ACADEMIC CV 1 Personal detailsgrant/longLeeds.pdf · My contribution 100% of lectures and exam, preparation, delivery and assessment. MATH2450 Mathematics for Geophysics III Number

ACADEMIC CV

1 Personal detailsDr. Grant LytheSCHOOL: MathematicsFACULTY: MAPSWORK TELEPHONE NUMBER: (0113) 3435132WORK EMAIL ADDRESS: [email protected] OF CURRENT POST: Professor of Applied MathematicsWEB PAGE: http://www1.maths.leeds.ac.uk/˜grant

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Contents

1 Personal details 1

2 Biographical information 3

3 Teaching 4i Summary of undergraduate teaching since 2011 . . . . . . . . . . . . . . 4ii Summary of postgraduate teaching since 2011 . . . . . . . . . . . . . . . 5iii Undergraduate teaching, supervision and tutoring . . . . . . . . . . . . . 6iv MSc and level-5 teaching and supervision . . . . . . . . . . . . . . . . . 8v Postgraduate teaching . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

4 Research 11i Principal Publications . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

i.1 Current articles: submitted, under revision, in final preparation . . 11i.2 Refereed contributions to journals . . . . . . . . . . . . . . . . . 11i.3 Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18i.4 Parts of Books . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

ii Presentations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19iii Supervision of postdoctoral workers . . . . . . . . . . . . . . . . . . . . 28iv Supervision of research students . . . . . . . . . . . . . . . . . . . . . . 29v PhD Transfer interviews . . . . . . . . . . . . . . . . . . . . . . . . . . 29vi Grant income . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29vii Some unsuccessful proposals . . . . . . . . . . . . . . . . . . . . . . . . 34

5 Scholarship 36

6 Enterprise and Knowledge Transfer 36

7 Academic Leadership 37i School . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

i.1 Mentoring/observation of peers . . . . . . . . . . . . . . . . . . 37ii Faculty and University . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

ii.1 Internal examiner . . . . . . . . . . . . . . . . . . . . . . . . . . 38ii.2 Postgraduate tutor, applied mathematics. 2012- . . . . . . . . . . 38ii.3 Socrates/Erasmus coordinator 2010-2012 . . . . . . . . . . . . . 39ii.4 Programme coordinator, Mathematics and Biology . . . . . . . . 39ii.5 Undergraduate Admissions 2005-2009 . . . . . . . . . . . . . . . 39

iii External . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40iii.1 Editorial and Referee service . . . . . . . . . . . . . . . . . . . . 40iii.2 External examiner . . . . . . . . . . . . . . . . . . . . . . . . . 41iii.3 External teaching . . . . . . . . . . . . . . . . . . . . . . . . . . 42

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2 Biographical informationPrevious employment

2000 Fellowship, Spanish Ministry of Education and Culture. Held at the UniversidadCarlos III de Madrid, Spain

1996-9 Director’s Postdoc, Los Alamos National Laboratory, USA

1995-6 Postdoc, Optique nonlineaire theorique, Universite Libre de Bruxelles, Belgium.

Qualifications

1994 Completed Ph.D Thesis Stochastic slow-fast dynamics,

Department of Applied Mathematics and Theoretical Physics,

University of Cambridge, U.K. (Trinity College)

Senior Rouse-Ball Scholar 1993, Knight Prize 1992

1990 Master of Science (Physics, 1st Class Hons), University of Auckland, New Zealand.

Commonwealth Scholarship 1990

1988 Visiting Scholarship, Nuclear Physics, Australian National University.

1987 Bachelor of Science, University of Auckland, New Zealand.

Senior Scholarship Physics 1987, Senior Prize Mathematics 1987

Membership of professional bodies

2006 Society for Industrial and Applied Mathematics

2007 London Mathematical Society

2009 British Society for Immunology

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3 Teaching

i Summary of undergraduate teaching since 2011

MATH3001 Final-year projects

I have acted as primary supervisor of the maximum number of students, 6 per year,and secondary supervisor of 6 more, every year since the module’s inception in2015-2016.

MATH3565 Mathematical Biology

Number of students 30-50

My contribution 100% of lectures and exam, preparation, delivery and assessment.

MATH2450 Mathematics for Geophysics III

Number of students 25

My contribution: 100% of lectures, course materials and exam, preparation, deliv-ery and assessment.

MATH2601 Computational Numerical Analysis

2015, 2017

Number of students 25-50

My contribution: 100% of lectures, course materials and exam, preparation, deliv-ery and assessment.

MATH1050 tutorials Calculus

Number of students groups of about 12

My contribution: tutor: biweekly tutorials, assessment of coursework

MATH1055 tutorials Numbers and Vectors

2016



MATH1015 tutorials Linear Algebra I



Assessor

• MATH1400 Modelling with Differential Equations (2015, 2016, 2017, 2018)

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• MATH1055 Numbers and Vectors (2014, 2015)

• MATH0380 (2018)

Exam marking: MATH2600, MATH5567

Relief lectures: MATH1920 (2012), MATH3396 (2013).

MATH3000 projects supervised: Hongwei Chen, Rong Shi, Christoforos Soutziss,Louis Kinsella, Amy Farrell.

Summer student project supervision

• Ruolin Wang (University of Sheffield) summer project on Green functions.

Final-year undergraduate project assessor

MATH3422 Victoria Green (2012)

MATH3422 Sorcha O’Sullivan (2013)

MATH3422 Abdul-Qadir Girach (2012)

MATH3422 Rebecca Scopes (2011)

MATH3422 Robin Johnson (2011)

Programme Coordinator I have designed and now coordinate the degree programme inBiology and Mathematics.

Study Abroad Coordinator I had overall responsibilty for MATH9001 and MATH9004,Year abroad for BSc programmes and Year abroad for MMath programme, in 2010-2011 and 2011-2012. In 2012-2013 and 2013-2014 I was part of the committeecharged with deciding on module marks.

ii Summary of postgraduate teaching since 2011

• MATH5566 Advanced Mathematical Biology

Number of students: 25-35My contribution: 100% of lectures, course materials and exam, preparation, deliv-

ery and assessment.

• Final-year undergraduate/Masters project supervision (level 5)

2014-2015 Laura Jarman “Branching Processes and Mathematical Medicine”

2013-2014 Mark Pierzchalski “Stochastic processes” (MATH5004)

2012-2013 Rhys Lleision-Jones “Stochastic Processes and Branching Processes inBiology” (MATH5004)

2012 Steph Dyson (MSc) “Stochastic Modelling in Immunology” (MATH5871)

• MAGIC065 Stochastic processes

My contribution: 4-8 lectures lectures per year, teleconferenced over the MAGICgrid, to a consortium of Universities.

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iii Undergraduate teaching, supervision and tutoring

• MATH3565 Mathematical Biology

2010, 2011, 2012, 2014, 2016, 2017, 2018 Typical number of students: 40.

• MATH2450 Mathematics for Geophysics III

Service teaching

2009, 2010, 2011 Number of students: 20

• MATH1915/6/7 Basic use of Computers for Mathematics.

First year, G100, 1MK and Joint Honours.

2004,5,6. Number of students: 100.

This course on use of software, including MAPLE, has been modernised and aug-mented with the addition of LATEX.

http://www1.maths.leeds.ac.uk/Applied/1916/

• MATH1970 Differential Equations

First year, G100, Engineering and Theoretical Physics.

2004, 2005 Number of students: 125-150.

In 2003, G100 was rearranged and two new courses, MATH1960 and MATH1970,created from the ashes of MATH1932 and MATH1942. I had to produce a newlecture course, plus examples sheets and answers for the G100 tutorials. I haveproduced a quantum leap forward in the quality of handouts and notes, typing upLaTeX versions of the examples and answers and making them available on theweb.


• MATH1942 Further ODEs and Multivariable Calculus

First year, G100, Engineering and Theoretical Physics.

2002, 2003.

• MATH0380 Foundation Applied Mathematics for Business

Foundation year.

2001, 2002, 2003, 2016 Number of students: 60-120.

This course did not exist before I taught it. It involved teaching large groups of for-eign students the basics of matrix algebra and quantitative techniques. Two lecturesand one examples class per week. Most students go on to the Business School, butsome have been accepted into the MK and MM programs. I found a large numberof capable students that could be a future source of foreign students for the Schoolof Maths.


• ad-hoc teaching for colleagues, away or on leave, including MATH1382 (2006),MATH3397 (2011), MATH1920 (2012), MATH3396 (2013).

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• Study Abroad CoordinatorI had overall responsibilty for MATH9001 and MATH9004, Year abroad for BScprogrammes and Year abroad for MMath programme, in 2010-2011 and 2011-2012.

• Exam marker, MATH2600 (2014)

• Exam marker, MATH5567 (2014)

• Assessor MATH1400 (2013-2016)

• Assessor MATH1055 (2012-2015)

• Assessor MATH1150 (2004-2008).

• Assessor MATH0370 (2001-2006).

• Research Council funded summer project supervision

1. David Franco 2008

2. Mark Day 2009

• Final-year level 3 project supervision

2012 Victoria Green (3MK) “Branching Processes and Biology”

2007-2008 Debra McDonagh (3MM) “Stochastic Differential Equations and Fi-nance”

2006-2007 Stephen Ryder (3MK) “First-order Stochastic Differential Equations andMaple Applications”

2004-2005 Eleanor Walton (3MK) “Stochastic calculus and Stochastic DifferentialEquations”

• Short Project supervision (MATH3000)

2014-2015 Amy Farrell, Sam Watson

2012-2013 Hon Wei Chen, Rong Shi

2010-11 Christoforos Soutzis, Louis Kinsella

2008-9 Alasdair Hunter

2006-7 Sarah Holian, Laura Smithson, Mark Wells.

2005-6 Alexander Wood, Claire Pacini, Xu Jianyun, Zeki Tezcan.

• Small group teaching (tutorials)The tutorial system has evolved iover the years and my responsibilities have in-cluded, most recently, MATH1055 and MATH1015. I have experience with G100,Joint Honours, G150 and theoretical physics tutorials and tutorials for students tak-ing maths modules as electives.

In addition, 2nd-, 3rd- and 4th-year students come to see me on a one-to-one basiswhen they have difficulties, whether my assigned personal tutees or not.

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• Personal tuteesAll students on the Biology and Mathematics degree programme are my personaltutees. I also have personal tutees on the Mathematics and Economics programme.

My current tutees are

Meng Hao Mathematics with Finance 1st year

Benjamin Martin Mathematics with Finance 1st year

Adam Nakhuda Mathematics with Finance 1st year

Zhao Xiao Mathematics with Finance 1st year

Kunyuan Yu Mathematics with Finance 1st year

Yuwei Zhang Mathematics with Finance 1st year

Jessica Bird Abroad/Industry 3rd Year Mathematics (Industrial)

Jack Blagbrough 2nd Year Biology and Mathematics

Sarah Brown 2nd Year Biology and Mathematics

Shannah Cunningham 3rd Year Mathematics

William Kirkham 3rd Year Mathematics

Georgina McCormick 3rd Year Mathematics

Emily McKechnie 2nd Year Mathematical Studies

Matthew Norman Abroad/Industry 3rd Year Biology and Mathematics (Industrial)

Michael O’Brien 3rd Year Mathematical Studies

Jack O’Donnell 3rd Year Mathematics

Tomas O’Neill 3rd Year Economics and Mathematics

Calum Pringle Abroad/Industry 3rd Year Mathematics (International)

Matthew Pye Abroad/Industry 3rd Year Economics and Mathematics (Industrial)

Nischal Shrestha Abroad/Industry 3rd Year Economics and Mathematics (Interna-tional)

Andrew Smith Abroad/Industry 3rd Year Economics and Mathematics (Industrial)

Edward Wright 3rd Year Economics and Mathematics

iv MSc and level-5 teaching and supervision

• MATH5566 Advanced Mathematical Biology

15-25 students, 2010, 2011, 2012, 2014, 2016, 2017, 2018.

• MATH5300 Applied Financial Modelling

Graduate level course, Business School.

2004, 2005, 2006, 2007, 2008, 2009 Number of students: 10-30.

[Project supervision]

2013-2014 Mark Pierzchalski Stochastic processes

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2012-2013 Rhys Williams Stochastic Processes and Branching Processes in Biol-ogy

2012, co-supervisor Steph Dyson (MSc. MATH5871) Exploring a stochastic modelof competing T-cell clonotypes

2008-2009 Mark Day (MNatSci) “Stochastic Modelling in Immunology”

2003-2004 Paula West (4MM) “Stochastic modelling of particle collisions”

v Postgraduate teaching

• Tutorials on mathematical modelling

given to PhD students on the four-year PhD Programme in Cardiovascular diseaseand diabetes

2015

• MATH5565 Mathematical Biology

15-25 students, 2010, 2011, 2012, 2014.

• Branching processes. Q-bio summer school.

Santa Fe, USA. 3 August 2013

• MAGIC065 Stochastic processes

Four lectures given, over the MAGIC grid, to a consortium of Universities. (Corecourse.)

October-November 2010, 2011, 2012.

• MAGIC047 Stochastic Modelling in Biology

Six lectures given, over the MAGIC grid, to a consortium of Universities.

October-November 2008, October-November 2009.

• Summer School: Theoretical and Experimental Immunology

School of Mathematics, University of Leeds

31 Aug-4 Sep 2009.

• Numerical methods for stochastic dynamics

Opening tutorial, SAMSI programme.

North Carolina, USA. 30 Aug 2009

• Stochastics and Modelling

Graduate School: Nonlinear and Stochastic Systems in Biology School of Mathe-matics, University of Leeds

30th March - 1st April 2009

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• Markov chains and stochastic processes

Intensive two-day course, part of the European Phd Programme in ComputationalBiology, given at the Gulbenkian Institute, Lisbon, Portugal.

24-24 November 2008

• I have been teaching one-day LATEX courses, 4-5 times per year since 2006. Theseare given to graduate students from across the University.

http://www1.maths.leeds.ac.uk/LaTeX/

• Assessor, first year PhD reports: Naglu Jagjit (2004), Wang Wen Kai (2007), MarkWebster (2013), Anna Longjaloux (2014).

• LUBS PhD Transfer panel chair 2009-2011: Martin Anastosov, Zhidi Du, TongyaWang, James Fung

For a list of PhD students supervised, please see Section 4iv.For a list of PhD vivas in which I have acted as internal examiner, please see Section7 ii.1.

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4 Research

i Principal Publications

i.1 Current articles: submitted, under revision, in final preparation

i.2 Refereed contributions to journals

1. Authors: Pedro Goncalves, Marco Ferrarini, Carmen Molina-Parıs, Grant Lythe,Florence Vasseur, Annik Lima, Benedita Rocha, Orly Azogui

Title: A new mechanism shapes the naive CD8+ T cell repertoire: The selection forfull diversity

Journal: Molecular Immunology 85 6–80 (2017)

2. Authors: Mario Castro, Grant Lythe, Carmen Molina-Pars, Ruy M. Ribeiro

Title: Mathematics in modern immunology

Journal: Royal Society Interface focus 6 (2016)

3. Authors: H. Hamlet Chu, Shiao-Wei Chan, John Paul Gosling, Nicolas Blanchard,Alexandra Tsitsiklis, Grant Lythe, Nilabh Shastri, Carmen Molina-Pars, Ellen A.Robey

Title: Continuous Effector CD8+ T Cell Production in a Controlled Persistent In-fection Is Sustained by a Proliferative Intermediate Population

Journal: Immunity 45 159–171 (2016)

4. Authors: Grant Lythe, Robin E. Callard, Rollo L. Hoare and Carmen Molina-Parıs

Title: How many TCR clonotypes does a body maintain?

Journal: Journal of Theoretical Biology 389 214 (2016)

5. Authors:

Kim Pham, Raz Shimoni, Mirren Charnley, Mandy J. Ludford-Menting, Edwin D.Hawkins, Kelly Ramsbottom, Jane Oliaro, David Izon, Stephen B. Ting, JosephReynolds, Grant Lythe, Carmen Molina-Paris, Heather Melichar, Ellen Robey PatrickO. Humbert, Min Gu and Sarah M. Russell Title: Asymmetric cell division duringT cell development controls downstream fate

Journal: Journal of Cell Biology 210 933 (2015)

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6. Authors: Joseph Gillard, Tom Laws, Grant Lythe, and Carmen Molina-Parıs.

Title: Modelling early events in Francisella tularensis pathogenesis

Journal: Frontiers in Cellular and Infection Microbiology 4 169–177 (2014)

7. Authors: Kevin Burrage and Grant Lythe

Title: Accurate stationary densities with partitioned numerical methods for stochas-tic partial differential equations

Journal: Stochastic Partial Differential Equations: Analysis and Computations 2262–280 (2014)

8. Authors: Mario Castro, Hisse van Santen, Marıa Ferez, Balbino Alarcon, GrantLythe, and Carmen Molina-Parıs.

Title: Receptor pre-clustering and T cell responses: insights into molecular mecha-nisms.

Journal: Frontiers in Immunology 5 (2014)

9. Authors: Carmen Molina-Parıs, Grant Lythe, Maria Sawicka, Joseph Reynolds,Niloufar Abourashchi, Kristin Hogquist, Gretta Stritesky

Title: From pre-DP, post-DP, SP4 and SP8 thymocyte cell counts to a dynamicalmodel of cortical and medullary selection


10. Authors: Joseph Reynolds, Ines Amado, Antonio Freitas, Grant Lythe, and CarmenMolina-Parıs.

Title: A mathematical perspective on CD4+ T cell quorum-sensing.

Journal: Journal of Theoretical Biology 347 160–175 (2014)

11. Authors: Carmen Molina-Parıs, Joseph Reynolds, Grant Lythe and Mark Coles

Title: Mathematical model of naive T cell division and survival IL-7 thresholds.


12. Authors: Susanna Celli, Mark Day, Carmen Molina-Parıs, Grant Lythe and PhilippeBousso,

Title: How many dendritic cells are required to initiate a T cell response?

Journal: Blood 120 3945 (2012)

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13. Authors: Joseph Reynolds, Mark Coles, Grant Lythe and Carmen Molina-Parıs

Title: Deterministic and stochastic naive T cell population dynamics: symmetricand asymmetric cell division

Journal: Dynamical Systems 27 75-103 (2012)

14. Authors: Afonso R. M. Almeida, Ines F. Amado, Joseph Reynolds, Julien Berges,Grant Lythe, Carmen Molina-Parıs and Antonio A. Freitas

Title: Quorum-sensing in CD4+ T cell homeostasis: a hypothesis and a model


15. Authors: Graham Donovan and Grant Lythe

Title: T-cell movement on the reticular network

Journal: Journal of Theoretical Biology 295 59 (2012)

16. Authors: Emily Stirk, Grant Lythe, Hugo van den Berg and Carmen Molina-Parıs.

Title: Stochastic competitive exclusion in the maintenance of the nave T cell reper-toire

Journal: Journal of Theoretical Biology 265 396-410 (2010)

17. Authors: Emily Stirk, Grant Lythe, Hugo van den Berg, Gareth Hurst and CarmenMolina-Parıs.

Title: The limiting conditional distribution in a stochastic model of T cell repertoiremaintenance

Journal: Mathematical Biosciences 224 74-86 (2010)

18. Authors: Kevin Burrage and Grant Lythe

Title: Accurate Stationary Densities with Partitioned Numerical Methods for Stochas-tic Differential Equations

Journal: SIAM1 Journal on Numerical Analysis 47 1601-1618 (2009)

19. Authors: Mario Castro and Grant Lythe

Title: Numerical experiments on noisy chains: from collective transitions to nucleation-diffusion,

Journal: SIAM Journal on Applied Dynamical Systems 7 207-219 (2008)

1Society for Industrial and Applied Mathematics

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20. Authors: Kevin Burrage, Ian Lenane and Grant Lythe

Title: Numerical methods for second-order stochastic differential equations

Journal: SIAM Journal on Scientific Computing 29 245-264 (2007)

21. Authors: Grant Lythe

Title: Diffusion-limited reaction in one dimension

Journal: Physica D 222 159-163 (2006)

22. Authors: Grant Lythe and Salman Habib

Title: Kink stochastics

Journal: Computing in Science and Engineering 8,3 10-15 (2006)

23. Authors: Kalvis Jansons and Grant Lythe

Title: Multidimensional exponential timestepping with boundary test

Journal: SIAM Journal on Scientific Computing 27 793–808 (2005)

24. Authors: Alp T. Fındıkoglu, Roberto Camassa, Grant Lythe and Q.X. Jia

Title: Transmission, reflection and second-harmonic generation in a nonlinear waveg-uide

Journal: SIAM Journal on Applied Mathematics 66 1–28 (2005)


Title: Exponential timestepping with boundary test for stochastic differential equa-tions

Journal: SIAM Journal on Scientific Computing 24 1809–1822 (2003)

26. Authors: Grant Lythe and Franz Mertens

Title: Rice’s ansatz for overdamped φ4 kinks at finite temperature

Journal: Physical Review E 67 027601–027604 (2003)

27. Authors: Alp T. Fındıkoglu, Roberto Camassa, Grant Lythe and Q.X. Jia

Title: Dielectric nonlinearity and stochastic effects in strontium titanate

Journal: Applied Physics Letters 80 3391–3393 (2002)

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28. Authors: Salman Habib, Katja Lindenberg, Grant Lythe and Carmen Molina-Parıs

Title: Diffusion-limited reaction in one dimension: paired and unpaired nucleation

Journal: J. Chem. Phys. 115 73–89 (2001)


Title: Stochastic PDEs: convergence to the continuum?

Journal: Computer Physics Communications 142 29–35 (2001)


Title: Efficient numerical solution of stochastic differential equations using expo-nential timestepping

Journal: Journal of Statistical Physics 100 1097–1109 (2000)

31. Authors: Salman Habib and Grant Lythe

Title: Dynamics of kinks: nucleation, diffusion and annihilation

Journal: Physical Review Letters 84 1070–1073 (2000)

32. Authors: Luıs Bettencourt, Salman Habib and Grant Lythe

Title: Controlling one-dimensional Langevin dynamics on the lattice

Journal: Physical Review D 60 105039 (1999)

33. Authors: Grant Lythe and M.R.E. Proctor

Title: Predictability of noise-controlled dynamics

Journal: Physica D 133 362 (1999)

34. Authors: Esteban Moro and Grant Lythe

Title: Dynamics of defect formation

Journal: Physical Review E 59 R1303–1306 (1999)


Title: Stochastic Stokes’ drift


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36. Authors: J.C. Celet, D. Dangoisse, P. Glorieux, Grant Lythe and T. Erneux

Title: Slowly passing through resonance strongly depends on noise


37. Authors: A. T. Fındıkoglu, Q. X. Jia, D. W. Reagor, Y. Fan, Grant Lythe, R. A.Camassa, D. Cai, N. Gronbech-Jensen and A. R. Bishop

Title: New potential applications of nonlinear dielectrics: microwave solitons andstochastic resonance

Journal: Integrated Ferroelectrics 22 259–268 (1998)


Title: Stochastic Calculus: application to dynamic bifurcations and threshold cross-ings

Journal: Journal of Statistical Physics 90 227–251 (1998)

39. Authors: Grant Lythe, T. Erneux, A. Gavrielides and V. Kovanis

Title: Low pump limit of the bifurcation to periodic intensities in a semiconductorlaser subject to external optical feedback

Journal: Physical Review A 55 4443–4448 (1997)

40. Authors: A. Gavrielides, V. Kovanis, P.M. Varangis, T.Erneux and Grant Lythe

Title: Coexisting periodic attractors in injection-locked diode lasers

Journal: Quantum and semiclassical optics 9 785–796 (1997)

41. Authors: A. Gavrielides, V. Kovanis, P.M. Varangis, T.Erneux and Grant LytheTitle: Quasiperiodicity in semiconductor lasers

Journal: Proceedings of the SPIE 2994 624-634 (1997)

42. Author: Grant Lythe

Title: Domain formation in dynamic transitions with noise

Journal: Physical Review E 53 R4271–4274 (1996)


Title: Dynamics controlled by additive noise

Journal: Nuovo Cimento D 17 855–861 (1995)

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Title: A noise-controlled dynamic bifurcation

Journal: Nonlinear Science B, 7 147–158 (1994)

45. Authors: M.R.E.Proctor and Grant Lythe

Title: Noise and resonant mode interactions

Journal: Annals New York Academy of Sciences 706 42–53 (1993)

46. Authors: Grant Lythe and M.R.E. Proctor

Title: Noise and slow-fast dynamics in a three-wave resonance problem

Journal: Physical Review E 47 3122–3127 (1993)

47. Authors: Allen WH, Bond IA, Budding E, Conway MJ, Daniel A, Fenton KB,Fujii H, Fujii Z, Hayashida N, Hibino K, Honda M, Humble JE, Kabe S, KasaharaK, Kifune T, Lythe GD, Masaike A, Matsubara Y, Mitsui K, Miura Y, Mori M,Muraki Y, Nagano M, Nakamura T, Nishizawa M, Morris PM, Ogio S, Saito T,Sakata M, Sato H, Shimizu HM, Spencer M, Storey JR, Tanimori T, Teshima M,Torii S, Wadsworth A, Watase Y, Woodhams MD, Yamamoto Y, Yock PCM andYuda T

Title: Upper limits on TeV gamma-ray emission from Cen A, Vela X-1, Cen X-3,Cir X-1

Journal: The Astrophysical Journal 405 554–557 (1993)

48. Authors: Allen WH, Bond IA, Budding E, Conway MJ, Daniel A, Fenton KB,Fujii H, Fujii Z, Hayashida N, Hibino K, Honda M, Humble JE, Kabe S, KasaharaK, Kifune T, Lythe GD, Masaike A, Matsubara Y, Mitsui K, Miura Y, Mori M,Muraki Y, Nagano M, Nakamura T, Nishizawa M, Morris PM, Ogio S, Saito T,Sakata M, Sato H, Shimizu HM, Spencer M, Storey JR, Tanimori T, Teshima M,Torii S, Wadsworth A, Watase Y, Woodhams MD, Yamamoto Y, Yock PCM andYuda T

Title: Survey of ultra-high-energy gamma-ray emission in the Magellanic clouds

Journal: The Astrophysical Journal 403 239–248 (1993)

49. Authors: Bond IA, Budding E, Conway MJ, Daniel A, Fenton KB, Fujii H, FujiiZ, Hayashida N, Hibino K, Honda M, Humble JE, Kabe S, Kasahara K, Kifune T,Lythe GD, Masaike A, Matsubara Y, Mitsui K, Miura Y, Mori M, Muraki Y, NaganoM, Nakamura T, Nishizawa M, Morris PM, Ogio S, Saito T, Sakata M, Sato H,Shimizu HM, Spencer M, Storey JR, Tanimori T, Teshima M, Torii S, WadsworthA, Watase Y, Woodhams MD, Yamamoto Y, Yock PCM and Yuda T

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Title: Search for point sources of ultra high energy γ rays in the southern sky

Journal: Physical Review D 48 466–478 (1993)

50. Authors: Bond IA, Budding E, Conway MJ, Daniel A, Fenton KB, Fujii H, FujiiZ, Hayashida N, Hibino K, Honda M, Humble JE, Kabe S, Kasahara K, Kifune T,Lythe GD, Masaike A, Matsubara Y, Mitsui K, Miura Y, Mori M, Muraki Y, NaganoM, Nakamura T, Nishizawa M, Morris PM, Ogio S, Saito T, Sakata M, Sato H,Shimizu HM, Spencer M, Storey JR, Tanimori T, Teshima M, Torii S, WadsworthA, Watase Y, Woodhams MD, Yamamoto Y, Yock PCM and Yuda T

Title: Upper limits for ultra-high-energy gamma-rays from SN1987A obtained byCerenkov technique at large zenith angles

Journal: The Astrophysical Journal 344 L17–L19 (1989)

i.3 Editor

Mathematical models and immune cell biologyC. Molina-Parıs and Grant Lythe (Springer 2011).

i.4 Parts of Books

1. Authors: C. Molina-Parıs, E. Stirk, K. Quinn and G. Lythe

Title:Continuous-Time Birth and Death Processes: Diversity Maintenance of NaiveT Cells in the Periphery

In: Mathematical Models and Immune Cell Biology (Springer 2011) pp. 171–186

2. Authors: C. Molina-Parıs, G. Lythe and E. Stirk

Title: Multivariate Competition Processes: A Model for Two Competing T CellClonotypes


3. Authors: M. Day and G. Lythe

Title: Timescales of the Adaptive Immune Response



Title: Kinks in a stochastic PDE

In: Proceedings of the IUTAM symposium on Nonlinear Stochastic Dynamics N.Sri Namachchivaya and Y.K.LIN (Eds.) (Kluwer, Dordrecht 2003), pp435–444.

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Title: Stochastic PDEs: domain formation in dynamic transitions

In: Proceedings of FISES 97, J.A. Cuesta and A Sanchez, eds.(Editorial del CIEMAT, Madrid, 1998)

6. Authors: Grant Lythe

Title: Noise and dynamic transitions

In: Stochastic Partial Differential Equations, A. Etheridge (ed.) (Cambridge Univer-sity Press, 1995), pp181–188

ii Presentations

• How many TCR clonotypes does a body maintain?NIH, MA. 7 August 2018

• How many TCR clonotypes does a body maintain?St Jude hospital, TN. 22 August 2018

•• The T-cell repertoire: measurements and simulationsSystems Immunology Workshop: Adaptive Immune Repertoires and BeyondUniversity of Surrey. 27-28 March 2018.

• Agent-based modelling: cellular and subcellularEMBO Modelling infectious diseases in the cell and host Singapore. 22-24 Jan 2018.

• Agent-based modelling and immunologyMathematical Models of Infection, Inflammation and Immunity 5-7 April, 2017 Indian

Institute of Science, Bangalore• Is Immunology like Astronomy?

BSSE Symposium, IISc Bangalore, 27 Jan 2017• Mathematical and Computational Immunology

QUT, Brisbane, Australia. 2 Sep 2016.• The T-cell repertoire: measurements and simulations

Conference:International Congress of Immunology, Melbourne, Australia. 22 Aug 2016.

• The T-cell repertoire: measurements and simulationsAuckland Bioengineering Institute, Auckland, New Zealand. 18 Aug 2016.

• The T-cell repertoireConference: ECMTBUniversity of Nottingham. 14 Jul 2016.

• The T-cell repertoire: measurements and simulationsConference: Bordeaux Modelling WorkshopUniversity of Bordeaux, France. 2 Jun 2016.

• Stochastic models and immunologyAstra-Zeneca, Cambridge. 13 Mar 2016.

• Stochastic modelling and immunology IIIsaac Newton Institute, Cambridge. 23 Feb 2016.

• How many TCR clonotypes does a body maintain?Conference: Quantitative Immunology

Lythe page 19 of 42

KITP, Santa Barbara, USA. 5 Feb 2016• Stochastic modelling and immunology I

Isaac Newton Institute, Cambridge. 26 Jan 2016.• How many TCR clonotypes does a body maintain?

Seminar: Division of Infection and Immunity, University College London, 25 Jan2016.• Stochastic modelling and immunology

Conference: Numerical Modeling in Evolutionary Problems: perspectives and appli-cations

Fisciano, Italy. 26 Oct 2015.• How many TCR clonotypes does a body maintain?

Conference: European Congress on ImmunologyVienna, Austria. 9 Sep 2015

• Modelling the T-cell repertoireConference: Bio-Modeling Workshop.Los Alamos, New Mexico. 7 Aug 2015.

• Stochastic modelling, mathematical and computationalConference: Stochastic single-cell dynamics in immunologyAmsterdam, Netherlands. 19 Jun 2015

• Competition model of the T-cell repertoireConference: Mathematics for health and disease.16 Apr 2015, International Centre for Mathematical Sciences, Edinburgh

• Competition model of the T-cell repertoireConference: Probability in the North-East.9 Jan 2015, University of York.

• Stochastic modelling and immunology: how many populations? how many cells? howmany encounters?

Seminar: Mathematics Institute, University of Warwick.23 October 2014

• Stochastic modeling and immunology: How many populations? How many cells? Howmany encounters?

Conference: Ecology, Evolution and Dynamics of Dengue and other Related Dis-eases.

Arizona State University, USA. 4-5 Aug 2014• Stochastic modelling, Brownian motion and immunology

Conference: Quantitative Immunology annual meeting.NUI Galway, Ireland. 24 June 2014

• IL-7 thresholds and naive T cell homeostasisConference: Bordeaux Modelling Workshop.Bordeaux, France. 6 June 2014

• How many TCR clonotypes does a body maintain?Conference: Systems Approaches in Immunology and Infectious Diseases.Santa Fe, NM, USA. 11 Jan 2014


Seminar: Department of Mathematics and Statistics, University of Limerick.25 November 2013

Lythe page 20 of 42


Seminar: Hamilton Institute, National University of Ireland (NUI), Maynooth.27 November 2013


Seminar: School of Mathematics, Statistics and Applied Mathematics, NUI, Galway.28 November 2013

• Branching processesQ-bio summer school. Santa Fe, USA.3 August 2013

• Stochastic dynamics and the adaptive immune systemConference: Stochastic, statistical and computational approaches to Immunology.ICMS, Edinburgh. 22-26 Jul 2013

• Stochastic modelling of T cell homeostasisConference: Modelling in immunology.Bordeaux, France. 18 Jun 2013

• New numerical methods for stochastic DEs and PDEsConference: Fusion of knowledge in stochastic modelling of large complex systemsZif Bielefeld, Germany, 13 Jun 2013.

• New numerical methods for stochastic DEs and PDEsConference: SIAM dynamical systemsSnowbird, USA. 29 May 2013.

• Stochastic dynamics and the adaptive immune systemSeminar: University of Nottingham5 Feb 2013

• Timescales of the immune responseConference: Lymphocyte development.Max Planck Institute for Complex Systems, Dresden, Germany. Aug 2012

• Stochastic Dynamics and the Adaptive Immune SystemConference: Stochastic dynamics in actionZif Bielefeld, Germany. 24 May 2012

• Computational model of large-scale clonal competitionConference: Computational ImmunologyWalter and Eliza Hall Institute, Melbourne, Australia. Apr 2012

• Stochastic dynamics and the adaptive immune systemSeminar: Department of Mathematics, University of Auckland, New Zealand.15 March 2012

• Stochastic dynamics and T cellsSeminar: IIMS, Massey University, New Zealand.14 March 2012

• Stochastic dynamics and the adaptive immune systemSeminar: Astra-Zeneca, Alderley Park.11 Nov 2011

• Brownian motion and the adaptive immune systemConference: Theoretical and Experimental Immunology,Indian Institute of Science, Bangalore. 16 Aug 2011

Lythe page 21 of 42

• Stochastic Dynamics in the Immune SystemConference: ICIAM.Vancouver, Canada. 20 Jul 2011

• Diffusive lymphocyte movement and interactions, in silico and in vivoConference: Imaging, Interpretation and Modeling in Modern ImmunologyBanff, Canada. 14 April 2011

• Timescales of the immune responseConference: Physics of Immunity.Max Planck Institute for Complex Systems, Dresden, Germany. 4-8 April 2011

• Kinks and nucleation in a stochastic PDEConference: Random Dynamical SystemsBielefeld, Germany, 4-5 November 2010

• Stochastic Dynamics and T CellsConference: International Network in Theoretical Immunology meetingLos Alamos, USA. 6 Aug 2010

• Kink stochasticsConference: Coherent StructuresLorentz Center, Leiden. 12-16 Jul 2010

• Kink stochasticsConference: Stochastic Partial Differential Equations: Approximation, Asymptotics

and ComputationIsaac Newton Institute for Mathematical Sciences, Cambridge. 28 Jun - 2 Jul 2010

• Stochastic Dynamics and T CellsConference: SIAM DSPDEsBarcelona, May 31 - 4 Jun 2010

• Stochastic dynamics and T cellsSeminar: Department of Mathematics, University of Auckland4 March 2010

• Kink stochasticsSeminar: Applied Mathematics and Mathematical Physics, Imperial College London3 Nov 2009

• Discrete and continuous stochastic modellingLeeds Summer School, Theoretical and experimental immunology. 4 Sep 2009

• Numerical methods for stochastic dynamicsOpening tutorial, SAMSI programme.North Carolina, USA. 30 Aug 2009

• A Taste of Mathematical ImmunologySeminar: Department of Biochemistry, Indian Institute of Science, Bangalore.12th Aug 2009

• Stochastic modelling in immunologySeminar: Department of Mathematics, Indian Institute of Science, Bangalore.6th Aug 2009

• Mathematical ImmunologySeminar: Instituto Superior Tecnico, Lisbon, Portugal26 Jun 2009

• Timescales of lymphocyte motion and collisions in a lymph nodeSeminar: John Innes Centre, Norwich

Lythe page 22 of 42

19 Jun 2009• Timescales of lymphocyte motion and collisions in a lymph node

Conference: British Society for Immunology Congress 2008Glasgow. 24 Nov 2008

• Timescales of the Immune responseSeminar: Leeds MathBiol seminars, Faculty of Biological Sciences13 Nov 2008

• Kink StochasticsConference: SIAM nonlinear waves and coherent structuresRome, Italy. 21 Jul 2008

• Modelos Matematicos en Immunologıa: homeostasis e interaccion entre celulas T ycelulas dendrıticas

Seminar: Centro de Biologıa Molecular, Madrid24 Jul 2008

• Inmunologıa MatematicaConference: Nolineal 2008Barcelona, Spain15 Jun 2008

• Kink stochastics and diffusion-limited reactionSeminar: Engineering Mathematics, University of Bristol6 Jun 2008

• Seminar: Kink stochastics and diffusion-limited reactionMathematics, University of Strathclyde19 Mar 2008

• Kink stochastics and diffusion-limited reactionSeminar: Mathematics, University of Essex13 Mar 2008

• Kink stochastics and diffusion-limited reactionSeminar: Fluids and MHD seminars, School of Mathematics, Leeds.24 Jan 2008

• Kink stochasticsSeminar: Mathematics and Statistics, University of Limerick, Ireland13 Dec 2007

• Long-term dynamics of a stochastic PDE with kinksConference: Numerical analysis of Stochastic PDEsMIMS, Manchester. 3-4 Sep 2007

• Diffusion-limited reaction in one dimensionConference: SciCADE 2007St Malo, France. 9-13 Jul 2007

• Statistics and Dynamics of KinksMSRI workshop Mathematical Issues in Stochastic Approaches for Multiscale Mod-

ellingBerkeley, USA. 21-25 May 2007

• Stochastic Modelling in ImmunologyConference: Host-pathogen interactionsBiopolis, Singapore. 19 March 2007

• Noisy kinks and diffusion-limited reaction

Lythe page 23 of 42

Conference: macsdiem 2007Brighton. 22-24 Feb 2007

• Noisy kinks and diffusion-limited reactionDepartment of Mathematics, University of Sussex, 9 Nov 2006

• Eventos de nucleacion en cadenas de particulas sujetas a fluctuacionesConference: Fısica EstadısticaGranada 14-16 Sep 2006

• Noisy kinks and diffusion-limited reactionConference: First-Passage and Extreme-Value problems in Random ProcessesIsaac Newton Institute, Cambridge. 29 June 2006

• Dinamica estocastica de kinksSeminar: E.T.S.I. Aeroauticos, Universidad Politecnica de Madrid, Spain31 May 2006

• Timescales and lengthscales from noiseConference: UK-German Frontiers of Science (Royal Society-von Humboldt Foun-

dation)Robinson Centre, Wyboston. 30 March-1 April 2006http://www.avh.de/en/netzwerk/frontiers/index.htm

• φ4 kinks and diffusion-limited reaction in one dimensionSeminar: Physics, University of Manchester2 Nov 2005http://theory.phy.umist.ac.uk/index.php?doc=seminars

• Diffusion-limited reaction in one dimensionSeminar: Applied Mathematics, University of Manchester9 Nov 2005http://www.maths.man.ac.uk/Research/seminars.html

• Diffusion-limited reaction in one dimensionSeminar: Mathematics, University of Glasgow17 Jun 2005http://www.maths.gla.ac.uk/events/seminars

• Numerical methods for second-order stochastic equationsConference: Computational Stochastic Differential EquationsBanach Centre, Bedlewo, Poland. 19-24 September 2005http://www.nada.kth.se/ szepessy/spde work.html

• Diffusion-limited reaction in one dimensionConference: Workshop on Coagulation-Fragmentation Processes: Theory and Ap-

plicationsICMS, Edinburgh, 4 - 8 July 2005http://www.icms.org.uk/meetings/2005/coagfrag/index.html

• Diffusion-limited reaction in one dimensionSeminar: University of Glasgow17 June 2005http://www.maths.gla.ac.uk/events/seminars

• Diffusion-limited reaction in one dimensionMathematics Colloquium, Heriot-Watt University, 4 March 2005http://www.ma.hw.ac.uk/maths/maths.html

Lythe page 24 of 42

• Transmision, reflexion y generacion del segundo harmonico en una guıa de ondas nolineal

Seminar: GISC (in Spanish).Departamento de Matematicas, Universidad Carlos III de Madrid, Spain, 22 Nov 2004http://www.gisc.es

• Dielectric nonlinearity and stochastic effects in Strontium TitanateSeminar: Superconductivity Technology CenterLos Alamos National Laboratory20 Aug 2004

• Transmision, reflexion y generacion del segundo harmonico en una guıa de ondas nolineal

Conference: Nolineal 2004 (in Spanish).Toledo, Spain, 31 May 2004http://matematicas.uclm.es/nolineal2004/

• Exponential timestepping for SDEsSeminar: School of Mathematics and Computer Science, University of Leicester20 May 2004http://www.mcs.le.ac.uk/seminars/applicable/Programme.html

• Exponential timestepping for SDEsSeminar: Department of Mathematical Sciences, University of Bath21 May 2004http://www.bath.ac.uk/ massch/Seminars/Formal

• Dynamic bifurcations: lengthscales from noiseConference: Multiscale Analysis for Stochastic DynamicsMathematics Institute, University of Warwick, UK, 14 Aug 2003http://www.maths.warwick.ac.uk/miraw

• Kink dynamics: from an SPDE to diffusion-limited reactionConference: Workshop on Stochastic Partial Differential Equations and Related

TopicsMathematics Institute, University of Warwick, 20 Oct 2003http://www.maths.warwick.ac.uk/research/

• Exponential timestepping for stochastic differential equationsConference: SIAM dynamical systemsSnowbird, USA. 27 May 2003http://www.siam.org/meetings/ds03

• Timescales and lengthscales from noisePANDA Meeting, University of Leeds, 1 August 2003http://www.maths.leeds.ac.uk/˜alastair/03 lms/

• Exponential timestepping for stochastic differential equationsConference: SDEs and SPDEs : Numerical Methods and ApplicationsEdinburgh, 4 Apr 2003http://www.ma.hw.ac.uk/icms/meetings/2003/sde/

• Dynamics of kinks at finite temperatureSeminar: Facultat de FısicaUniversitat de Barcelona, Spain21 Oct 2002

• Stochastic PDEs: convergence to the continuum?

Lythe page 25 of 42

Conference: IUTAM Symposium on Nonlinear Stochastic DynamicsUrbana-Champaign, Illinois, USA. August 2002http://bacmac.aae.uiuc.edu/iutam/

• Exponential timestepping for stochastic differential equationsConference: Scientific ComputationUniversity of Geneva, 26-29 June 2002

• Dynamics of KinksSeminar: Departement de Physique Theorique University of Geneva, Switzerland23 June 2002

• Resolucion de ecuaciones diferenciales estocasticas con el metodo exponencialConference: NoLineal 2002, Cuenca, Spain. 5-8 June 2002 (in spanish).http://matematicas.uclm.es/nolineal2002/

• Exponential timestepping for stochastic differential equationsConference: Half-day stochastic meetingUniversity of Strathclyde, Glasgow, UK. 1 Dec 2001

• Introduccion a la ecuacion de Langevin (in spanish).Seminar: Grupo de Fisica del plasma, Universidad Carlos III de Madrid.2 March 2001

• Stochastic PDEs: convergence to the continuum?Conference: Conference on Computational Physics 2000Gold Coast, Australia. 2000

• Resolucion de ecuaciones diferenciales estocasticas con el metodo exponencialConference: Fısica Estadıstica (poster, in spanish).Universidad de Santiago de Compostela, Spain. 2000http://fmares.usc.es/ fises2000/

• Dynamics of defect formationConference: Peyresq workshopHaute Provence, France Jul 2000

• Dinamica de kinks calientesConference: Nolineal 2000 (in spanish).Almagro, Castilla-La Mancha, Spain 2000http://www.uclm.es/cursos/nolineal/

• Dynamics of kinks at finite temperatureConference: Computational issues in stochastic processesCECAM, Ecole Normale Superieure de Lyon, France. 2000http://www.gst.net/˜algarcia/cecam/abstract.htm

• Exponential timestepping for stochastic DEsConference: ANODE 99Auckland, New Zealand. 1999

• Exponential timestepping for stochastic DEs “Young talent” award.Conference: SciCADE (Scientific Computation and Differential Equations)Fraser Island, Australia. 1999

• Stochastic PDEsConference: Stochastic Evolutionary EquationsLos Alamos, USA 1999

• Dynamics of defect formationWake Forest University, North Carolina. 31 Aug 1999

Lythe page 26 of 42

• Vida y muerte de los kinks (poster, in spanish).Conference: Fısica EstadısticaInstituto de Fısica, Santander. 1999

• Secret lives of kinksConference: SIAM dynamical systemsSnowbird, Utah, USA. 1999http://www.siam.org/meetings/ds99/cp21.htm

• Stochastic Stokes’ driftConference: American Physical Society Centennial MeetingAtlanta, USA. 1999

• Real time dynamics of kinksConference: Nonequilibrium quantum field theoryITP, Santa Barbara, USA 1999http://online.itp.ucsb.edu/online/noneq99/lythe/

• The secret lives of kinksSeminar: Department of Mathematics, Massey UniversityPalmerston North, New Zealand.1 Dec 1998

• Finite-temperature dynamics of kinksConference: IGPP/NPACI Workshop: Accurate Simulation and Modeling of Physical

SystemsSan Diego, USA. 19 Nov 1998

• Dynamics of defect formationSeminar: Theoretical Division T6.Los Alamos, USA.21 Oct 1998.

• Dynamique tres sensible au bruit (in French).Seminar: Laboratoire de Physique, ENS.Lyon, FranceAug 1998

• Passage through resonance in a driven Nd:YAGConference: Laser Optics 98St. Petersburg, Russia. 1998http://www.ilph.spb.ru/lo98/lo98call.htm

• EDP estocasticas (in spanish).Conference: Fısica EstadısticaUniversidad Carlos III, Getafe (Madrid), Spain. 1997

• Stochastic Calculus: Application to Dynamic Bifurcations and Neuron Dynamics.Conference: SIAM Annual ConferenceStanford, USA. 1997http://www.siam.org/meetings/archives/an97/ms12.htm

• Effect of Noise on Bifurcations in Spatially Extended Systems.Conference: SIAM, Applications of dynamical systemsSnowbird, USA. 1997http://www.siam.org/meetings/archives/ds97/ms12.htm

• Noise-controlled dynamics in normal forms.Conference: SIAM, Applications of dynamical systems

Lythe page 27 of 42

Snowbird, USA. 1997http://www.siam.org/meetings/archives/ds97/ms48.htm

• Slow passage through resonance in a periodically modulated laserConference: Noise and NonlinearityHeraklion, Greece. 1996

• Domain formation with noise and time-dependent bifurcation parameter.Conference: New Developments and Applications in Stochastic PDEsLos Alamos, USA. 1996

• Noise, dynamics bifurcations and pattern formationSeminar: Institute for marine and atmospheric researchUtrecht, Netherlands.29 Mar 1996.

• Dynamic transitionsConference: International Conference on Industrial and Applied MathematicsHamburg, Germany 1995)

• Dynamics of stability lossConference: Mathematical Theory of Phase TransitionsBrighton, UK. 1994.

• Dynamics controlled by additive noiseConference: Fluctuations in Physics and BiologyElba, Italy 1994.

• Noise-controlled dynamics of stability lossConference: Stochastic partial differential equationsICMS, Edinburgh, UK. 1994.

• A noise-controlled dynamic bifurcationConference: Euromech 308: Chaos and noise in dynamical systemsSpała, Poland. 1993.

• A noise-controlled dynamic bifurcationConference: Fluctuations and OrderLos Alamos, USA. 1993.

• Noise-controlled dynamicsConference: British Applied Mathematics ColloquiumGlasgow, UK. 1993.

• The effect of noise on solutions of some ODEsConference: IAAS Workshop on Stochastic NumericsGosen, Germany. 1992.

iii Supervision of postdoctoral workers

• Martin Lopez-Garcıa, Leverhulme trust PDRA (2013-).

• Edgar Delgado-Eckert, ESF research fellow (2013-)

• Sheeja Krishnan, Unilever (2012-).

• Ed Clark, Unilever (2010-2011).

Lythe page 28 of 42

iv Supervision of research students

1. Josh L (2017-)

2. Polly G (2017-)

3. Remus Stana (2015-)

4. Jonty Carruthers (2015-2018)

5. Marco Ferrarini (2014-2018) Evaluation of CD8+ numbers and repertoires

6. Dr. Luis de la Higuera (2013-2017)Stochastic models for CD4+ T cells

7. Dr. Maria Sawicka (2012-2017)Mathematical models of receptor mediated processes in vascular endothelial cells

8. Dr. Joseph Reynolds (2010-2014)Mathematical models of the roles of IL-2 and IL-7 in T cell homeostasis

9. Dr. Mark Day (2009-2013)Stochastic modelling of lymphocyte dynamics and interactions

10. Dr. James Currie (2008-2012)Stochastic modelling of TCR binding

11. Dr. Emily Stirk (2006-2010)Stochastic modelling of diversity and ageing in the naive T cell repertoire

v PhD Transfer interviews

1. Robert West (June 2017)

2. Fabio Peruzzo (July 2016)

3. Mark Webster (July 2013)

vi Grant income

Funded projects: 2014

May 2013 - Apr 2017 Principal investigator:

FP7-PEOPLE-2012-ITN, Quantitative T cell Immunology (QuanTI).

Monetary Value: e4,013k.

Feb 2012 - Jan 2015 Co-investigator:

Stochastic modelling of T cell responses: chemical skin sensitisation.

Unilever, CH-2011-0828. Monetary value: £450k.

Lythe page 29 of 42

May 2013 - Apr 2017 Co-investigator:

FP7-PEOPLE-2012-IRSES, Mathematics for Health and Disease (INDOEUROPEAN-MATHDS).

Monetary Value: e290k.

Sep 2013 - Aug 2016 Co-investigator:

Vascular receptor-ligand programming: stochastic modelling of cellular fate,

Leverhulme Trust. Monetary Value: £247k.

Apr 2013 - Mar 2015 Co-investigator:

FP7-PEOPLE-2011-IEF, Vascular endothelial growth factor receptor: mathemati-cal modelling (VEGFR).

Monetary Value: e209k.

1 Oct 2013 - 31 Mar 2014 Principal investigator:

Modelling pathogenesis and host-response within the human body

Defence Science and Technology Laboratories, DSTLX-1000074213

£46k

Sep 2012 - Mar 2016 Co-investigator:

Stochastic modelling of receptor-ligand interactions in the VEGFR system.

EPSRC CASE studentship, with industrial partner AstraZeneca. Monetary value:£23k.

Jan 2012-Dec 2014 Principal investigator:

Stochastic modelling of T cell responses: in vivo imaging of T cell and antigen-presenting cell interactions

University of Leeds WUN research fund. Monetary Value: £12k.

Projects recently submitted to funding bodies

2015-2020 Co-investigator:

Systems Immunology Research On T Cell hOmeostasis: Understanding the disease,optimizing the interventions (SIROCO)

Participants:1 (Coordinator) University of Bordeaux, France2 University College London, UK3 Imperial College London, UK4 University of Leeds, UK5 University of Glasgow, UK6 Utrecht University, The Netherlands7 University Medical Center Utrecht, The Netherlands8 Institut National de la sante et de la Recherche Medicale, France

Total funding requested for Horizon2020 H2020-PHC: 6 million euros.

Lythe page 30 of 42


Role of the vascular endothelial growth factor receptor tyrosine kinases in cardiacand endothelial cell fate: an experimental and mathematical study

BBSRC Industrial Partnership £996848

(with FBS and Astra-Zeneca)

Projects in preparation

• Francisella Tularensis infection: an experimental and mathematical study

with Joe Gillard, Tom Laws and C. Molina-Parıs

to be submitted to MRC in May 2015

• Modelling the immune response to oncolytic viruses and other immuno-therapies

with Alan Melcher, C. Molina-Parıs, Stephen Smye, Charles Taylor

Outline proposal accepted by Cancer Research UK, November 2014

FEC Salary contributions: 2014

• I am the principal scientific coordinator of the Initial Training Network QuanTI:Quantitative T cell Immunology, with 11 partners and 6 associated partners, fromindustry and academia across Europe, with 4 million euros of FP7 funding. Themanagement budget, allocated to the University of Leeds, is paying twenty-five per-cent of my salary and paying the salary of our administrator for the project. Two ofthe Early Stage Researchers, Luis de la Higuera and Marco Ferrarini, are PhD stu-dents in applied maths at Leeds as part of the network. Network training and skillsevents, management and scientific direction are coordinated by us at Leeds. We re-cently held a successful mid-term review meeting, bringing together all fellows andPIs with the European project Officer, Sandrine Jacobs.

FEC: 25 %

• Twenty-five percent of my time is currently allocated to the Dstl-funded project“Modelling pathogenesis and host-response within the human body”, begun on ashort-term basis in 2012-13 and now part of Dstl’s core programme. Our task isto construct a stochastic agent-based model of Francisella Tularensis inhalationalinfection, pathogenesis and host immune response (both innate and adaptive). Mycomputation modelling identifies stages of infection and pathogenesis, and the corre-sponding timescales. The Defence Science and Technology Laboratory (Dstl) max-imises the impact of science and technology for the defence and security of the UK,supplying sensitive and specialist services for the Ministry of Defence and widergovernment.

FEC: 25 % in 2014, figure for 2015 to be confirmed.

Lythe page 31 of 42

• Unilever are providing £400,000 funding for the Research Project Stochastic mod-elling of T cell responses: chemical skin sensitisation starting in 2012. The aim ofthis project is to estimate the size, quality and diversity of the antigen specific T cellpopulation response in humans (cell numbers in blood and skin, T cell subsets in-volved and T cell receptor diversity), as a function of time, following exposure to anovel chemical sensitiser. The project will involve the following scenarios: differentfrequencies of exposure to the novel chemical sensitiser and different sizes of skinpatch exposed to the novel chemical sensitiser.

FEC: Currently 10 %, expected to be increased to 20% in 2015.

Recently completed funded projects




£46k




£31k

2012-2014 Principal investigator:

Stochastic modelling of T cell responses: in vivo imaging of T cell and antigen-presenting cell interactions

£12k

University of Leeds WUN research fund

Sep 2010 - Sep 2013 Co-investigator:

White Rose Studentship – White Rose Immune Modelling Network.

Monetary value: £145k.

Sep 2010 - Sep 2013 Co-investigator:

Interface dynamics out of equilibrium with applications to condensed matter andbiosystems,

Spanish Research Council. Monetary Value: e40k.

2009 Co-investigator:

New in vivo imaging techniques: challenges for experimental and theoretical im-munology

European Science Foundation, Exploratory Workshop

Lythe page 32 of 42


International Network in Theoretical Immunology

FP7 Marie Curie Actions (People) PIRSES-GA-2008-230665 230ke

http://www1.maths.leeds.ac.uk/applied/INTI


Immunology Imaging and Modelling Network – I2M

BBSRC £100k

http://www1.maths.leeds.ac.uk/applied/I2M


New imaging techniques: challenges for experimental and theoretical immunology

£13.5K from the University of Leeds’ pump-priming WUN International ResearchCollaboration fund.

2006 Principal investigator:

Stochastic Models of intercellular signalling and cell motility.

British Council Collaboration Development Award


EPSRC Conference grant

SDEs and SPDEs: numerical methods and applications

GR/R91106/01

Used to hold the conference SDEs and SPDEs: Numerical methods and applica-tions, in Edinburgh, 31 March to 4th April 2003.


PPARC MHD Turbulence and the generation of large-scale magnetic fields in theSun

PP/D00179X/1


Ethel Raybould travelling fellowship, Department of Mathematics, University ofQueensland (2002).


Nuffield Foundation, Newly Appointed Lecturer’s Award

Theory, numerics and applications of stochastic differential equations and stochas-tic partial differential equations

NAL/00496/G

Lythe page 33 of 42


European Infrastructure program (Framework 4)

Large scale solutions of stochastic partial differential equations

HPRI-1999-CT-00071

Used to visit the Large Scale Computing Facility CESCA-CEPBA, Barcelona, 2002.Collaborator: Jordi Garcıa-Ojalvo.


Los Alamos National Laboratory, LDRD-IP

Stochastic Resonance in Arrays with Tunable Nonlinearity and Coupling 1998-2001$600,000.

vii Some unsuccessful proposals

1. Grant title Mechanisms controlling homeostasis of T cells

Funding body Medical Research Council, partnership grant

Applicants Ben Seddon (PI), Robin Callard, Nigel Klein, Joe Standing (UCL)Andrew Yates (Albert Einstein, New York)Grant Lythe, Carmen Molina-Parıs (Leeds)

Date 2013

% contribution Leeds 25%

2. Grant title Understanding the long-term maintenance of immunity in vivo

Funding body Human Frontiers of Science

Applicants Miles Davenport (Sydney)Brian Rudd (Cornell)Grant Lythe (Leeds)

Date 2012

% contribution 33% Leeds

3. Grant title T cell diversity and homeostasis in the periphery: a mathematical study

Funding body BBSRC

Applicants Grant Lythe, Carmen Molina-Parıs (Leeds)

Date 2012


4. Grant title New computational tools for Stochastic PDEs

Funding body EPSRC

Applicants Grant Lythe

Date 2011

% contribution 100% Leeds, 100% GDL

Lythe page 34 of 42

5. Grant title Stochastic dynamics of immune cells

Funding body BBSRC

Applicants Paul Garside, James Brewer, Pasquale Maffia (Glasgow). Grant Lythe,Carmen Molina-Parıs (Leeds)

Date 2011


6. Grant title T cell diversity and homeostasis

Funding body BBSRC

Applicants Grant Lythe, Carmen Molina-Parıs (Leeds)

Date 2012


7. Grant title Applied systems analysis of reconstitution in human and mouse to iden-tify key mechanisms of T cell homeostasis in health and disease

Funding body Medical Research Council

Applicants Ben Seddon (PI), Robin Callard, Nigel Klein, Joe Standing (UCL)Andrew Yates (Albert Einstein, New York)Grant Lythe, Carmen Molina-Parıs (Leeds)

Date 2010

% contribution Leeds 25%

8. Grant title Modelling adaptive immune responses: crossing the industrial-academicdivide

Funding body EU Marie Curie (Industry Academic Partnership IAPP)

Applicants Grant Lythe, Carmen Molina-Parıs (Leeds)European and industrial partners

Date 2009


9. Grant title IMMUNOTRAIN

Funding body EU FP7 (ITN)


Date 2009


10. Grant title Quantitative immunology and in vivo imaging

Funding body EU FP7 (ITN)


Date 2008


Lythe page 35 of 42

5 ScholarshipI have an international reputation as an academic leader, a sustained record of publicationsand a varied and growing portfolio of funded research projects and networks, collabora-tions and roles. Scholarship, research and collaborations have borne fruit in joint papersand research funding with scientists and mathematicians in the UK and elsewhere, andin my appointment as editor of the SIAM journal on applied mathematics. I am leadingan FP7-funded collaboration with Indian scientists and immunologists. I am also leadingcollaborations outside academia, obtaining significant funding from Unilever and Dstl.

• Academic Editor, SIAM Journal on Applied Mathematics

• Academic Editor, PLoS ONE

• Chair, North British Differential Equations Seminar

http://www1.maths.leeds.ac.uk/applied/NBDES

• Editor, UK Nonlinear News

http://www1.maths.leeds.ac.uk/applied/news.dir

6 Enterprise and Knowledge Transfer

EKT activities

My major continuing research activities are industrial-academic partnerships that havesignificant knowledge transfer components. Medium and large-scale projects funded byUnilever and Dstl, will continue to be an important part of my research portfolio. My linkswith AstraZeneca are strengthening, resulting in a CASE studentship and an applicationto the BBSRC Industrial Partnerships Scheme.

I co-founded the British Society for Immunology’s Mathematical Modelling Affinitygroup, that enables transfer of ideas between mathematicians and immunologists. Mi-crosoft Research Cambridge has hosted our most recent meetings.

I co-coordinate INDOMATH, the EU-funded Research Staff Exchange scheme withIndia. Two-way visits under the umbrella of the scheme, with institutions such as IndianInstitute of Science (Bangalore) and University of Hyderabad are transferring knowledgeacross fields and continents. The EPSRC and the Indian Academy of Sciences have ac-cepted our request to fund international conferences in Edinburgh (April 2015) and Chen-nai (November 2015).

I am the principal scientific coordinator of the FP7 network, QuanTI, that is acting asa platform for the development of a coordinated inter-sectorial initiative to model humanimmune responses in health and disease. QuanTI has a total of four industrial partners:Bayer, Microsoft Research Cambridge, AstraZeneca, Unilever and TalaveraScience. Allof them are involved at their highest possible level. The network outreach activities aimto create awareness in the general public of the importance of research to society andpromote research careers. We aim to generate knowledge that will be applied in healthand medicine, to improve quality of life, ensuring that the results of biomedical researchwill ultimately benefit all citizens.

Lythe page 36 of 42

• Why do maths at University? talk at Higher Education Day at Notre Dame SixthForm College 25/6/13

• Why do maths at University? talk at Higher Education Day at Notre Dame SixthForm College, June 2012

• One-day visit including talks to Year 10,11 and 12 students at King’s school, Peter-borough. 20 June 2007.

• Why do maths at University?, talk given at Haberdashers boys’ school, Hertsford-shire. 1 March 2007.

• Why do maths at University?, talk given at UCAS Convention, Harrogate, 27 April2007.

Websites that I developed and maintain:

1. http://www.maths.leeds.ac.uk/Applied/I2M

2. http://www.maths.leeds.ac.uk/Applied/INTI

3. http://www.maths.leeds.ac.uk/Applied/NBDES

4. http://www.maths.leeds.ac.uk/˜grant/immunet

Patents

None.

7 Academic Leadership

i School

In the last 10 years, I have undertaken some of the most demanding and important admin-istrative tasks in the School of Mathematics: undergraduate admissions, study abroad andpostgraduate.

According to the most recent School of Mathematics workload model (2014), my al-location was 2168 hours, compared to the target of 1600 and the school average of 1761.

i.1 Mentoring/observation of peers

• P. Walker, teaching fellow since 2011.

(Including ULTA-2 mentor meetings.)

• Edgar Delgado-Eckert, ESF research fellow (2013-)

(Including probation meetings.)

• Elena Issoglio, lecturer in financial mathematics.

(Including ULTA mentor meetings.)

I am a trained SRDS reviewer, acting recently as reviewer for Dr. Venelina Koleva andJessica Brennan.

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ii Faculty and University

ii.1 Internal examiner

Internal Examiner of PhD theses

• Mark Webster, 2016

Convergence Properties of Approximate Bayesian Computation

• Mohammed Sabah Hussein, 2015

Coefficient Identification Problems in Heat Transfer

• Robin Archibald Richardson, 2014

A mesoscale model for coarse-grained protein dynamics

(Independent Chair)

• Bartosz Sznesny, 2014

Coevolutionary Dynamics in Structured Populations of Three Species

• R.C. Oliver, 2013

A stochastic finite element model for the dynamics of globular proteins

• Elizabeth Elliott (FBS), 2013

Evolution at shifting range margins

• Niloufar Abouraschi, 2009

Stability of Stochastic Differential Equations

• Georgios Aivaliotis, 2009

Controlled Markov Diffusions and Mean-Variance Optimisation

Course Effective Research Student Supervision: Role of the Internal Examiner, 11 May2007.

ii.2 Postgraduate tutor, applied mathematics. 2012-

As postgraduate tutor for applied mathematics, I have responsibility for co-ordinating ad-mission, pastoral care, and recording and monitoring progress of postgraduate researchstudents and for liaison with Research Student Administration (RSA). I help devise strat-egy and policy, participating in annual planning exercises, and leading on recruitment andstudentship matters for PGR students to support school strategic objectives for postgradu-ate research.

I am responsible raising the profile and importance of postgraduate research as ‘seniorsupervisor’ in the School with responsibility for all PGR matters, including strategic devel-opment, student experience, submission and qualification rates, the efficient and effectivedevelopment of arrangements and policy within the School, for the management of post-graduate research degree candidatures, and for ensuring compliance with the UniversitysCode of Practice for Research Degree Candidatures.

In the postgradute admissions process, my role is

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1. Coordinating admissions, including circulation of prospective PGR applications topotential supervisors where appropriate, approving acceptability of the application,supervisory team and research project

2. Considering applications, with the potential supervisor as appropriate

3. Ensuring that all decisions taken on admissions are timely and in line with Univer-sity, Faculty and School policy.

ii.3 Socrates/Erasmus coordinator 2010-2012

The School sends an increasing number of students each year to destinations in Europe(Erasmus) and Worldwide (US, Canada and Australia). We host between 10 and 20 in-coming students from many countries, for ine or two semesters. I am personal tutor to allof them.

ii.4 Programme coordinator, Mathematics and Biology

Biology and Mathematics, now parented by School of Maths. I am redesigned the degree,in consultation with FBS, and all of the students on the programme are my personal tutees.

ii.5 Undergraduate Admissions 2005-2009

This was a 52-week-per-year responsibility, particularly intense in August and September(A level results and clearing), October (processing of UCAS applications), Novemberand February (Post-Application visit days by prospective students). In addition, we gavemultiple talks as part of the University’s open days in September and June and organise thecreation and editing of the School’s publicity material. I tutored secondary-school studentson the “Access to Leeds” programme.

The number of applications to mathematics at Leeds increased to over 1100. Thequality of our intake, as measured by their Alevel scores, also improved. We evaluateapplicants with a myriad of qualifications, EU and overseas.

Other administrative tasks

• Health and Safety committee (2015-)

• Faculty Internationalisation Student Education Group

• Space group 2013-

• Special Circumstances Committee 2011-2013

• Committee, Annual Teaching Software Upgrade (ATSU) 2009-2011

• Learning and Teaching Committee 2007-9

• MAPS faculty board 2006-9.

• Seminar co-organiser 2001-2005.

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• “Webmaster” for the Applied Maths web pages 2003-5.

• Admissions interviewing 2003-2005.

• Organised new students’ party 2002, 2003, 2004.

• Fire Warden since 2003 (attended university training courses 2003, 2004, 2010).Induction talk to new students 2007.

iii External

iii.1 Editorial and Referee service

I Academic journals

• Academic editor of SIAM Journal on Applied Mathematics.

• Academic Editor of PLoS ONE.

• Referee for Applied Numerical Mathematics, Bioinformatics, Bulletin of Math-ematical Biology, Clinical and Translational Immunology, Communications inComputational Physics, Computers and Mathematics with Applications, Com-putational and Mathematical Methods in Medicine, Electronic Transactions onNumerical Analysis, Europhysics Letters, Fluctuation and Noise Letters, Fron-tiers of Immunology, Garland Science, IMA Journal of Applied Mathematics,Journal of Chemical Physics, Journal of Computational and Applied Mathe-matics, Journal of Computational Physics, Journal of Mathematical Biology,Journal of Physics A, Journal of the Royal Society Interface, Journal of Sta-tistical Physics, Journal of Theoretical Biology, Mathematika, Methodologyand Computing in Applied Probability Natural Computing, Nature Communi-cations, Nonlinear differential equations and applications Nonlinearity, Quar-terly Journal of Mechanics and Applied Mathematics, Physica A and PhysicaD, Physical Review E, Physics Letters A, PLoS Computational Biology, Proba-bilistic Engineering Mechanics, Proceedings of the Royal Society A, ScientificReports SIAM Journal of Numerical Analysis, SIAM Journal of Scientific Com-puting, SIAM Multiscale Modelling and Simulation, Springer books, Theoreti-cal Ecology.

II Research funding

• Action Medical Research

• MRC

• BBSRC

• EPSRC

• European Science Foundation

• Research Foundation Flanders

• Wellcome trust

• Research Foundation Flanders

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iii.2 External examiner

External course examiner/scrutineer

• University College London

Mathematics, Computers and Medicine (iBSc) Bd -new (INFNUMCM)

• University of Swansea,

• University of Limerick.

• Integrated BSc: Mathematics, Computers and Medicine, UCL

External Examiner of PhD theses

• Edward Lee, University of Glasgow, 29 May 2018 Quantifying the Development,Size, and Repertoire Diversity of T Cell Populations

• Ryan Howitt, University of Nottingham, 18 Dec 2017

Stochastic modelling of repeat-mediated phase variation in Campylobacter Jejuni

• Adedeji Oluwaseun Majekodunmi, University College London, 15 Sep 2017

Mathematical and Statistical Modelling of factors affecting CD4 T-cell Reconstitu-tion in HIV-Infected Children starting Anti-retroviral Therapy

• Katherine Best, University College London, 22 Apr 2016

Computational approaches to the analysis of the T cell receptor repertoire

• Daniel Laydon, Imperial College London, 20 Mar 2015

Modelling the diversity and persistence of the human T-lymphotropic virus type-1

• Siu Kwan Yip, University of Warwick, 6 Feb 2014

On the Pfaffian property of annihilating random walk and coalescing random walk

• Joanna Lewis, University College London, 31 Jan 2013

Mathematical and Statistical Modelling of CD4 T-cell Reconstitution in HIV-infectedChildren Starting Antiretroviral Therapy

• Ciara Dangefeld, University of Oxford, 13 Dec 2012

Stochastic models of ion channel dynamics and their role in short-term repolarisa-tion variability in cardiac cells

• Bartolomeus Hirt, University of Nottingam, 18 Oct 2012

Mathematical Modelling of Cell Cycle and Telomere Dynamics

• Hasan Alzambaidi, Manchester University, 19 Sep 2011

Numerical simulations of the spiking activity and the related first exit time of stochas-tic neural systems

• Iyabo Adamu, Heriot-Watt University, 16 Dec 2010

Numerical simulations of the spiking activity and the related first exit time of stochas-tic neural systems

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iii.3 External teaching

• Numerical methods for stochastic dynamics

Opening tutorial, SAMSI programme.

North Carolina, USA. 30 Aug 2009

• Markov chains and stochastic processes

Intensive two-day course, part of the European Phd Programme in ComputationalBiology, given at the Gulbenkian Institute, Lisbon, Portugal.

24-24 November 2008

END

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Documents

ACADEMIC CV 1 Personal detailsgrant/longLeeds.pdf · My contribution 100% of lectures and exam, preparation, delivery and assessment. MATH2450 Mathematics for Geophysics III Number