Research Outputs for May 2014

Hydrodynamic persistence within very dilute two-dimensional suspensions of squirmers

RJ Clarke, MD Finn, M MacDonald
Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 10.1098/rspa.2013.0508

In this study, we consider suspensions of swimming microorganisms in situations where we might expect the promotion of two-dimensional flow, such as within thin fluid films. Given that two-dimensional, inertialess flows are notoriously long-ranged (although not afflicted by Stokes paradox in the case of self-motile bodies), this raises interesting questions around the care which must be taken with the semi-dilute assumption in such situations. Adopting the prototype squirmer as a model of a swimming microorganisms of the type previously considered, we find that although the flowfield decays algebraically with the characteristic separation distance between microorganisms, there remains a finite interaction between the squirmers even at asymptotically large distances. This finding is further borne out by asymptotic analysis, which confirms that the limiting form of the far-field interaction depends solely upon the relative orientation between the microorganisms. Those which swim in the same general direction are seen to experience very large lateral displacements (many times the size of the displacements experienced owing to interactions between less well-aligned swimmers). This clearly has potential implications for very dilute suspensions in which squirmers become broadly aligned in their swimming direction (e.g. during chemotaxis). We show that hydrodynamically enhanced cell spreading, previously reported for denser suspensions, can persist even at extreme dilutions. Moreover, we demonstrate that this induced spreading can continue in the presence of potentially decohering Brownian effects.

Efficient Bayesian inference under the structured coalescent

TG Vaughan, D Kühnert, A Popinga, D Welch, AJ Drummond
Bioinformatics 10.1093/bioinformatics/btu201

MOTIVATION: Population structure significantly affects evolutionary dynamics. Such structure may be due to spatial segregation, but may also reflect any other gene-flow-limiting aspect of a model. In combination with the structured coalescent, this fact can be used to inform phylogenetic tree reconstruction, as well as to infer parameters such as migration rates and sub-population sizes from annotated sequence data. However, conducting Bayesian inference under the structured coalescent is impeded by the difficulty of constructing Markov Chain Monte Carlo sampling algorithms (samplers) capable of efficiently exploring the state space.

 

RESULTS: In this paper, we present a new MCMC sampler capable of sampling from posterior distributions over structured trees: timed phylogenetic trees in which lineages are associated with the distinct sub-population in which they lie. The sampler includes a set of MCMC proposal functions which offer significant mixing improvements over a previously published method. Furthermore, its implementation as a BEAST 2 package ensures maximum flexibility with respect to model and prior specification. We demonstrate the usefulness of this new sampler by using it to infer migration rates and effective population sizes of H3N2 influenza between New Zealand, New York and Hong Kong from publicly-available HA sequences under the structured coalescent.

 

AVAILABILITY: The sampler has been implemented as a publicly-available BEAST 2 package which is distributed under version 3 of the GNU General Public License (GPL) at http://compevol.github.io/MultiTypeTree.

The use of Numerical Weather Prediction and a Lagrangian transport (NAME-III) and dispersion (ASHFALL) models to explain patterns of observed ash deposition and dispersion following the August 2012 Te Maari, New Zealand eruption

Richard Turner, Stuart Moore, Natalia Pardo, Gabor Kereszturi, Michael Uddstrom, Tony Hurst, Shane Cronin
Journal of Volcanology and Geothermal Research 10.1016/j.jvolgeores.2014.05.017

The August 6, 2012 Te Maari, New Zealand eruption produced a very small ash-dominated plume (~ 230,000 m3, 8-10 km high) that was rapidly and widely dispersed, covering 1600 km2 within an hour. This paper documents for the August 6, 2012 Te Maari eruption the upper level (troposphere) plume movement based on ash-detection algorithms applied to IR satellite imagery. It also presents the distribution of airborne ash and wind-influenced ashfall as determined by NAME-III aerial dispersion modelling using observed particle characteristics and grainsize distribution measurements (that are also presented) and compares the ashfall with observations.

The upper level (troposphere) ash movement was also evaluated from ash-detection algorithms, applied to infra-red satellite imagery and the resulting distributions were compared to those forecast by the numerical dispersion models. Forecasts of upper level ash-dispersion patterns explained the satellite imagery observations well, predicting the correct altitudes when using plausible ash size distributions and release levels. Patterns in proximal ashfall could only be partly explained by aerial dispersal of large particles released at low altitudes in the eruption column. The extreme distal (100-150 km away) observed ashfall distributions also cannot be fully explained by NAME-III when using; reasonably prescribed initial particle size distributions, eruption column height, eruption timing, well forecast winds, and dry sedimentation processes. Aggregation and ice nucleation effects (observed in deposits) were not included in the ash dispersion model, but appear as a plausible mechanism to account for the observed fraction of wind dispersed ash particles < 30 μm deposited but not captured by the models.

Optimal composition of atomic orbital basis sets for recovering static correlation energies

Andrew J Wallace, Deborah L Crittenden
The journal of physical chemistry. A 10.1021/jp500686m

Static correlation energies (Estat) are calculated in a range of basis sets for a chemically diverse collection of atoms and molecules. The reliability of a basis set in capturing Estat is assessed according to the following: mean and maximum absolute deviations from near-exact Estat estimates, monotonic convergence to the complete basis set limit, and ability to capture Estat accurately independent of changes in geometry, molecular size, and electronic configuration. Within the polarization and correlation-consistent basis set series, triple-ζ basis sets are the smallest that can reliably capture Estat. The cc-pVTZ basis set performs particularly well, recovering Estat to chemical accuracy for all atoms and molecules in our data set. A series of customized basis sets are constructed by stripping polarization functions from, and swapping polarization functions among, existing basis sets. Basis sets without polarization functions are incapable of accurately recovering Estat. Basis sets with a near-complete set of s, p, and d functions can approach chemical accuracy in maximum absolute error. However, this may be achieved at lower computational cost by using a well balanced triple-ζ basis set including f functions, along with a smaller number of s, p, and d functions. Recommended basis sets for calculating Estat with increasing accuracy at increasing computational cost are 6-311G(2d,2p), cc-pVTZ, and cc-pVQZ stripped of g functions.