Forthcoming events in this series
OCCAM Group Meeting
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
OCCAM Group Meeting
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
OCCAM Group Meeting
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
OCCAM Group Meeting
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
OCCAM Group Meeting
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
OCCAM Group Meeting
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
OCCAM Group Meeting
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
OCCAM Group Meeting
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
OCCAM Group Meeting
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’
Transport through composite membranes: Support properties, film morphology and their impact on flux, rejection and fouling
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.
OCCAM Group Meeting
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
Universal behavior of topological defects in nematic liquid crystals
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).
OCCAM Group Meeting
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
OCCAM Group Meeting
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
OCCAM Group Meeting
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
OCCAM Group Meeting
Abstract
- Chong Luo - Microscopic models for planar bistable liquid crystal device
- Laura Gallimore - Modelling Cell Motility
- Yi Ming Lai - Stochastic Oscillators in Biology
Stability of periodic structures: from composites to crystal lattices
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.
OCCAM Group Meeting
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
Some symmetry results for the Ginzburg Landau equations
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.
OCCAM Group Meeting
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'
Solution of Hyperbolic Systems of Equations on Sixty-Five Thousand Processors... In Python!
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.
OCCAM Group Meeting
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
OCCAM Group Meeting
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
OCCAM Group Meeting
Abstract
- Ian Griffiths - Control and optimization in filtration and tissue engineering
- Vladimir Zubkov - Comparison of the Navier-Stokes and the lubrication models for the tear film dynamics
- Victor Burlakov - Applying the ideas of 1-st order phase transformations to various nano-systems
OCCAM Group Meeting
Abstract
- Derek Moulton - "Growth and morphology of seashells"
- Simon Cotter - "A Hybrid stochastic finite element method for solving Fokker-Planck equations"
- Apala Majumdar -"The theory of liquid crystals - analysis, computation and applications"
11:15
OCCAM Group Meeting
Abstract
- Rob Style - "Drying and freezing stuff - the wrap up"
- Maria Bruna-Estrach - “Including excluded-volume effects into diffusion of hard spheres"
- Patricio Farrell - “Multiscale Analysis for Elliptic Boundary Value Problems using Radial Basis Functions"
OCCAM Group Meeting
Abstract
- Benjamin Franz - "Hybrid modelling of individual movement and collective behaviour"
- Ingrid Von Glehn - "Image Inpainting on Surfaces"
- Rita Schlackow - "Genome-wide analysis of transcription termination regions in fission yeast"
OCCAM Group Meeting
Abstract
- James Kirkpatrick - "Drift Diffusion modelling of organic solar cells: including electronic disorder".
- Timothy Reis - "Moment-based boundary conditions for the Lattice Boltzmann method".
- Matthew Moore - "Introducing air cushioning to Wagner theory".
- Matthew Hennessy - “Organic Solar Cells and the Marangoni Instability”.
OCCAM Group Meeting
Abstract
- Wan Chen - “From Brownian Dynamics to Transition Rate Theory: An Ion Channel Example”
- Thomas Lessinnes - "Neuronal growth: a mechanical perspective"
- Savina Joseph - “Current generation in solar cells”
- Shengxin Zhu - “The Numerical Linear Algebra of Approximation involving Radial Basis Functions”
OCCAM Group Meeting
Abstract
- Thomas Maerz - ‘Some scalar conservation laws on some surfaces - Closest Point Method’
- Chong Luo - ‘Numerical simulation of bistable switching in liquid crystals’
- Radek Erban - ‘Half-way through my time at OCCAM: looking backwards, looking forwards’
- Hugh McNamara - ‘Challenges in locally adaptive timestepping for reservoir simulation’
OCCAM Group Meeting
Abstract
- Laura Gallimore - Modelling Cell Motility
- Y. M. Lai - Stochastic Synchronization of Neural Populations
- Jay Newby - Quasi-steady State Analysis of Motor-driven Transport on a 2D Microtubular Network
OCCAM Group Meeting
Abstract
- Chris Farmer - Numerical simulation of anisotropic diffusion
- Jean-Charles Seguis - Introduction to the Fictitious Domain Method for Finite Elements Method
- Amy Smith - Multiscale Models of Cardiac Contraction and Perfusion
- Mark Curtis - Developing a novel Slender Body Theory incorporating regularised singularities
OCCAM Group Meeting
Abstract
- Nick Hale - 'Rectangular pseudospectral differentiation matrices' or, 'Why it's not hip to be square'
Boundary conditions in pseudospectral collocation methods
are imposed by removing rows of the discretised differential operator and
replacing them with others to enforce the required conditions at the boundary.
A new approach, based upon projecting the discrete operator onto a lower-degree
subspace to create a rectangular matrix and applying the boundary condition
rows to ‘square it up’, is described.
We show how this new projection-based method maintains
characteristics and advantages of both traditional collocation and tau methods.
- Cameron Hall - 'Discrete-to-continuum asymptotics of functions defined as sums'
When attempting to homogenise a large number of dislocations, it becomes important to express the stress in a body due to the combined effects of many dislocations. Assuming linear elasticity, this can be written as a simple sum over all the dislocations. In this talk, a method for obtaining an asymptotic approximation to this sum by simple manipulations will be presented. This method can be generalised to approximating one-dimensional functions defined as sums, and work is ongoing to achieve the same results in higher dimensions.
- Vladimir Zubkov - 'On the tear film modeling'
A great number of works about the tear film behaviour was published. The majority of these works based on modelling with the use of the lubrication approximation. We explore the relevance of the lubrication tear film model compare to the 2D Navier-Stokes model. Our results show that the lubrication model qualitatively describe the tear film evolution everywhere except region close to an eyelid margin. We also present the tear film behaviour using Navier-Stokes model that demonstrates that here is no mixing near the MCJ when the eyelids move relative to the eyeball.
- Kostas Zygalakis - 'Numerical methods for stiff stochastic differential equations'
Multiscale differential equations arise in the modelling of many important problems in the science and engineering. Numerical methods for such problems have been extensively studied in the deterministic case. In this talk, we will discuss numerical methods for (mean-square stable) stiff stochastic differential equations. In particular we will discuss a generalization of explicit stabilized methods, known as Chebyshev methods to stochastic problems.
OCCAM Group Meeting
Abstract
- Ian Griffiths - "Taylor Dispersion in Colloidal Systems".
- James Lottes - "Algebraic multigrid for nonsymmetric problems".
- Derek Moulton - "Surface growth kinematics"
- Rob Style - "Ice lens formation in freezing soils"
OCCAM Group Meeting
Abstract
- Simon Cotter presents: “Chemical Fokker-Planck equation and multiscale modelling of (bio)chemical systems”
- Lian Duan presents: “History matching problems using Bspline Parameterization”
- Chris Prior presents: “Helices, tubes and the Fourier Transform”
Volcanic test of climate mechanisms
Abstract
Strong explosive volcanic eruptions could inject in the lower stratosphere million tons of SO2, which being converted to sulfate aerosols, affect radiative balance of the planet for a few years. During this period the volcanic radiative forcing dominates other forcings producing distinct detectable climate responses. Therefore volcanic impacts provide invaluable natural test of climate nonlinearities and feedback mechanisms. In this talk I will overview volcanic impacts on tropospheric and strsatospheric temperature, ozone, high-latitude circulation, stratosphere-troposphere dynamic interaction, and focus on the long-term volcanic effect on ocean heat content and sea level.
10:10
An Introduction to multi-level simulation methods for problems with distorted grids or tensor coefficients
New numerical and asymptotic methods in applied PDEs
Abstract
1. "Approximate approximations" and accurate computation of high dimensional potentials.
2. Iteration procedures for ill-posed boundary value problems with preservation of the differential equation.
3. Asymptotic treatment of singularities of solutions generated by edges and vertices at the boundary.
4. Compound asymptotic expansions for solutions to boundary value problems for domains with singularly perturbed boundaries.
5. Boundary value problems in perforated domains without homogenization.
16:30
A stochastic model of large-scale brain activity
Abstract
We have recently found a way to describe large-scale neural
activity in terms of non-equilibrium statistical mechanics.
This allows us to calculate perturbatively the effects of
fluctuations and correlations on neural activity. Major results
of this formulation include a role for critical branching, and
the demonstration that there exist non-equilibrium phase
transitions in neocortical activity which are in the same
universality class as directed percolation. This result leads
to explanations for the origin of many of the scaling laws
found in LFP, EEG, fMRI, and in ISI distributions, and
provides a possible explanation for the origin of various brain
waves. It also leads to ways of calculating how correlations
can affect neocortical activity, and therefore provides a new
tool for investigating the connections between neural
dynamics, cognition and behavior
