Forthcoming events in this series


Wed, 29 Jan 2014
10:15
L4

Two exact solutions in the theory of biogenic mixing by microorganisms

Mitya Pushkin
(Department of Physics)
Abstract

Suspensions of active particles, such as swimming microorganisms, turn out to be efficient stirrers of the surrounding fluid. This fact may be directly relevant to the feeding and evolutionary strategies of swimming cells. Microfluidic devices exploring swimmers-induced mixing have been proposed. The possibility of a significant biogenic contribution to the ocean circulation is currently under intense debate. However, understanding fluctuations and the effective tracer diffusion in these non-equilibrium systems remains a challenge.  

In this talk we focus on the fundamentals of these processes.  We discuss the impediments to stirring by force-free microswimmers and give a classification of the possible stirring mechanisms. We show that enhanced mixing may arise due to entrainment of the surrounding fluid by individual swimmers moving on infinite straight trajectories. Our first exact result shows that the total amount of fluid entrained by a swimmer, also know as its Darwin drift, is finite and can be decomposed into a universal and model-dependent parts that have a clear physical meaning.

A different stirring mechanism arises for swimmers having curved trajectories. We show that the previously suggested model of swimmers moving in straight finite runs interspersed with random reorientations can be solved exactly. In particular, we calculate the effective tracer diffusion coefficient for a suspension of dipolar swimmers and show that swimmers confined to a plane give rise to a Levy flight process.

Our results provide a quantitative description of the enhanced tracer mixing in dilute suspensions of microswimmers. They agree with the results of numerical simulations and recent experiments with suspension of E. coli.

Wed, 17 Jul 2013

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

Dispersion of particles dropped on a liquid

Benoit Darrasse
(Ecole Polytechnique)
Abstract

The good use of condiments is one of the secrets of a tasty quiche. If you want to delight your guests, add a pinch of ground pepper or cinnamon to the yellow liquid formed by the mix of the eggs and the crème fraiche. Here, is a surprise : even if the liquid is at rest, the pinch of milled pepper spreads by itself at the surface of the mixture. It expands in a circular way, and within a few seconds, it covers an area equal to several times its initial one. Why does it spread like that ? What factors influence this dispersion ? I will present some experiments and mathematical models of this process.

Tue, 16 Jul 2013

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

Coarsening rates for the dynamics of interacting slipping droplets

Georgy Kitavtsev
(Max Planck Institute)
Abstract

*****     PLEASE NOTE THIS SEMINAR TAKES PLACE ON TUESDAY     *****

Reduced ODE models describing coarsening dynamics of droplets in nanometric polymer film interacting on solid substrate in the presence of large slippage at the liquid/solid interface are derived from one-dimensional lubrication equations. In the limiting case of the infinite slip length corresponding to the free suspended films a collision/absorption model then arises and is solved explicitly. The exact collision law is derived. Existence of a threshold at which the collision rates switch from algebraic to exponential ones is shown.

*****     PLEASE NOTE THIS SEMINAR TAKES PLACE ON TUESDAY     *****

Mon, 15 Jul 2013

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

Measuring ultralow interfacial tensions in microfluidics with magnetic particles

Scott Tsai
(Ryerson University)
Abstract

*****     PLEASE NOTE THIS SEMINAR TAKES PLACE ON MONDAY     *****

Ultralow interfacial tension mixtures have interfacial tensions that are 1,000 times, or more, lower than typical oil-water systems. Despite the recent utility of ultralow interfacial tension mixtures in industry and research, quantifying the interfacial tension remains challenging. Here I describe a technique that measures ultralow interfacial tensions by magnetically deflecting paramagnetic spheres in a co-flow microfluidic device. This method involves the tuning of the distance between the co-flowing interface and the magnetic field source, and observing the behavior of the magnetic particles as they approach the liquid-liquid interface--the particles either pass through or are trapped. I demonstrate the effectiveness of this technique for measuring very low interfacial tensions by testing solutions of different surfactant concentrations, and show that the results are comparable with measurements made using a spinning drop tensiometer.

*****     PLEASE NOTE THIS SEMINAR TAKES PLACE ON MONDAY     *****

Mon, 24 Jun 2013

10:00 - 10:30
OCCAM Common Room (RI2.28)

Energy equations and their fast solution

Prof. Tongxiang Gu
(Beijing)
Abstract

*****     PLEASE NOTE THIS SEMINAR WILL TAKE PLACE ON MONDAY 24TH JUNE 2013     *****

Energy equations describing magnetic and inertial confinement functions (ICF) are strongly coupled, time dependent non-linear PDEs. The huge disparity of the coefficients in the coupled non-linear equations brings tremendous numerical difficulties to get high resolution solutions. It results in highly ill-conditioned linear systems in each non-linear iteration. Solving the resulted non-linear systems is time-consuming which takes up to 90% in the total simulation time. Many customized numerical techniques have to be employed to get a robust and accurate solution.This talk will present an inexact Newton-Krylov-Schwarz framework to solve the problem, demonstrating how to integrate preconditioning, partial Jacobian matrix forming techniques, parallel computing techniques with the Newton-Krylov solvers to solve the challenging problem. The numerical results will be shown and other numerical problems will be mentioned.

*****     If anyone is planning to take the 11.36 train after the seminar to the NA conference in Glasgow a taxi from the Gibson building is being arranged. Please contact Jude, @email, to book a place in the taxi.     *****

Wed, 19 Jun 2013

12:00 - 13:00
OCCAM Common Room (RI2.28)

Swimming droplets and chimera clocks

Shashi Thutupalli
(Mechanical and Aerospace Engineering)
Abstract

*****     PLEASE NOTE THIS SEMINAR WILL COMMENCE AT 12.00     *****

I will present experimental work on collective dynamics in two different systems: (i) a collection of self propelled droplets and (ii) coupled mechanical oscillators.  

In the first part, I will talk about microswimmers made from water-in-oil emulsion droplets. Following a brief description of the swimming mechanism, I will discuss some of the collective effects that emerge in quasi 1 and 2 dimensional confinements of swimming droplets. Specifically, I dwell on hydrodynamic and volume exclusion interactions, only through which these droplets can couple their motions. 

In the second part, I will present recent results about an intriguing dynamic known as a chimera state. In the world of coupled oscillators, a chimera state is the co-existence of synchrony and asynchrony in a population of identical oscillators, which are coupled nonlocally. Following nearly 10 years of intense theoretical research, it has been an imminent question whether these chimera states exist in real systems. Recently, we built an experiment with of springs, swings and metronomes and realised, for the first time, these symmetry breaking states in a purely physical system.

*****     PLEASE NOTE THIS SEMINAR WILL COMMENCE AT 12.00     *****

Mon, 17 Jun 2013

12:00 - 13:00
OCCAM Common Room (RI2.28)

Multiscale Dataflow Computing

Dr Oskar Menser
(Imperial College London)
Abstract

*****     PLEASE NOTE THIS SEMINAR WILL TAKE PLACE ON MONDAY 17TH JUNE 2013     *****

Computing is an exercise of discretization of the real world into space, time, and value. While discretization in time and space is well understood in the sciences, discretization of value is a scientific domain full of opportunity. Maxeler's Multiscale Dataflow Computing allows the programmer to finely trade off discretization of value with real performance measured in wallclock time.

In this talk I will show the connection between discretization of value and Kolmogorov Complexity on one hand and approximation theory on the other. Utilizing the above concepts together with building general purpose computing systems based on dataflow concepts, has enabled us to deliver production systems for Oil & Gas imaging (modelling, multiple elimination, RTM, Geomechanics), Finance Risk (derivatives modelling and scenario analysis), as well as many scientific application such as computing weather models, Astrochemistry, and brain simulations. Algorithms range from 3D Finite Difference, Finite Elements (sparse matrix solvers), pattern matching, conjugate gradient optimization, to communication protocols and bitcoin calculations. Published results of users of our machines show a 20-50x total advantage in computations per unit space (1U) and computations per Watt.

*****     PLEASE NOTE THIS SEMINAR WILL TAKE PLACE ON MONDAY 17TH JUNE 2013     *****

Tue, 11 Jun 2013

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

In silico study of macromolecular crowding effects on biochemical signaling

Koichi Takahashi
(RIKEN)
Abstract

***** PLEASE NOTE THAT THIS WILL TAKE PLACE ON TUESDAY 11TH JUNE ****

Signal transduction pathways are sophisticated information processing machinery in the cell that is arguably taking advantage of highly non-idealistic natures of intracellular environments for its optimum operations. In this study, we focused on effects of intracellular macromolecular crowding on signal transduction pathways using single-particle simulations. We have previously shown that rebinding of kinases to substrates can remarkably increase processivity of dual-phosphorylation reactions and change both steady-state and transient responses of the reaction network. We found that molecular crowding drastically enhances the rebinding effect, and it shows nonlinear time dependency although kinetics at the macroscopic level still follows the conventional model in dilute media. We applied the rate law revised on the basis of these calculations to MEK-ERK system and compared it with experimental measurements.

***** PLEASE NOTE THAT THIS WILL TAKE PLACE ON TUESDAY 11TH JUNE ****

Wed, 13 Mar 2013

14:00 - 15:00
OCCAM Common Room (RI2.28)

Exact solutions to the total generalised variation minimisation problem

Konstantinos Papafitsoros
(University of Cambridge)
Abstract

********** PLEASE NOTE THE SPECIAL TIME **********

Total generalised variation (TGV) was introduced by Bredies et al. as a high quality regulariser for variational problems arising in mathematical image processing like denoising and deblurring. The main advantage over the classical total variation regularisation is the elimination of the undesirable stairscasing effect. In this talk we will give a small introduction to TGV and provide some properties of the exact solutions to the L^{2}-TGV model in the one dimensional case.

Wed, 06 Mar 2013

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

Using mathematics to understand, treat, and avoid hematological disease

Prof. Michael Mackey
(McGill)
Abstract

In this talk aimed at a general audience I will discuss the ways in which we have used mathematical models of the regulation of haematopoiesis (blood cell production) to understand haematological diseases, and suggest successful treatment strategies for these diseases. At the end I will talk about our current work on tailoring chemotherapy so that it has less damaging effects on the haematopoietic system and, consequently, improve the quality of life for patients being treated for a variety of tumours.

Tue, 05 Mar 2013

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

Accelerated Landweber methods based on co-dilated orthogonal polynomials

Dr Wolfgang Erb
(Universität zu Lübeck)
Abstract

******************** PLEASE NOTE THIS SEMINAR WILL TAKE PLACE ON TUESDAY ********************

Well-known iterative schemes for the solution of ill-posed linear equations are the Landweber iteration, the cg-iteration and semi-iterative algorithms like the $\nu$-methods. After introducing these methods, we show that for ill-posed problems a slight modification of the underlying three-term recurrence relation of the $\nu$-methods provides accelerated Landweber algorithms with better performance properties than the $\nu$-methods. The new semi-iterative methods are based on the family of co-dilated ultraspherical polynomials. Compared to the standard $\nu$-methods, the residual polynomials of the modified methods have a faster decay at the origin. This results in an earlier termination of the iteration if the spectrum of the involved operator is clustered around the origin. The convergence order of the modified methods turns out to be the same as for the original $\nu$-methods. The new algorithms are tested numerically and a simple adaptive scheme is developed in which an optimal dilation parameter is determined. At the end, the new semi-iterative methods are used to solve a parameter identification problem obtained from a model in elastography.

Wed, 27 Feb 2013

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

A model for a protein oscillator in Myxococcus xanthus

Dr Peter Rashkov
(Philipps-Universität Marburg)
Abstract

Cell polarity in the rod-shaped bacterium Myxococcus xanthus is crucial for the direction of movement of individual cells. Polarity is governed by a regulatory system characterized by a dynamic spatiotemporal oscillation of proteins between the opposite cell poles. A mathematical framework for a minimal macroscopic model is presented which produces self-sustained regular oscillations of the protein concentrations. The mathematical model is based on a reaction-diffusion PDE system and is independent of external triggers. Necessary conditions on the reaction terms leading to oscillating solutions are derived theoretically. Possible scenarios for protein interaction are numerically tested for robustness against parameter variation. Finally, possible extensions of the model will be addressed.

Wed, 20 Feb 2013

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

Multiscale challenges and the hybrid method for stochastic simulation of biochemical systems

Yang Cao
(Virginia Tech)
Abstract

Complex systems emerging from many biochemical applications often exhibit multiscale and multiphysics (MSMP) features: The systems incorporate a variety of physical processes or subsystems across a broad range of scales. A typical MSMP system may come across scales with macroscopic, mesoscopic and microscopic kinetics,
deterministic and stochastic dynamics, continuous and discrete state space, fastscale and slow-scale reactions, and species of both large and small populations. These complex features present great challenges in the modeling and simulation practice. The goal of our research is to develop innovative computational methods and rigorous fundamental theories to answer these challenges. In this talk we will start with introduction of basic stochastic simulation algorithms for biochemical systems and multiscale
features in the stochastic cell cycle model of budding yeast. With detailed analysis of these multiscale features, we will introduce recent progress on simulation algorithms and computational theories for multiscale stochastic systems, including tau-leaping methods, slow-scale SSA, and the hybrid method. 

Tue, 19 Feb 2013

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

Mathematical modelling with fully anisotropic diffusion

Thomas Hillen
(University of Alberta)
Abstract

***** PLEASE NOTE THIS SEMINAR WILL TAKE PLACE ON TUESDAY 19TH FEBRUARY *****

With "fully anisotropic" I describe diffusion models of the form u_t=\nabla \nabla (D(x) u), where the diffusion tensor appears inside both derivatives. This model arises naturally in the modeling of brain tumor spread and wolf movement and other applications. Since this model does not satisfy a maximum principle, it can lead to interesting spatial pattern formation, even in the linear case. I will present a detailed derivation of this model and discuss its application to brain tumors and wolf movement. Furthermore, I will present an example where, in the linear case, the solution blows-up in infinite time; a quite surprising result for a linear parabolic equation (joint work with K.J. Painter and M. Winkler).

Wed, 13 Feb 2013

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

Diffusion, aggregation, clustering of telomeres and polymer dynamics in the cell nucleus

David Holcman
(Ecole Normale Superieure)
Abstract

I propose to present modeling and experimental data about the organization of telomeres (ends of the chromosomes): the 32 telomeres in Yeast form few local aggregates. We built a model of diffusion-aggregation-dissociation for a finite number of particles to estimate the number of cluster and the number of telomere/cluster and other quantities. We will further present based on eingenvalue expansion for the Fokker-Planck operator, asymptotic estimation for the mean time a piece of a polymer (DNA) finds a small target in the nucleus.

Wed, 06 Feb 2013

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

Coalescence of drops on a substrate

Jacco Snoeijer
(University of Twente)
Abstract

When two drops come into contact they will rapidly merge and form a single drop. Here we address the coalescence of drops on a substrate, focussing on the initial dynamics just after contact. For very viscous drops we present similarity solutions for the bridge that connects the two drops, the size of which grows linearly with time. Both the dynamics and the self-similar bridge profiles are verified quantitatively by experiments. We then consider the coalescence of water drops, for which viscosity can be neglected and liquid inertia takes over. Once again, we find that experiments display a self-similar dynamics, but now the bridge size grows with a power-law $t^{2/3}$. We provide a scaling theory for this behavior, based on geometric arguments. The main result for both viscous and inertial drops is that the contact angle is important as it determines the geometry of coalescence -- yet, the contact line dynamics appears irrelevant for the early stages of coalescence.

Wed, 23 Jan 2013

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

Dielectrowetting driven spreading of droplets and shaping of liquid interfaces

Glen McHale
(Northumbria University)
Abstract

The contact angle of a liquid droplet on a surface can be controlled by making the droplet part of a capacitive structure where the droplet contact area forms one electrode to create an electrowetting-on-dielectric (EWOD) configuration [1]. EWOD introduces a capacitive energy associated with the charging of the solid-liquid interface, in addition to the surface free energy, to allow the contact angle, and hence effective hydrophilicity of a surface, to be controlled using a voltage. However, the substrate must include an electrode coated with a thin, and typically hydrophobic, solid insulating layer and the liquid must be conducting, typically a salt solution, and have a direct electrical contact. In this seminar I show that reversible voltage programmed control of droplet wetting of a surface can be achieved using non-conducting dielectric liquids and without direct electrical contact. The approach is based on non-uniform electric fields generated via interdigitated electrodes and liquid dielectrophoresis to alter the energy balance of a droplet on a solid surface (Fig. 1a,b). Data is shown for thick droplets demonstrating the change in the cosine of the contact angle is proportional to the square of the applied voltage and it is shown theoretically why this equation, similar to that found for EWOD can be expected [2]. I also show that as the droplet spreads and becomes a film, the dominant change in surface free energy to be expected occurs by a wrinkling/undulation of the liquid-vapor interface (Fig. 1c) [3,4]. This type of wrinkle is shown to be a method to create a voltage programmable phase grating [5]. Finally, I argue that dielectrowetting can be used to modify the dynamic contact angle observed during droplet spreading and that this is described by a modified form of the Hoffman-de Gennes law for the relationship between edge speed and contact angle. In this dynamic situation, three distinct regimes can be predicted theoretically and are observed experimentally. These correspond to an exponential approach to equilibrium, a pure Tanner’s law type power law and a voltage determined superspreading power law behavior [6]. 

Acknowledgements

GM acknowledges the contributions of colleagues Professor Carl Brown, Dr. Mike Newton, Dr. Gary Wells and Mr Naresh Sampara at Nottingham Trent University who were central to the development of this work. EPSRC funding under grant EP/E063489/1 is also gratefully acknowledged.

References

[1]   F. Mugele and J.C. Baret, “Electrowetting: From basics to applications”, J. Phys.: Condens. Matt., 2005, 17, R705-R774.

[2]  G. McHale, C.V. Brown, M.I. Newton, G.G. Wells and N. Sampara, “Dielectrowetting driven spreading of droplets”, Phys. Rev. Lett., 2011, 107, art. 186101.

[3]  C.V. Brown, W. Al-Shabib, G.G. Wells, G. McHale and M.I. Newton, “Amplitude scaling of a static wrinkle at an oil-air interface created by dielectrophoresis forces”, Appl. Phys. Lett., 2010,  97, art. 242904.

[4]  C.V. Brown, G. McHale and N.J. Mottram, “Analysis of a static wrinkle on the surface of a thin dielectric liquid layer formed by dielectrophoresis forces”, J. Appl. Phys. 2011, 110 art. 024107.

[5]  C.V. Brown, G. G. Wells, M.I. Newton and G. McHale, “Voltage-programmable liquid optical interface”, Nature Photonics, 2009, 3, 403-405.

[6]  C.V. Brown, G. McHale and N. Sampara, “Voltage induced superspreading of droplets”, submitted (2012)

Wed, 14 Nov 2012

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

A purely mechanical approach to the formation and propagation of aneurysms

Jose Merodio
(Universidad Politécnica de Madrid)
Abstract

One of the main problems occurring in the aorta is the development of aneurysms, in which case the artery wall thickens and its diameter increases. Suffice to say that many other factors may be involved in this process. These include, amongst others, geometry, non-homogeneous material, anisotropy, growth, remodeling, age, etc. In this talk, we examine the bifurcation of inflated thick-walled cylindrical shells under axial loading and its interpretation in terms of the mechanical response of arterial tissue and the formation and propagation of aneurysms. We will show that this mechanical approach is able to capture features of the mechanisms involved during the formation and propagation of aneurysms.

Wed, 07 Nov 2012

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

Non-linear modelling of active biohybrid materials

Luis Dorfmann
(Tufts)
Abstract

Recent advances in engineered muscle tissue attached to a synthetic substrate motivates the development of appropriate constitutive and numerical models. Applications of active materials can be expanded by using robust, non-mammalian muscle cells, such as those of Manduca sexta. In this talk we present a   continuum model that accounts for the stimulation of muscle fibers by introducing multiple stress-free reference configurations and for the hysteretic response by specifying a pseudo-elastic energy function. A simple example representing uniaxial loading-unloading is used to validate and verify the characteristics of the model. Then, based on experimental data of muscular thin films, a more complex case shows the qualitative potential of Manduca muscle tissue in active biohybrid constructs.

Wed, 31 Oct 2012

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

Reduced-order robust real time control

Professor Dennis McLaughlin
(Parsons Laboratory)
Abstract

Although the importance of hydrologic uncertainty is widely recognized it is rarely considered in control problems, especially real-time control. One of the reasons is that stochastic control is computationally expensive, especially when control decisions are derived from spatially distributed models. This talk reviews relevant control concepts and describes how reduced order models can make stochastic control feasible for computationally demanding applications. The ideas are illustrated with a classic problem -- hydraulic control of a moving contaminant plume.