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Reconstructing transmission trees for communicable diseases using densely sampled genetic data (2016)
Journal Article
Worby, C. J., O'Neill, P. D., Kypraios, T., Robotham, J. V., De Angelis, D., Cartwright, E. J., …Cooper, B. S. (2016). Reconstructing transmission trees for communicable diseases using densely sampled genetic data. Annals of Applied Statistics, 10(1), https://doi.org/10.1214/15-AOAS898

Whole genome sequencing of pathogens from multiple hosts in an epidemic offers the potential to investigate who infected whom with unparalleled resolution, potentially yielding important insights into disease dynamics and the impact of control measur... Read More about Reconstructing transmission trees for communicable diseases using densely sampled genetic data.

On expected durations of birth-death processes with applications to branching processes and SIS epidemics (2016)
Journal Article
Ball, F., Britton, T., & Neal, P. (2016). On expected durations of birth-death processes with applications to branching processes and SIS epidemics. Journal of Applied Probability, 53(1), https://doi.org/10.1017/jpr.2015.19

We study continuous-time birth–death type processes, where individuals have independent and identically distributed lifetimes, according to a random variable Q, with E[Q] = 1, and where the birth rate if the population is currently in state (has size... Read More about On expected durations of birth-death processes with applications to branching processes and SIS epidemics.

Evolution and spherical collapse in Einstein-Æther theory and Hořava gravity (2016)
Journal Article
Bhattacharyya, J., Coates, A., Colombo, M., & Sotiriou, T. P. (2016). Evolution and spherical collapse in Einstein-Æther theory and Hořava gravity. Physical Review D, 93(6), Article 64056. https://doi.org/10.1103/PhysRevD.93.064056

We compare the initial value formulation of the low-energy limit of (nonprojectable) Hořava gravity to that of Einstein-æther theory when the æther is assumed to be hypersurface orthogonal at the level of the field equations. This comparison clearly... Read More about Evolution and spherical collapse in Einstein-Æther theory and Hořava gravity.

Inertial effects on thin-film wave structures with imposed surface shear on an inclined plane (2016)
Journal Article
Sivapuratharasu, M., Hibberd, S., Hubbard, M. E., & Power, H. (2016). Inertial effects on thin-film wave structures with imposed surface shear on an inclined plane. Physica D: Nonlinear Phenomena, 325, 86-97. https://doi.org/10.1016/j.physd.2016.03.008

This study provides an extended approach to the mathematical simulation of thin-film flow on a flat inclined plane relevant to flows subject to high surface shear. Motivated by modelling thin-film structures within an industrial context, wave structu... Read More about Inertial effects on thin-film wave structures with imposed surface shear on an inclined plane.

Discrete structures in continuum descriptions of defective crystals (2016)
Journal Article
Parry, G. P. (2016). Discrete structures in continuum descriptions of defective crystals. Philosophical Transactions A: Mathematical, Physical and Engineering Sciences, 374(2066), https://doi.org/10.1098/rsta.2015.0172

I discuss various mathematical constructions that combine together to provide a natural setting for discrete and continuum geometric models of defective crystals. In particular I provide a quite general list of `plastic strain variables', which quant... Read More about Discrete structures in continuum descriptions of defective crystals.

Variational finite element methods for waves in a Hele-Shaw tank (2016)
Journal Article
Kalogirou, A., Moulopoulou, E. E., & Bokhove, O. (2016). Variational finite element methods for waves in a Hele-Shaw tank. Applied Mathematical Modelling, 40(17-18), 7493-7503. https://doi.org/10.1016/j.apm.2016.02.036

The damped motion of driven water waves in a Hele-Shaw tank is investigated variationally and numerically. The equations governing the hydrodynamics of the problem are derived from a variational principle for shallow water. The variational principle... Read More about Variational finite element methods for waves in a Hele-Shaw tank.

Pointed Hopf Algebras with Triangular Decomposition: A Characterization of Multiparameter Quantum Groups (2016)
Journal Article
Laugwitz, R. (2016). Pointed Hopf Algebras with Triangular Decomposition: A Characterization of Multiparameter Quantum Groups. Algebras and Representation Theory, 19(3), 547-578. https://doi.org/10.1007/s10468-015-9588-x

© 2016, The Author(s). In this paper, we present an approach to the definition of multiparameter quantum groups by studying Hopf algebras with triangular decomposition. Classifying all of these Hopf algebras which are of what we call weakly separable... Read More about Pointed Hopf Algebras with Triangular Decomposition: A Characterization of Multiparameter Quantum Groups.

The spatiotemporal order of signaling events unveils the logic of development signaling (2016)
Journal Article
Zhu, H., Owen, M. R., & Mao, Y. (in press). The spatiotemporal order of signaling events unveils the logic of development signaling. Bioinformatics, 32(15), https://doi.org/10.1093/bioinformatics/btw121

Motivation: Animals from worms and insects to birds and mammals show distinct body plans; however, the embryonic development of diverse body plans with tissues and organs within is controlled by a surprisingly few signaling pathways. It is well recog... Read More about The spatiotemporal order of signaling events unveils the logic of development signaling.

A spectral boundary integral method for inviscid water waves in a finite domain (2016)
Journal Article
Im, J., & Billingham, J. (2016). A spectral boundary integral method for inviscid water waves in a finite domain. International Journal for Numerical Methods in Fluids, 82(7), 437-448. https://doi.org/10.1002/fld.4225

In this paper, we show how the spectral formulation of Baker, Meiron and Orszag can be used to solve for waves on water of infinite depth confined between two flat, vertical walls, and also how it can be modified to take into account water of finite... Read More about A spectral boundary integral method for inviscid water waves in a finite domain.

Multicellular mathematical modelling of mesendoderm formation in amphibians (2016)
Journal Article
Brown, L., Middleton, A., King, J., & Loose, M. (2016). Multicellular mathematical modelling of mesendoderm formation in amphibians. Bulletin of Mathematical Biology, 78(3), 436-467. doi:10.1007/s11538-016-0150-8

The earliest cell fate decisions in a developing embryo are those associated with establishing the germ layers. The specification of the mesoderm and endoderm is of particular interest as the mesoderm is induced from the endoderm, potentially from an... Read More about Multicellular mathematical modelling of mesendoderm formation in amphibians.

Neural field models with threshold noise (2016)
Journal Article
Thul, R., Coombes, S., & Laing, C. R. (2016). Neural field models with threshold noise. Journal of Mathematical Neuroscience, 6, Article 3. https://doi.org/10.1186/s13408-016-0035-z

The original neural field model of Wilson and Cowan is often interpreted as the averaged behaviour of a network of switch like neural elements with a distribution of switch thresholds, giving rise to the classic sigmoidal population firing-rate funct... Read More about Neural field models with threshold noise.

Hierarchical Bayesian modelling of variability and uncertainty in synthetic action potential traces (2016)
Journal Article
Johnstone, R. H., Bardenet, R., Gavaghan, D. J., Polonchuk, L., Davies, M. R., & Mirams, G. R. (2016). Hierarchical Bayesian modelling of variability and uncertainty in synthetic action potential traces. Computing in cardiology, 43, 1089-1092

© 2016 CCAL. There are many sources of uncertainty in the recording and modelling of membrane action potentials (APs) from cardiomyocytes. For example, there are measurement, parameter, and model uncertainties. There is also extrinsic variability bet... Read More about Hierarchical Bayesian modelling of variability and uncertainty in synthetic action potential traces.

Quantum periods for 3-dimensional Fano manifolds (2016)
Journal Article
Coates, T., Corti, A., Galkin, S., & Kasprzyk, A. M. (2016). Quantum periods for 3-dimensional Fano manifolds. Geometry and Topology, 20(1), https://doi.org/10.2140/gt.2016.20.103

The quantum period of a variety X is a generating function for certain Gromov-Witten invariants of X which plays an important role in mirror symmetry. In this paper we compute the quantum periods of all 3-dimensional Fano manifolds. In particular we... Read More about Quantum periods for 3-dimensional Fano manifolds.

Statistics of eigenvectors in the deformed Gaussian unitary ensemble of random matrices (2016)
Journal Article
Truong, K., & Ossipov, A. (2016). Statistics of eigenvectors in the deformed Gaussian unitary ensemble of random matrices. Journal of Physics A: Mathematical and Theoretical, 49(14), https://doi.org/10.1088/1751-8113/49/14/145005

We study eigenvectors in the deformed Gaussian unitary ensemble of random matrices $H=W\tilde{H}W$, where $\tilde{H}$ is a random matrix from the Gaussian unitary ensemble and W is a deterministic diagonal matrix with positive entries. Using the supe... Read More about Statistics of eigenvectors in the deformed Gaussian unitary ensemble of random matrices.

Entanglement quantification made easy: polynomial measures invariant under convex decomposition (2016)
Journal Article
Regula, B., & Adesso, G. (2016). Entanglement quantification made easy: polynomial measures invariant under convex decomposition. Physical Review Letters, 116, Article 070504. https://doi.org/10.1103/PhysRevLett.116.070504

Quantifying entanglement in composite systems is a fundamental challenge, yet exact results are only available in few special cases. This is because hard optimization problems are routinely involved, such as finding the convex decomposition of a mixe... Read More about Entanglement quantification made easy: polynomial measures invariant under convex decomposition.

Assisted distillation of quantum coherence (2016)
Journal Article
Chitambar, E., Streltsov, A., Rana, S., Bera, M. N., Adesso, G., & Lewenstein, M. (2016). Assisted distillation of quantum coherence. Physical Review Letters, 116(7), https://doi.org/10.1103/PhysRevLett.116.070402

We introduce and study the task of assisted coherence distillation. This task arises naturally in bipartite systems where both parties work together to generate the maximal possible coherence on one of the subsystems. Only incoherent operations are a... Read More about Assisted distillation of quantum coherence.

Slowly rotating black holes in Einstein-æther theory (2016)
Journal Article
Barausse, E., Sotiriou, T. P., & Vega, I. (2016). Slowly rotating black holes in Einstein-æther theory. Physical Review D, 93(4), Article 44044. https://doi.org/10.1103/PhysRevD.93.044044

We study slowly rotating, asymptotically flat black holes in Einstein-æther theory and show that solutions that are free from naked finite area singularities form a two-parameter family. These parameters can be thought of as the mass and angular mome... Read More about Slowly rotating black holes in Einstein-æther theory.

Adaptive energy minimisation for hp-finite element methods (2016)
Journal Article
Houston, P., & Wihler, T. P. (2016). Adaptive energy minimisation for hp-finite element methods. Computers and Mathematics with Applications, 71(4), https://doi.org/10.1016/j.camwa.2016.01.002

This article is concerned with the numerical solution of convex variational problems. More precisely, we develop an iterative minimisation technique which allows for the successive enrichment of an underlying discrete approximation space in an adapti... Read More about Adaptive energy minimisation for hp-finite element methods.