The Mathematical Institute, University of Oxford, Eprints Archive

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Number of items: 92.

Kelly, S and Wickstead, B and Maini, P. K. and Gull, K (2011) Ab initio identification of novel regulatory elements in the genome of Trypanosma brucei by Bayesioan inference on sequence segmentation. PLOs One, 6 (10). e25666 (11 pages).

Cotter, S. L. and Vejchodsky, T. and Erban, R. (2011) Adaptive finite element method assisted by stochastic simulation of chemical systems. SIAM Journal on Scientific Computing . (Submitted)

Hall, C. L. (2011) Asymptotic analysis of a pile-up of edge dislocation. Materials Science and Engineering A . (Submitted)

Richardson, G. and Please, C. P. and Kirkpatrick, J. (2011) Asymptotic solution of a model for bilayer organic diodes and solar cells. SIAM Journal on Applied Mathematics . (Submitted)

Griffiths, I. M. and Bain, C. D. and Breward, C. J. W. and Chapman, S. J. and Howell, P. D. and Waters, S. L. (2011) An asymptotic theory for the re-equilibration of a micellar
surfactant solution.
SIAM Journal on Applied Mathematics . (Submitted)

Cotter, C. J. and Cotter, S. L. and Vialard, F. X. (2011) Bayesian data assimilation in shape registration. Inverse Problems . (Submitted)

Cooray, H. and Cicuta, P. and Vella, D. (2011) The Capillary Interaction Between Two Vertical Cylinders. Journal of Physics: Condensed Matter . (Submitted)

Davit, Y. and Quintard, M. (2011) Comment on “Frequency-dependent dispersion in porous media”. American Physical Society . (Submitted)

Murray, P J and Walter, A and Fletcher, A G and Edwards, C. M. and Tindall, M. J. and Maini, P. K. (2011) Comparing a discrete and continuum model of the intestinal crypt. Physical Biology, 8 (2). 026011 (11 pages. ISSN 1478-3975

Cotter, S. L. and Zygalakis, K. C. and Kevrekidis, I. G. and Erban, R. (2011) A Constrained Approach to Multiscale Stochastic Simulation of
Chemically Reacting Systems.
Journal of Chemical Physics . (Submitted)

Simpson, M J and Baker, R. E. (2011) Correcting mean-field approximations for spatially-dependent advection-diffusion-reaction processes. Physical Review E, 82 (4). 041905.

Duan, L. and Farmer, C. L. and Hoteit, I. and Luo, X. and Moroz, I. M. (2011) Data assimilation using bayesian filters and B-spline geological models. Institute of Physics: Conference Series . (Submitted)

MacNamara, S and Baker, R. E. and Maini, P. K. (2011) Distinguishing graded & ultrasensitive signalling cascade kinetics by the shape of morphogen gradients in Drosophila. Journal of Theoretical Biology, 285 (1). pp. 136-146.

Bassett, D S and Wymbs, N F and Porter, M A and Mucha, P J and Carlson, J M and Grafton , S T (2011) Dynamic reconfiguration of human brain networks during learning. Proceedings of the National Academy of Sciences of the USA, 118 (18). pp. 7641-7646.

Luo, C. and Majumdar, A. and Erban, R. (2011) The dynamics of bistable liquid crystal wells. Journal of Computational Physics . (Submitted)

Braun, R. J. (2011) Dynamics of the Tear Film. Annual Review of Fluid Mechanics . (Submitted)

Maini, P. K. (2011) Editorial. Bulletin of Mathematical Biology, 73 (1). p. 1. ISSN 0092-8240

Lai, Y. M. and Newby, J. M. and Bressloff, P. C. (2011) Effects of demographic noise on the synchronization of a metapopulation in a fluctuating environment. Physical Review Letters . (Submitted)

Soon, Y. W. and Clarke, T. M. and Zhang, W. and Agostinelli, T. and Kirkpatrick, J. and Dyer-Smith, C. and McCulloch, I. and Nelson, J. and Durrant, J. R. (2011) Energy versus electron transfer in organic solar cells: a comparison of the photophysics of two indenofluorene: fullerene blend films. Chemical Science . (Submitted)

Hamadeh, A. and Roberts, M.A.J. and August, E. and McSharry, P. E. and Maini, P. K. and Armitage, J. P. (2011) Feedback control architecture & the bacterial chemotaxis network. PLOS Computational Biology , 7 (5). 15 pages.

Murphy, K. E. and Hall, C. L. and Maini, P. K. and McCue, S. W. and McElwain, D. L. S. (2011) A fibrocontractive mechanochemical model of dermal wound
closure incorporating realistic growth factor kinetics.
Bulletin of Mathematical Biology . (Submitted)

Bressloff, P. C. and Newby, J. M. (2011) Filling of a Poisson trap by a population of random intermittent searchers. Physical Review E. . (Submitted)

Wagner, T. J. W. and Vella, D. (2011) Floating carpets and the delamination of elastic sheets. Physical Review Letters . (Submitted)

Neukirch, S. and Frelat, J. and Goriely, A. and Maurini, C. (2011) Frequency jumps in the planar vibrations of an elastic beam. Journal of Sound and Vibration . (Submitted)

Erban, R. and Haskovec, J. (2011) From individual to collective behaviour of coupled velocity jump processes: a locust example. Annales de l'Institut Henri Poincaré (C) Analyse Non Linéaire . (Submitted)

Bressloff, P. C. and Webber, M. (2011) Front propagation in stochastic neural fields. SIAM Journal on Applied Dynamical Systems . (Submitted)

Smith, N. A. S. and Peppin, S. S. L. and Ramos, A. M. (2011) Generalized enthalpy model of a high pressure shift freezing process. Royal Society . (Submitted)

Loessner, D. and Flegg, J. A. and Byrne, H. M. and Hall, C. L. and Moroney, T. J. and Clements, J. A. and McElwain, D. L. S. and Hutmacher, D. W. (2011) Growth of confined cancer spheroids: a combined experimental and mathematical modelling approach. Integrative Biology . (Submitted)

Goriely, A. and Neukirch, S. and Hausrath, A. (2011) Helices through 3 or 4 points? Note di Matematica . (Submitted)

Abdulle, A. and Cohen, D. and Vilmart, G. and Zygalakis, K. C. (2011) High order weak methods for stochastic differential equations based on modified equations. SIAM Journal on Scientific Computing . (Submitted)

Székely Jr., T. and Burrage, K. and Erban, R. and Zygalakis, K. C. (2011) Higher-order numerical methods for stochastic simulation of
chemical reaction systems.
Journal of Chemical Physics . (Submitted)

Cross, R. and McNamara, H. and Kalachev, L. and Pokrovski, A. (2011) Hysteresis and Post Walrasian Economics. Journal of Mathematical Economics . (Submitted)

Style, R. W. and Cocks, A. C. F. and Peppin, S. S. L. and Wettlaufer, J. S. (2011) Ice-lens formation and connement-induced supercooling in soils and other colloidal materials. Physical Review E . (Submitted)

März, T. (2011) Image inpainting based on coherence transport with adapted distance functions. SIAM Journal on Imaging Sciences . (Submitted)

Lippok, N. and Nielsen, P. and Vanholsbeeck, F. (2011) Improving the efficiency of optical coherence tomography by using the non-ideal behaviour of a polarising beam splitter. Optics Express .

Vella, D. and Ajdari, A. and Vaziri, A. and Boudaoud, A. (2011) The indentation of pressurized elastic shells: From polymeric capsules to yeast cells. Journal of the Royal Society Interface . (Submitted)

Woolley, T. E. and Baker, Ruth E. and Gaffney, E. A. and Maini, P. K. (2011) Influence of stochastic domain growth on pattern nucleation for diffusive systems with internal noise. Physical Review E, 84 (4). 041905-1. ISSN 1063-651X

Boston, E A J and Gaffney, E. A. (2011) The influence of toxicity constraints in models of chemotherapeutic protocol escalation. Mathematical Medicine & Biology, 28 (4). pp. 357-384.

Cho, S W and Kwak, S W and Woolley, T. E. and Lee, M J and Kim, E J and Baker, R. E. and Kim, H J and Shin, J S and Tickle, C and Maini, P. K. and Jung, H S (2011) Interactions between Shh, Sostdc1 and Wnt signaling and a new feedback loop for spatial patterning of the teeth. Development , 138 (9). pp. 1807-1816.

Newby, J. M. (2011) Isolating intrinsic noise sources in a stochastic genetic switch. Physical Biology . (Submitted)

Style, R. W. and Peppin, S. S. L. (2011) The kinetics of ice-lens growth in porous media. Journal of Fluid Mechanics . (Submitted)

McNamara, H. and Bower, G. and Dellar, P. J. (2011) A locally adaptive time-stepping algorithm for
petroleum reservoir simulations.
Applied Maths Journal . (Submitted)

Yates, C. A. and Burrage, K. (2011) Look before you leap: a confidence-based method for selecting species criticality while avoiding negative populations in $\tau$-leaping. The Journal of Chemical Physics, 134 (8). 084109-1.

Gaffney, E. A. and Gadelha, H and Smith, D J and Blake, J R and Kirkman-Brown, J C (2011) Mammalian Sperm Motility: Observation and Theory. Annual Review of Fluid Mechanics, 43 (2). pp. 501-528.

Sun, J and Bollt, E M and Porter, M A and Dawkins, M S (2011) A mathematical model for the dynamics and synchronization of cows. Physica D, 240 (19). pp. 1497-1509.

Martin, N K and Gaffney, E. A. and Gatenby, R A and Gillies, R. J. and Robey, I F and Maini, P. K. (2011) A mathematical model of tumour & blood pHe regulation: The HCO-3/CO2 buffering system. Mathematical Biosciences, 230 (1). pp. 1-11.

Venkatarman, C and Sekimura, T. and Gaffney, E. A. and Maini, P. K. (2011) Modeling parr-mark pattern formation during the early development of Amago trout. Physical Review E, 84 (4). 041923-1-049123-13. ISSN 1063-651X

Simpson, M J and Baker, R. E. and McCue, S. W. (2011) Models of collective cell spreading with variable cell aspect ration: a motivation for degenerate diffusion models. Physical Review E, 83 (2). 021901. ISSN 1063-651X

Giomi, L. and Bowick, M. J. and Ma, X. and Majumdar, A. (2011) Molecular Tilt on Monolayer-Protected Nanoparticles. A Letters Journal Exploring the Frontiers of Physics . (Submitted)

Hennessy, M. G. and Münch, A. (2011) A multiple scales approach to evaporation induced Marangoni convection. SIAM Journal on Applied Mathematics . (Submitted)

Perfahl, H and Byrne, H. M. and Chen, T and Estrella, V and Alarcon, T. and Lapin, A and Gatenby, R. A. and Gilles, R and Lloyd, M C and Maini, P. K. and Reuss, M and Owen, M. R. (2011) Multiscale modelling of vascular tumour growth in 3D: the roles of domain size & boundary condition. PLOs One, 6 (4). 17 pages.

Bressloff, P. C. and Webber, M. (2011) Neural field model of binocular rivalry waves. Journal of Computational Neuroscience . (Submitted)

Du, Q. and Gunzburger, M. and Lehoucq, R. B. and Zhou, K. (2011) A non-local vector calculus,non-local volume-constrained problems,and non-local balance laws. Mathematical Models and Methods in Applied Sciences . (Submitted)

Quezada de Luna, M. and Đuričković, B. and Goriely, A. (2011) Nonlinear waves in heterogeneous elastic rods via homogenization. International Journal of Nonlinear Mechanics . (Submitted)

Gallimore, L. S. and Whiteley, J. P. and Waters, S. L. and King, J. R. and Oliver, J. M. (2011) Nonuniqueness in a minimal model for cell motility. Mathematical Medicine and Biology . (Submitted)

Heath-Brown, D. R. (2011) A Note on the Chevalley--Warning Theorems. Uspekhi Matematicheskikh Nauk, 66 . pp. 223-232.

Hall, C. L. and Menon, S. N. and McCue, S. W. and McElwain, D. L. S. (2011) A novel model for one-dimensional morphoelasticity. Part I - Theoretical foundations. Journal of Mathematical Biology . (Submitted)

Menon, S. N. and Hall, C. L. and McCue, S. W. and McElwain, D. L. S. (2011) A novel model for one-dimensional morphoelasticity. Part II - Application to the contraction of fibroblast-populated collagen lattices. Journal of Mathematical Biology . (Submitted)

Fornberg, B. and Weideman, J. A. C. (2011) A Numerical Methodology for the Painlevé Equations. Journal of Computational Physics . (Submitted)

Luo, C. and Calderer, M. C. (2011) Numerical study of liquid crystal elastomers by a mixed finite element method. European Journal of Applied Mathematics . (Submitted)

Hall, C. L. and Markenscoff, X. (2011) On approaches to modelling lattice dislocations. Philosophical Magazine Letters . (Submitted)

Griffiths, I. M. and Bain, C. D. and Breward, C. J. W. and Colegate, D. M. and Howell, P. D. and Waters, S. L. (2011) On the predictions and limitations of the BeckerDoring model for reaction kinetics in micellar surfactant solutions. Journal of Colloid and Interface Science . (Submitted)

Prior, C. and Berger, M. A. (2011) On the shape of force–free field lines in the solar corona. Solar Physics . (Submitted)

Elliott, J. A. W. and Peppin, S. S. L. (2011) Particle trapping and banding in rapid solidification. Physical Review Letters . (Submitted)

Keener, J. P. and Newby, J. M. (2011) A perturbation analysis of spontaneous action potential initiation by stochastic ion channels. Physical Review E. . (Submitted)

Mihai, L. A. and Goriely, A. (2011) Positive or negative Poynting effect? The role of adscititious inequalities in hyperelastic materials. Proceedings of the Royal Society . (Submitted)

Woolley, T. E. and Baker, R. E. and Gaffney, E. A. and Maini, P. K. (2011) Power spectra methods for a stochastic description of diffusion on deterministically growing domains. Physical Review E, 84 (2). 021915-1-021915-15. ISSN 1063-651X

Davidovitch, B. and Schroll, R. D. and Vella, D. and Adda-Bedia, M. and Cerda, E. (2011) A prototypical model for tensional wrinkling in thin sheets. Proceeding of the National Academy of Sciences of the USA . (Submitted)

Bressloff, P. C. and Newby, J. M. (2011) Quasi-steady state analysis of two-dimensional random intermittent search processes. Physical Review E . (Submitted)

Kirchartz, T. and Pieters, B. E. and Kirkpatrick, J. and Rau, U. and Nelson, J. (2011) Recombination via tail states in polythiophene:fullerene solar cells. Physical Review B .

Yavari, A. and Goriely, A. (2011) Riemann-Cartan Geometry of nonlinear dislocation mechanics. Archive for Rational Mechanics and Analysis . (Submitted)

Epstein, M. and Goriely, A. (2011) Self-diffusion in remodelling and growth. Zeitschrift für angewandte Mathematik und Physik . (Submitted)

Plikus, M. V. and Baker, R. E. and Chen, C C and Fare, C and de La Cruz, D. and Andl, T and Maini, P. K. (2011) Self-organizing & stochastic behaviors during the regeneration of hair stem cells. Science, 332 (6029). p. 586.

Zygalakis, K. C. and Roose, T. (2011) A simple mathematical model for investigating the effect of cluster roots on plant nutrient uptake. European Journal of Physics . (Submitted)

Bron, A J and Gaffney, E. A. and Tiffany , J M and Yokoi, N (2011) A solute gradient in the tear meniscus I. A hypothesis to explain Marx's line. The Ocular Surface, 9 (2). pp. 70-91.

Bron, A J and Yokoi, N and Gaffney, E. A. and Tiffany , J M (2011) A solute gradient in the tear meniscus II. implications for lid margin disease, including meibomian gland dysfunction. The Ocular Surface, 9 (2). pp. 92-97.

Macdonald, C. B. and Brandman, J. and Ruuth, S. J. (2011) Solving Eigenvalue Problems on Curved Surfaces using the Closest Point Method. Journal of Computational Physics . (Submitted)

Goriely, A. and Tabor, M. (2011) Spontaneous rotational inversion in Phycomyces. Physical Review Letters . (Submitted)

Majumdar, A. and Prior, C. and Goriely, A. (2011) Stability estimates for a twisted rod under terminal loads: a three-dimensional study. Journal of Elasticity . (Submitted)

Woolley , T. E. and Baker, R. E. and Gaffney, E. A. and Maini, P. K. (2011) Stochastic reaction & diffusion on growing domains: understanding the breakdown of robust pattern formation. Physical Review E, 84 (4). 046216-1. ISSN 1063-651X

Klingbeil, G. and Erban, R. and Giles, M. B. and Maini, P. K. (2011) STOCHSIMGPU: parallel stochastic simulation for the sytems biology toolbox 2 for matlab. Bioinformatics, 27 (8). pp. 1170-1171.

Ketcheson, D. I. and Gottlieb, S. and Macdonald, C. B. (2011) Strong Stability Preserving Two-Step Runge-Kutta Methods. SIAM Journal on Numerical Analysis . (Submitted)

Moulton, D. E. and Goriely, A. (2011) Surface growth kinematics via local curve evolution. Journal of Mathematical Biology . (Submitted)

Henao, D. and Majumdar, A. (2011) Symmetry of uniaxial global Landau-de Gennes minimizers in the
theory of nematic liquid crystals.
SIAM Journal on Mathematical Analysis . (Submitted)

Burlakov, V. and Emptage, N. and Goriely, A. and Bressloff, P. C. (2011) Synaptic bistability due to nucleation and evaporation of receptor clusters. Physical Review Letters . (Submitted)

Soto, A M and Sonnenschein, C and Maini, P. K. (2011) Systems biology and cancer, [Editorial]. Progress in Biophysics & Molecular Biology, 106 (2). pp. 337-339.

Please, C. P. and Fulford, G. R. and McElwain, D. L. S. and Collins, M. J. (2011) Tear film thickness variations and the role of the tear meniscus. Mathematical Medicine and Biology - a Journal of the IMA . (Submitted)

Schofield, J W and Gaffney, E. A. and Gatenby, R A and Maini, P. K. (2011) Tumour angiogenesis: The gap between theory and experiment. Journal of Theoretical Biology, 274 (1). pp. 97-102.

Flegg, M. B. and Chapman, S. J. and Erban, R. (2011) The Two Regime method for optimizing stochastic reaction-diffusion simulations. Proceedings of the National Academy of Sciences . (Submitted)

Murphy, K. E. and Hall, C. L. and Maini, P. K. and McCue, S. W. and McElwain, D. L. S. (2011) A two-compartment mechanochemical model of the roles of
transforming growth factor β and tissue tension in dermal wound healing.
Journal of Theoretical Biology . (Submitted)

Flegg, J. A. and Byrne, H. M. and Flegg, M. B. and McElwain, D. L. S. (2011) Wound healing angiogenesis the clinical implications of a simple mathematical model. Journal of Theoretical Biology . (Submitted)

Vella, D. and Ajdari, A. and Vaziri, A. and Boudaoud, A. (2011) Wrinkling of pressurized elastic shells. Physical Review Letters . (Submitted)

This list was generated on Mon Apr 21 00:14:43 2014 BST.