examine this assumption, we analyse the issue of the competition between two strains differing in their transmission mode using a stochastic metapopulation model in which hosts may display different behaviours inside and outside their populations. We show that stochastic selection pressures may drive parasite evolution towards a transmission mode that maximizes the persistence of the parasite. We study the conditions under which stochastic selection pressures may surpass the deterministic ones. Our results are illustrated by the cases of feline immunodeficiency virus in cats and of sexually transmitted diseases in mammals.     

Properties of force networks in jammed granular media

Discrete element method simulations are conducted to investigate the effects of applied uniaxial compressive load, and bidisperse particle size distributions on force networks within jammed granular media. The differences between the strong and weak networks are examined through investigating the spatial correlation and distribution of contact angles, and emergence of chainlike structures. The simulation results show that the chainlike structures are more prevalent in the strong network due to the larger cumulative probabilities of contact angles, but not all the contacts belonging to the strong or weak networks are able to constitute the chainlike structures. Although the contacts of coarse-fine particles are dominant for the bidisperse systems, the contacts of coarse–coarse particles dominate the strong network, as well as the linear chainlike structures. Upon increasing the pressure from very low to high, the probability of contact orientations with respect to the compression direction in the strong network increases for contact orientation less than \(60^{\circ }\) and decreases for contact orientation greater than \(60^{\circ }\), while the opposite trends are observed in the weak network. The tails of normalized normal contact forces distributions are quantified by \(\hbox {P}(\hbox {f}) = \hbox {exp}(-\hbox {cf}^{\mathrm{n}})\), and it is found that the value of n depends on the applied pressure and particle size distribution. Statistical analysis shows that the degree of homogeneity of contact force increases with increasing pressure, which is also validated by participation number.     

Experiments and theory of undulatory locomotion in a simple structured medium

Undulatory locomotion of micro-organisms through geometrically complex, fluidic environments is ubiquitous in nature and requires the organism to negotiate both hydrodynamic effects and geometrical constraints. To understand locomotion through such media, we experimentally investigate swimming of the nematode Caenorhabditis elegans through fluid-filled arrays of micro-pillars and conduct numerical simulations based on a mechanical model of the worm that incorporates hydrodynamic and contact interactions with the lattice. We show that the nematode''s path, speed and gait are significantly altered by the presence of the obstacles and depend strongly on lattice spacing. These changes and their dependence on lattice spacing are captured, both qualitatively and quantitatively, by our purely mechanical model. Using the model, we demonstrate that purely mechanical interactions between the swimmer and obstacles can produce complex trajectories, gait changes and velocity fluctuations, yielding some of the life-like dynamics exhibited by the real nematode. Our results show that mechanics, rather than biological sensing and behaviour, can explain some of the observed changes in the worm''s locomotory dynamics.     

Disease transmission in territorial populations: the small-world network of Serengeti lions

Territoriality in animal populations creates spatial structure that is thought to naturally buffer disease invasion. Often, however, territorial populations also include highly mobile, non-residential individuals that potentially serve as disease superspreaders. Using long-term data from the Serengeti Lion Project, we characterize the contact network structure of a territorial wildlife population and address the epidemiological impact of nomadic individuals. As expected, pride contacts are dominated by interactions with neighbouring prides and interspersed by encounters with nomads as they wander throughout the ecosystem. Yet the pride–pride network also includes occasional long-range contacts between prides, making it surprisingly small world and vulnerable to epidemics, even without nomads. While nomads increase both the local and global connectivity of the network, their epidemiological impact is marginal, particularly for diseases with short infectious periods like canine distemper virus. Thus, territoriality in Serengeti lions may be less protective and non-residents less important for disease transmission than previously considered.     

The effect of individual variation on the structure and function of interaction networks in harvester ants

Social insects exhibit coordinated behaviour without central control. Local interactions among individuals determine their behaviour and regulate the activity of the colony. Harvester ants are recruited for outside work, using networks of brief antennal contacts, in the nest chamber closest to the nest exit: the entrance chamber. Here, we combine empirical observations, image analysis and computer simulations to investigate the structure and function of the interaction network in the entrance chamber. Ant interactions were distributed heterogeneously in the chamber, with an interaction hot-spot at the entrance leading further into the nest. The distribution of the total interactions per ant followed a right-skewed distribution, indicating the presence of highly connected individuals. Numbers of ant encounters observed positively correlated with the duration of observation. Individuals varied in interaction frequency, even after accounting for the duration of observation. An ant''s interaction frequency was explained by its path shape and location within the entrance chamber. Computer simulations demonstrate that variation among individuals in connectivity accelerates information flow to an extent equivalent to an increase in the total number of interactions. Individual variation in connectivity, arising from variation among ants in location and spatial behaviour, creates interaction centres, which may expedite information flow.     

A model for predicting uniaxial compression behavior of fused fibrous networks

Fused fibrous networks are increasingly being used for emerging industrial applications ranging from thermal/sound insulation, fluid filtration/separation, and energy conversion to tissue scaffolds. Majority of these applications need a deeper understanding of fused fibrous networks under compression loading. In this research work, a compression model of fused fibrous networks has been proposed by defining two distinct regions displaying the bending of free fiber segments between the fiber-to-fiber contacts followed by the transverse compression of fiber contacts through classical Hertzian contact mechanics approach. The mechanistic models developed in this study, have clearly elucidated the main fiber and structural parameters that control the compression behavior of fused fibrous networks. A comparison has also been made between the theoretical and experimental pressure–strain curves of randomly and preferentially aligned fused fibrous networks.     

Nanoscale Joule heating, Peltier cooling and current crowding at graphene-metal contacts

The performance and scaling of graphene-based electronics is limited by the quality of contacts between the graphene and metal electrodes. However, the nature of graphene-metal contacts remains incompletely understood. Here, we use atomic force microscopy to measure the temperature distributions at the contacts of working graphene transistors with a spatial resolution of ~ 10 nm (refs 5-8), allowing us to identify the presence of Joule heating, current crowding and thermoelectric heating and cooling. Comparison with simulation enables extraction of the contact resistivity (150-200 Ω μm2) and transfer length (0.2-0.5 μm) in our devices; these generally limit performance and must be minimized. Our data indicate that thermoelectric effects account for up to one-third of the contact temperature changes, and that current crowding accounts for most of the remainder. Modelling predicts that the role of current crowding will diminish and the role of thermoelectric effects will increase as contacts improve.     

A model for fibre contact in planar random fibre networks

A model is presented for the expected degree of contact between fibres in isotropic near-planar random fibre networks. The statistics of fibre contact in two-dimensional fibre networks are considered and the expressions derived are developed to allow the fractional contact area in structures formed by the superposition of two-dimensional structures to be derived. These expressions allow the fractional contact area to be expressed in terms of the network porosity only. For thin networks, the fractional contact area may be expressed in terms of network porosity and the expected coverage of the network. Theory permitting the determination of the expected area of one contact and hence the expected number of contacts per fibre is presented also. Good agreement is found between the expressions derived for the fractional contact area and data from the literature.     

Investigation of the fabric evolution and the stress-transmission behaviour of sands based on X-ray μCT images

This paper presents the use of X-ray micro-tomography (X-ray $\mu$CT) and image processing and analysis techniques to investigate the stress transmission and buckling of inter-particle contacts within a granular material. A triaxial testing of a miniature Leighton Buzzard sand (LBS) sample was carried out with full-field in-situ X-ray $\mu$CT scanning. High-spatial-resolution CT images of the sample were acquired at several loading stages of the test. Image processing and analysis techniques were used to quantify the inter-particle contact evolution (contact gain, contact loss and contact movement), fabric, contact duration and buckling of stress-transmission contacts based on the CT images. The results indicated that contact gain and loss, and contact movement played two competing roles in determining the overall fabric evolution of the sample. Contacts with a longer duration were more likely to orient in the major principal stress direction and form a stress-transmission contact network. A gradual decrease in the buckling rate of the stress-transmission contacts was observed outside of the shear band, and a relatively stable buckling rate was observed within the shear band during the shear. The results suggested that jamming occurred outside of the shear band and that unjamming occurred within the shear band.     

Theoretical characterization of the topology of connected carbon nanotubes in random networks

In recent years, a lot of attention has been paid to carbon nanotube (CNT) networks and their applications to electronic devices. Many studies concentrate on the percolation threshold and the characterization of the conduction in such materials. Nevertheless, no theoretical study has yet attempted to characterize the CNT features inside finite size CNT networks. We present a theoretical approach based on geometrical and statistical considerations. We demonstrate the possibility of explicitly determining some relations existing between two neighbor CNTs and their contact efficiency in random networks of identical CNTs. We calculate the contact probability of rigid identical CNTs and we obtain a probability of 0.2027, which turns out to be independent of the CNT density. Based on this probability, we establish also the dependence of the number of contacts per CNT as a function of the CNT density. All the theoretical results are validated by very good agreement with Monte Carlo simulations.     

The role of heterogeneity in contact timing and duration in network models of influenza spread in schools

Influenza poses a significant health threat to children, and schools may play a critical role in community outbreaks. Mathematical outbreak models require assumptions about contact rates and patterns among students, but the level of temporal granularity required to produce reliable results is unclear. We collected objective contact data from students aged 5–14 at an elementary school and middle school in the state of Utah, USA, and paired those data with a novel, data-based model of influenza transmission in schools. Our simulations produced within-school transmission averages consistent with published estimates. We compared simulated outbreaks over the full resolution dynamic network with simulations on networks with averaged representations of contact timing and duration. For both schools, averaging the timing of contacts over one or two school days caused average outbreak sizes to increase by 1–8%. Averaging both contact timing and pairwise contact durations caused average outbreak sizes to increase by 10% at the middle school and 72% at the elementary school. Averaging contact durations separately across within-class and between-class contacts reduced the increase for the elementary school to 5%. Thus, the effect of ignoring details about contact timing and duration in school contact networks on outbreak size modelling can vary across different schools.     

The interplay of cell–cell and cell–substrate adhesion in collective cell migration

Collective cell migration often involves notable cell–cell and cell–substrate adhesions and highly coordinated motion of touching cells. We focus on the interplay between cell–substrate adhesion and cell–cell adhesion. We show that the loss of cell-surface contact does not significantly alter the dynamic pattern of protrusions and retractions of fast migrating amoeboid cells (Dictyostelium discoideum), but significantly changes their ability to adhere to other cells. Analysis of the dynamics of cell shapes reveals that cells that are adherent to a surface may coordinate their motion with neighbouring cells through protrusion waves that travel across cell–cell contacts. However, while shape waves exist if cells are detached from surfaces, they do not couple cell to cell. In addition, our investigation of actin polymerization indicates that loss of cell-surface adhesion changes actin polymerization at cell–cell contacts. To further investigate cell–cell/cell–substrate interactions, we used optical micromanipulation to form cell–substrate contact at controlled locations. We find that both cell-shape dynamics and cytoskeletal activity respond rapidly to the formation of cell–substrate contact.     

A phase-field method for modeling cracks with frictional contact

We introduce a phase-field method for continuous modeling of cracks with frictional contacts. Compared with standard discrete methods for frictional contacts, the phase-field method has two attractive features: (i) it can represent arbitrary crack geometry without an explicit function or basis enrichment, and (ii) it does not require an algorithm for imposing contact constraints. The first feature, which is common in phase-field models of fracture, is attained by regularizing a sharp interface geometry using a surface density functional. The second feature, which is a unique advantage for contact problems, is achieved by a new approach that calculates the stress tensor in the regularized interface region depending on the contact condition of the interface. Particularly, under a slip condition, this approach updates stress components in the slip direction using a standard contact constitutive law, while making other stress components compatible with stress in the bulk region to ensure nonpenetrating deformation in other directions. We verify the proposed phase-field method using stationary interface problems simulated by discrete methods in the literature. Subsequently, by allowing the phase field to evolve according to brittle fracture theory, we demonstrate the proposed method's capability for modeling crack growth with frictional contact.     

Asynchronous collision integrators: Explicit treatment of unilateral contact with friction and nodal restraints

This article presents asynchronous collision integrators and a simple asynchronous method treating nodal restraints. Asynchronous discretizations allow individual time step sizes for each spatial region, improving the efficiency of explicit time stepping for finite element meshes with heterogeneous element sizes. The article first introduces asynchronous variational integration being expressed by drift and kick operators. Linear nodal restraint conditions are solved by a simple projection of the forces that is shown to be equivalent to RATTLE. Unilateral contact is solved by an asynchronous variant of decomposition contact response. Therein, velocities are modified avoiding penetrations. Although decomposition contact response is solving a large system of linear equations (being critical for the numerical efficiency of explicit time stepping schemes) and is needing special treatment regarding overconstraint and linear dependency of the contact constraints (for example from double‐sided node‐to‐surface contact or self‐contact), the asynchronous strategy handles these situations efficiently and robust. Only a single constraint involving a very small number of degrees of freedom is considered at once leading to a very efficient solution. The treatment of friction is exemplified for the Coulomb model. Special care needs the contact of nodes that are subject to restraints. Together with the aforementioned projection for restraints, a novel efficient solution scheme can be presented. The collision integrator does not influence the critical time step. Hence, the time step can be chosen independently from the underlying time‐stepping scheme. The time step may be fixed or time‐adaptive. New demands on global collision detection are discussed exemplified by position codes and node‐to‐segment integration. Numerical examples illustrate convergence and efficiency of the new contact algorithm. Copyright © 2013 The Authors. International Journal for Numerical Methods in Engineering published by John Wiley & Sons, Ltd.     

Temporal variation of contact networks in granular materials

For analogue granular materials simulated using DEM, contact networks are often drawn by joining the centroids of contacting particles. Although a limited amount of research has been done to characterise the temporal aspects of such contact networks at a micro-scale, many simple questions regarding the duration of contacts in evolving granular systems remain unanswered. This paper addresses this gap in the existing knowledge by using the open-source code LAMMPS to run and analyse nine (3D) triaxial simulations of 20,164 polydisperse spherical particles. Contacts which exist for a long duration are preferentially oriented in the direction of the major principal stress while the fabric anisotropy for contacts with a given duration increases with duration. Regardless of simulation conditions, there is a linear relationship between the percentage of contacts present for a given duration and contact duration, despite the non-linear overall behaviour of the material. The forces transmitted by contacts increase, on average, with increasing duration. The total number of unique contacts which appear during triaxial compression increases linearly after 10 % axial strain, although the number of contacts, both total and subdivided into strong and weak force subnetworks, remains quite stable. The majority of contacts in these evolving granular systems, even those participating in strong force chains, are formed and lost repeatedly.     

Simulating non‐holonomic constraints within the LCP‐based simulation framework

In this paper, we will extend the linear complementarity problem‐based rigid‐body simulation framework with non‐holonomic constraints. We consider three different types of such, namely equality, inequality and contact constraints. We show how non‐holonomic equality and inequality constraints can be incorporated directly, and derive formalism for how the non‐holonomic contact constraints can be modelled as a combination of non‐holonomic equality constraints and ordinary contacts constraints. For each of these three we are able to guarantee solvability, when using Lemke's algorithm. A number of examples are included to demonstrate the non‐holonomic constraints. Copyright © 2006 John Wiley & Sons, Ltd     

Spatial dynamics of the 1918 influenza pandemic in England,Wales and the United States

There is still limited understanding of key determinants of spatial spread of influenza. The 1918 pandemic provides an opportunity to elucidate spatial determinants of spread on a large scale.To better characterize the spread of the 1918 major wave, we fitted a range of city-to-city transmission models to mortality data collected for 246 population centres in England and Wales and 47 cities in the US. Using a gravity model for city-to-city contacts, we explored the effect of population size and distance on the spread of disease and tested assumptions regarding density dependence in connectivity between cities. We employed Bayesian Markov Chain Monte Carlo methods to estimate parameters of the model for population, infectivity, distance and density dependence. We inferred the most likely transmission trees for both countries.For England and Wales, a model that estimated the degree of density dependence in connectivity between cities was preferable by deviance information criterion comparison. Early in the major wave, long distance infective interactions predominated, with local infection events more likely as the epidemic became widespread. For the US, with fewer more widely dispersed cities, statistical power was lacking to estimate population size dependence or the degree of density dependence, with the preferred model depending on distance only. We find that parameters estimated from the England and Wales dataset can be applied to the US data with no likelihood penalty.     

Modeling particulate self-healing materials and application to uni-axial compression

Using an advanced history dependent contact model for DEM simulations, including elasto-plasticity, viscosity, adhesion, and friction, pressure-sintered tablets are formed from primary particles. These tablets are subjected to unconfined uni-axial compression until and beyond failure. For fast and slow deformation we observe ductile-like and brittle softening, respectively. We propose a model for local self-healing that allows damage to heal during loading such that the material strength of the sample increases and failure/softening is delayed to larger strains. Local healing is achieved by increasing the (attractive) contact adhesion forces for those particles involved in a potentially breaking contact. We examine the dependence of the strength of the material on (a) the damage detection sensitivity, (b) the damage detection rate, and (c) the (increased) adhesion between healed contacts. The material strength is enhanced, i.e., the material fails at larger strains and reaches larger maximal stress values, when any of the parameters (a)–(c) is increased. For very large adhesion between the healed contacts an interesting instability with strong (brittle) fluctuations of the healed material’s strength is observed.