Inferring epidemiological parameters from phylogenetic information for the HIV-1 epidemic among MSM

The HIV-1 epidemic in Europe is primarily sustained by a dynamic topology of sexual interactions among MSM who have individual immune systems and behavior. This epidemiological process shapes the phylogeny of the virus population. Both fields of epidemic modeling and phylogenetics have a long history, however it remains difficult to use phylogenetic data to infer epidemiological parameters such as the structure of the sexual network and the per-act infectiousness. This is because phylogenetic data is necessarily incomplete and ambiguous. Here we show that the cluster-size distribution indeed contains information about epidemiological parameters using detailed numberical experiments. We simulate the HIV epidemic among MSM many times using the Monte Carlo method with all parameter values and their ranges taken from literature. For each simulation and the corresponding set of parameter values we calculate the likelihood of reproducing an observed cluster-size distribution. The result is an estimated likelihood distribution of all parameters from the phylogenetic data, in particular the structure of the sexual network, the per-act infectiousness, and the risk behavior reduction upon diagnosis. These likelihood distributions encode the knowledge provided by the observed cluster-size distrbution, which we quantify using information theory. Our work suggests that the growing body of genetic data of patients can be exploited to understand the underlying epidemiological process.     

Conduction mechanisms in polyacetylene nanofibres

The current–voltage (I–V) characteristics of individual nanofibres of lightly-doped polyacetylene show very strong nonlinearities. At low temperatures the I–V characteristics are consistent with Zener-type tunnelling, and independent of temperature and magnetic field. We propose that this behaviour arises from tunnelling of a segment of the conjugated bond system in the presence of an electric field, in analogy to the soliton-pair creation mechanism proposed by Maki for conduction in charge-density-wave (CDW) materials. A comparison is made with analogous tunnelling conduction mechanisms reported in CDW and spin-density-wave systems at low temperatures. At higher temperatures the I–V characteristics deviate from Zener-type behaviour and are temperature dependent, so other conduction mechanisms are important.     

A numerical exploration of secondary separation in starting flow around a flat plate by the discrete vortex model

In the present work, a further numerical simulation of the starting flow around a flat plate normal to the direction of motion in a uniform fluid has been made by means of the discrete vortex method. The secondary separation occurring at rear surface of the plate is explored, and predicted approximately using Thwait's method. The calculated results show that in the early stages of the flow secondary separation does occur. The evolution of flow field, the vortex growing process and the characteristics of secondary vortices have been described. The time dependent drag coefficients, the vorticity shed from the edges and rear surface, and the separation positions are calculated as well as the distributions of velocity and pressure on the plate. In the case of flow normal to the plate, the calculated secondary vortices are weak. Their existence will change the local velocity distributions and affect pressure distributions. However, the effect on drag coefficient is negligible.     

Unified scaling law in the coherent noise model

The waiting time distribution between successive events and the unified scaling law is studied using the coherent noise model. It is shown that, although this model generates uncorrelated event sizes and does not exhibit criticality, it still provides the unified scaling law. We argue the role of characteristic kink observed in the unified scaling law and the meaning of the parameter C$C$ used to fix the peak of the kink to unity. Our results indicate that the parameter C$C$ is indeed a physical quantity localizing the end of the linear tendency in the scaling law, which corresponds to the completion of the dominance of correlated events in time.     

Modelling the spreading rate of controlled communicable epidemics through an entropy-based thermodynamic model

A model based on a thermodynamic approach is proposed for predicting the dynamics of communicable epidemics assumed to be governed by controlling eforts of multiple scales so that an entropy is associated with the system.All the epidemic details are factored into a single and time-dependent coefcient,the functional form of this coefcient is found through four constraints,including notably the existence of an inflexion point and a maximum.The model is solved to give a log-normal distribution for the spread rate,for which a Shannon entropy can be defined.The only parameter,that characterizes the width of the distribution function,is uniquely determined through maximizing the rate of entropy production.This entropy-based thermodynamic(EBT)model predicts the number of hospitalized cases with a reasonable accuracy for SARS in the year 2003.This EBT model can be of use for potential epidemics such as avian influenza and H7N9 in China.     

Optical extensometer and elimination of the effect of out-of-plane motions

A novel optical extensometer is developed to estimate the local uniform strain on planar surface accurately. The proposed system consists of a shared large format lens and two image sensors, which acquire pairs of images of two isolated small regions on the object surface simultaneously. Digital image correlation (DIC) algorithm is applied to determine the relative displacement between gauge points designated on recorded pairs of images. Then local strain can be extracted after dividing the relative displacement by the scale distance. Moreover, a special experimental setup called “correction sheet” is used to eliminate the virtual strain induced by out-of-plane motions. Uni-axial tensile experiments are performed to validate the reliability and resolution of the optical extensometer, and the measurement results demonstrate that the resolution of the optical extensometer achieves 2–3 με.     

Simulation of front motion in a reacting condensed two phase mixture

The computational technique is developed in order to provide the scale capturing for numerical simulation of the thermal processes. The thermal front motion and gas flow dynamics as well as the rate of particle growth during the Carbon Combustion Synthesis of Oxides (CCSO) were predicted using the numerical simulation. In CCSO the exothermic oxidation of carbon nanoparticles generates a self-sustained thermal reaction front that propagates through the solid reactant mixture converting it to the desired complex oxides. The combusted carbon is emitted from the sample as carbon dioxide and its high rate of release increases the product porosity and friability. It was shown that the complicated finger front instability can be developed during the carbon combustion synthesis. This phenomenon results from a vortex gas flow in the reaction zone fed by the carbon dioxide co-flow and oxygen counter-flow filtration.     

Regularization of reaction progress variable for application to flamelet-based combustion models

Many combustion models that are based on the flamelet paradigm employ a reaction progress variable. While such a progress variable is well defined for one-step reaction kinetics, this is typically not the case for complex chemical mechanisms. Consequently, several expressions for a progress variable have been utilized. In this paper a formal method for the generation of a reaction progress variable is proposed that is optimal with respect to a set of constraints. The potential of the method is demonstrated in applications to partially premixed and diffusion flames, and the extension to premixed combustion is discussed. It is shown that the proposed method can lead to significant improvements in the definition of an optimal progress variable over conventional formulations, essentially eliminating the expert knowledge previously required in identifying such quantities.     

Dynamic behavior of triple-walled carbon nanotubes conveying fluid

In this study, the instability of triple-walled carbon nanotubes (TWCNTs) conveying fluid is studied based on an Euler–Bernoulli beam model. The van der Waals (vdW) interactions between different carbon nanotubes (CNTs) are taken into account in the analysis, and the Galerkin discretization approach is used to solve the coupled equations of the motions. Numerical simulations show that the interlayer vdW interactions play a significant role in the natural frequencies and the stability of TWCNTs. The critical flow velocities—associated with divergence, restabilization and flutter—are determined. The effects of different inner radius and the value of mode N used in Galerkin discretization on the dynamical behaviors of the fluid-conveyed TWCNTs are also examined in detail. Results reveal that the internal moving fluid plays an important role in the instability of TWCNTs.     

Predicting the Mechanical Properties of Binary Blends of Immiscible Polymers

We couple a morphological study of an immiscible binary AB mixture with a micromechanical simulation to determine how the spatial distribution of the A and B domains and the interfacial region (interphase) affects the mechanical behavior of the blend. The morphological studies are conducted through a three-dimensional Cahn-Hilliard (CH) simulation. Through the CH calculations, we obtain the size and structure of the domains for different blend compositions. The output of the CH model serves as the input to the Lattice Spring Model (LSM), which consists of a three-dimensional network of springs. In particular, the location of the different phases is mapped onto the LSM lattice and the appropriate force constants are assigned to the LSM sites. A stress is applied to the LSM lattice and we calculate the elastic response of the material. We find that the local stress and strain fields are highly dependent on the morphology of the system. By integrating the morphological and mechanical models, we can isolate how modifications in the composition of the mixture affect the macroscopic behavior. Thus, we can establish how choices made in the components affect the ultimate performance of the material.