Forthcoming events in this series

Thu, 20 Jun 2013

09:30 - 10:30
OCCAM Common Room (RI2.28)

### Understanding organogenesis in the kidney at the level of the components

Melissa Little
(Institute for Molecular Bioscience)
Fri, 14 Jun 2013

11:30 - 13:00
OCCAM Common Room (RI2.28)

### OCCAM Group Meeting

Various
(University of Oxford)
Abstract
• Fabian Spill - Stochastic and continuum modelling of angiogenesis
• Matt Saxton - Modelling the contact-line dynamics of an evaporating drop
• Almut Eisentraeger - Water purification by (high gradient) magnetic separation
Fri, 10 May 2013

11:30 - 13:00
OCCAM Common Room (RI2.28)

### OCCAM Group Meeting

Various
(University of Oxford)
Abstract
• Sean Lim - Full waveform inversion: a first look
• Alex Raisch - Bistable liquid crystal displays: modelling, simulation and applications
• Vladimir Zubkov - Mathematical model of kidney morphogenesis
Fri, 12 Apr 2013

11:30 - 13:00
OCCAM Common Room (RI2.28)

### OCCAM Group Meeting

Various
Abstract
• Jen Pestana - Fast multipole method preconditioners for discretizations of elliptic PDEs
• Derek Moulton - A tangled tale: hunt for the contactless trefoil
• Thomas Lessines - Morphoelastic rods - growing rings, bilayers and bundles: foldable tents, shooting plants, slap bracelets & fibre reinforced tubes
Fri, 08 Mar 2013

11:30 - 13:00
OCCAM Common Room (RI2.28)

### OCCAM Group Meeting

Various
(OCCAM)
Abstract
• Wonjung Lee - Adaptive approximation of higher order posterior statistics
• Amy Smith - Multi-scale modelling of fluid transport in the coronary microvasculature
• Mark Curtis - The Stokes flow around arbitrary slender bodies
Fri, 08 Feb 2013

11:30 - 13:00
OCCAM Common Room (RI2.28)

### OCCAM Group Meeting

Various
(OCCAM, University of Oxford)
Abstract
• Jean-Charles Seguis - Simulation in chemotaxis and comparison of cell models
• Laura Kimpton (née Gallimore) - A viscoelastic two-phase flow model of a crawling cell
• Benjamin Franz - Particles and PDEs and robots
Fri, 11 Jan 2013

11:30 - 13:00
OCCAM Common Room (RI2.28)

### OCCAM Group Meeting

Various
Abstract
• Kiran Singh - Multi-body dynamics in elastocapillary systems
• Graham Morris - Investigating a catalytic mechanism using voltammetry
• Thomas Woolley - Cellular blebs: pressure-driven axisymmetric, membrane protrusions
Fri, 14 Dec 2012

11:30 - 13:00
OCCAM Common Room (RI2.28)

### OCCAM Group Meeting

Various
Abstract
• Victor Burlakov - Understanding the growth of alumina nanofibre arrays
• Brian Duffy - Measuring visual complexity of cluster-based visualisations
• Chris Bell - Autologous chemotaxis due to interstitial flow
Fri, 09 Nov 2012

11:30 - 13:00
OCCAM Common Room (RI2.28)

### OCCAM Group Meeting

Various
Abstract
• Joseph Parker - Numerical algorithms for the gyrokinetic equations and applications to magnetic confinement fusion
• Rita Schlackow - Global and functional analyses of 3' untranslated regions in fission yeast
• Peter Stewart - Creasing and folding of fibre-reinforced materials
Fri, 12 Oct 2012

11:30 - 13:00
OCCAM Common Room (RI2.28)

### OCCAM Group Meeting

Various
Abstract
• Matt Webber - ‘Stochastic neural field theory’
• Yohan Davit - ‘Multiscale modelling of deterministic problems with applications to biological tissues and porous media’
• Patricio Farrell - ‘An RBF multilevel algorithm for solving elliptic PDEs’
Thu, 20 Sep 2012

10:15 - 11:15
OCCAM Common Room (RI2.28)

### Transport through composite membranes: Support properties, film morphology and their impact on flux, rejection and fouling

Guy Ramon
(Princeton)
Abstract

Composite membranes comprised of an ultra-thin coating film formed over a porous support membrane are the basis for state-of-the-art reverse osmosis (RO) and nanofiltration (NF) membranes, offering the possibility to independently optimize the support membrane and the coating film. However, limited information exists on transport through such composite membrane structures. Numerical calculations have been carried out in order to probe the impacts of the support membrane skin-layer pore size and porosity, support membrane bulk micro-porosity, and coating film thickness and morphology (i.e. surface roughness) on solvent and solute transport through composite membranes. Results suggest that the flux and rejection of a composite membrane may be fine-tuned, by adjusting support membrane skin layer porosity and pore size, independent of the properties of the coating film. Further, the water flux over the membrane surface is unevenly distributed, creating local ‘hot spots’ of high flux that may govern initial stages of membrane fouling and scaling. The analysis provides important insight on how the non-trivial interaction of support properties and film roughness may result in widely varying transport properties of the composite structure. In particular, the simulations reveal inherent trade-offs between flux, rejection and fouling propensity (the latter due to ‘hot spots’), which are purely consequences of geometrical factors, irrespective of materials chemistry.

Fri, 14 Sep 2012

11:30 - 13:00
OCCAM Common Room (RI2.28)

### OCCAM Group Meeting

Various
Abstract
• Alfonso Bueno - Recent advances in mathematical modelling of cardiac tissue: A fractional step forward
• Matt Moore - Oblique water entry
• Matt Hennessy - Mathematical problems relating to organic solar cell production
Tue, 11 Sep 2012

10:15 - 11:15
OCCAM Common Room (RI2.28)

### Universal behavior of topological defects in nematic liquid crystals

Samo Kralj
(University of Maribor)
Abstract

Topological defects (TDs) are unavoidable consequence of continuous symmetry breaking phase transitions. They exhibit several universal features and often span apparently completely different systems. Particularly convenient testing ground to study basic physics of TDs are liquid crystals (LCs) due to their softness, liquid character and optical anisotropy. In the lecture I will present our recent theoretical studies of TDs in nematic LCs, which are of interest also to other branches of physics.

I will first focus on coarsening dynamics of TDs following the isotropic-nematic phase transition. Among others we have tested the validity of the Kibble-Zurek [1,2] prediction on the size of the so called protodomains, which was originally derived to estimate density of TDs as a function of inflation time in the early universe. Next I will consider nematic LC shells [3]. These systems are of interest because they could pave path to mm sized scaled crystals exhibiting different symmetries. Particular attention will be paid to curvature induced unbinding of pairs of topological defects. This process might play important role in membrane fission processes.

[1] W.H. Zurek, Nature 317, 505 (1985).

[2] Z. Bradac et al.,  J.Chem.Phys 135, 024506 (2011)

[3] S. Kralj et al.,  Soft Matter 7, 670 (2011); 8, 2460  (2012).

Fri, 27 Jul 2012

11:00 - 13:00
OCCAM Common Room (RI2.28)

### OCCAM Group Meeting

Various
Abstract
• James Herterich         -           Mathematical modelling of water purification
• Paul Roberts               -           Mathematical models of retinal oxygen distribution
• Stephen O'Keeffe       -           Mathematical modelling of growth and stability in biological structures
• Andrey Melnik             -           Dynamics of anisotropic remodelling in elastic tissues

Fri, 13 Jul 2012

11:30 - 13:00
OCCAM Common Room (RI2.28)

### OCCAM Group Meeting

Various
Abstract
• Yujia Chen - Solving Surface Poisson's Equation via the Closest Point Method
• Alex Lewis - Modelling liquid crystal devices
• Georgina Lang - Modelling of Brain Tissue Swelling
Fri, 08 Jun 2012

11:30 - 13:00
OCCAM Common Room (RI2.28)

### OCCAM Group Meeting

Various
Abstract
• Savina Joseph - Current generation in solar cells
• Shengxin Zhu - Spectral distribution, smoothing effects and smoothness matching for radial basis functions
• Ingrid von Glehn - Solving surface PDEs with the closest point method
Fri, 11 May 2012

11:30 - 13:00
OCCAM Common Room (RI2.28)

### OCCAM Group Meeting

Various
Abstract
• Chong Luo - Microscopic models for planar bistable liquid crystal device
• Laura Gallimore - Modelling Cell Motility
• Yi Ming Lai - Stochastic Oscillators in Biology
Tue, 08 May 2012

10:15 - 11:15
OCCAM Common Room (RI2.28)

### Stability of periodic structures: from composites to crystal lattices

Nicolas Triantafyllidis
(Ecole Polytechnique)
Abstract

Stability plays an important role in engineering, for it limits the load carrying capacity of all kinds of structures. Many failure mechanisms in advanced engineering materials are stability-related, such as localized deformation zones occurring in fiber-reinforced composites and cellular materials, used in aerospace and packaging applications. Moreover, modern biomedical applications, such as vascular stents, orthodontic wire etc., are based on shape memory alloys (SMA’s) that exploit the displacive phase transformations in these solids, which are macroscopic manifestations of lattice-level instabilities.

The presentation starts with the introduction of the concepts of stability and bifurcation for conservative elastic systems with a particular emphasis on solids with periodic microstructures. The concept of Bloch wave analysis is introduced, which allows one to find the lowest load instability mode of an infinite, perfect structure, based solely on unit cell considerations. The relation between instability at the microscopic level and macroscopic properties of the solid is studied for several types of applications involving different scales: composites (fiber-reinforced), cellular solids (hexagonal honeycomb) and finally SMA's, where temperature- or stress-induced instabilities at the atomic level have macroscopic manifestations visible to the naked eye.

Fri, 27 Apr 2012

10:15 - 11:15
OCCAM Common Room (RI2.28)

### Lymphatic system biomechanics and pumping

Jimmy Moore
(Texas A&M)
Fri, 20 Apr 2012

11:30 - 13:00
OCCAM Common Room (RI2.28)

### OCCAM Group Meeting

Various
Abstract
• Thomas März - Calculus on surfaces with general closest point functions
• Jay Newby - Modeling rare events in biology
• Hugh McNamara - Stochastic parameterisation and variational multiscale
Tue, 13 Mar 2012

10:15 - 11:15
OCCAM Common Room (RI2.28)

### Some symmetry results for the Ginzburg Landau equations

(University of Rome Sapienza)
Abstract

We discuss new symmetry results for nonconstant entire local minimizers of the standard Ginzburg-Landau functional  for maps in ${H}^{1}_{\rm{loc}}(\mathbb{R}^3;\mathbb{R}^3)$ satisfying a natural energy bound.

Up to  translations and rotations, such solutions of the Ginzburg-Landau system are given by an explicit map equivariant under the action of the orthogonal group.

More generally, for any $N\geq 3$ we  characterize the $O(N)-$equivariant vortex solution for Ginzburg-Landau type equations in the $N-$dimensional Euclidean space and we prove its local energy minimality for the corresponding energy functional.

Fri, 09 Mar 2012

11:00 - 13:00
OCCAM Common Room (RI2.28)

### OCCAM Group Meeting

Various
Abstract
• Graham Morris - 'Topics in Voltammetry'
• James Lottes - 'Algebraic Multigrid for Nonsymmetric Systems'
• Amy Smith - 'Multi-scale modelling of blood flow in the coronary microcirculation'
Thu, 01 Mar 2012

10:15 - 11:15
OCCAM Common Room (RI2.28)

### Solution of Hyperbolic Systems of Equations on Sixty-Five Thousand Processors... In Python!

(KAUST)
Abstract

As Herb Sutter predicted in 2005, "The Free Lunch is Over", software programmers can no longer rely on exponential performance improvements from Moore's Law.  Computationally intensive software now rely on concurrency for improved performance, as at the high end supercomputers are being built with millions of processing cores, and at the low end GPU-accelerated workstations feature hundreds of simultaneous execution cores.  It is clear that the numerical software of the future will be highly parallel, but what language will it be written in?

Over the past few decades, high-level scientific programming languages have become an important platform for numerical codes. Languages such as MATLAB, IDL, and R, offer powerful advantages: they allow code to be written in a language more familiar to scientists and they permit development to occur in an evolutionary fashion, bypassing the relatively slow edit/compile/run/plot cycle of Fortran or C. Because a scientist’s programming time is typically much more valuable than the computing cycles their code will use, these are substantial benefits. However, programs written in such languages are not portable to high performance computing platforms and may be too slow to be useful for realistic problems on desktop machines. Additionally, the development of such interpreted language codes is partially wasteful in the sense that it typically involves reimplementation (with associated debugging) of some algorithms that already exist in well-tested Fortran and C codes.  Python stands out as the only high-level language with both the capability to run on parallel supercomputers and the flexibility to interface with existing libraries in C and Fortran.

Our code, PyClaw, began as a Python interface, written by University of Washington graduate student Kyle Mandli, to the Fortran library Clawpack, written by University of Washington Professor Randy LeVeque.  PyClaw was designed to build on the strengths of Clawpack by providing greater accessibility.  In this talk I will describe the design and implementation of PyClaw, which incorporates the advantages of a high-level language, yet achieves serial performance similar to a hand-coded Fortran implementation and runs on the world's fastest supercomputers. It brings new numerical functionality to Clawpack, while making maximal reuse of code from that package.  The goal of this talk is to introduce the design principles we considered in implementing PyClaw, demonstrate our testing infrastructure for developing within PyClaw, and illustrate how we elegantly and efficiently distributed problems over tens of thousands of cores using the PETSc library for portable parallel performance.  I will also briefly highlight a new mathematical result recently obtained from PyClaw, an investigation of solitary wave formation in periodic media in 2 dimensions.

Fri, 10 Feb 2012

11:30 - 13:00
OCCAM Common Room (RI2.28)

### OCCAM Group Meeting

Various
Abstract
• Jean Charles Seguis - The fictitious domain method applied to hybrid simulations in biology
• Chris Farmer - Data assimilation and parameter estimation
• Mark Curtis - Stokes' flow, singularities and sperm
Fri, 13 Jan 2012

11:30 - 13:00
OCCAM Common Room (RI2.28)

### OCCAM Group Meeting

Various
Abstract
• Cameron Hall - Dislocations and discrete-to-continuum asymptotics: the summary
• Kostas Zygalakis - Multi scale methods: theory numerics and applications
• Lian Duan - Barcode Detection and Deconvolution in Well Testing