# School of Mathematics

## Prof Carmen Molina-Paris

Professor in Applied Mathematics

Applied Mathematics

### Contact details

Room: Satellite 10.21

Tel: +44 (0)113 3435151

Email: C.MolinaParis @ leeds.ac.uk

### Keywords

Quantum field theory

Early universe

Applied mathematics

Stochastic Markov processes

T cell development

T cell receptor signalling

T cell receptor diversity

Thymic selection

## Research interests

My main current interest is modelling immune responses.

Three main themes are of special interest:

[1] T cell receptor-ligand binding and T cell receptor

signalling, What determines the ability of T cells

to discriminate different antigens.

[2] Size and receptor diversity of the different T cell populations.

[3] Interactions, in vivo and in real time, between dendritic cells (that display antigens on their membrane) and T cells (that display on their membrane T cell receptors).

As a theoretical physicist I am interested in understanding particle production in the Early Universe and the validity of the semi-classical approximation to Einstein's equation.

## Current postgraduate students

Haifaa Alrihieli (2016)

Luis De La Higuera Romero (2013)

Marco Ferrarini (2014)

Maria Nowicka (2012)

## Publications

**Gonçalves P, Ferrarini M, Molina-Paris C, Lythe G, Vasseur F, Lim A, Rocha B, Azogui O** A new mechanism shapes the naïve CD8^{+}T cell repertoire: The selection for full diversity *Molecular Immunology*, **85**, 66-80, 2017

DOI:10.1016/j.molimm.2017.01.026

View abstract

**Artalejo JR, Gómez-Corral A, López-García M, Molina-París C** Stochastic descriptors to study the fate and potential of naive T cell clonotypes in the periphery *Journal of Mathematical Biology*, **74**, 673-708, 2017

DOI:10.1007/s00285-016-1020-6

View abstract

**Chu HH, Chan SW, Gosling JP, Blanchard N, Tsitsiklis A, Lythe G, Shastri N, Molina-París C, Robey EA** Continuous Effector CD8^{+}T Cell Production in a Controlled Persistent Infection Is Sustained by a Proliferative Intermediate Population *Immunity*, **45**, 159-171, 2016

DOI:10.1016/j.immuni.2016.06.013

View abstract

**Castro M, Lythe G, Molina-París C, Ribeiro RM** Mathematics in modern immunology *Interface Focus*, **6**, 14, 2016

DOI:10.1098/rsfs.2015.0093

View abstract

**Lythe G, Callard RE, Hoare RL, Molina-París C** How many TCR clonotypes does a body maintain? *Journal of Theoretical Biology*, **389**, 214-224, 2016

DOI:10.1016/j.jtbi.2015.10.016

View abstract

**Anderson PR, Molina-París C, Sanders DH** Breakdown of the semiclassical approximation during the early stages of preheating *Physical Review D - Particles, Fields, Gravitation and Cosmology*, **92**, 2015

DOI:10.1103/PhysRevD.92.083522

View abstract

**Pham K, Shimoni R, Charnley M, Ludford-Menting MJ, Hawkins ED, Ramsbottom K, Oliaro J, Izon D, Ting SB, Reynolds J, Lythe G, Molina-Paris C, Melichar H, Robey E, Humbert PO, Gu M, Russell SM** Asymmetric cell division during T cell development controls downstream fate *Journal of Cell Biology*, **210**, 933-950, 2015

DOI:10.1083/jcb.201502053

View abstract

**Reynolds J, Amado IF, Freitas AA, Lythe G, Molina-París C** A mathematical perspective on CD4(+) T cell quorum-sensing. *J Theor Biol*, **347**, 160-175, 2014

DOI:10.1016/j.jtbi.2013.12.019

View abstract

**Sawicka M, Stritesky GL, Reynolds J, Abourashchi N, Lythe G, Molina-París C, Hogquist KA** From pre-DP, post-DP, SP4, and SP8 Thymocyte Cell Counts to a Dynamical Model of Cortical and Medullary Selection. *Front Immunol*, **5**, 19, 2014

DOI:10.3389/fimmu.2014.00019

View abstract

**Castro M, van Santen HM, Férez M, Alarcón B, Lythe G, Molina-París C** Receptor Pre-Clustering and T cell Responses: Insights into Molecular Mechanisms. *Front Immunol*, **5**, 132, 2014

DOI:10.3389/fimmu.2014.00132

View abstract

**Gillard J, Laws TR, Lythe G, Molina-París C** Modelling early events in Francisella tularensis pathogenesis *Frontiers in Cellular and Infection Microbiology*, **4**, 2014

DOI:10.3389/fcimb.2014.00169

View abstract

**Reynolds J, Coles M, Lythe G, Molina-París C** Mathematical Model of Naive T Cell Division and Survival IL-7 Thresholds. *Front Immunol*, **4**, 434, 2013

DOI:10.3389/fimmu.2013.00434

View abstract

**Celli S, Day M, Müller AJ, Molina-Paris C, Lythe G, Bousso P** How many dendritic cells are required to initiate a T-cell response? *Blood*, **120**, 3945-3948, 2012

DOI:10.1182/blood-2012-01-408260

View abstract

**Molina-Paris C** A stochastic T cell response criterion *Journal of the Royal Society Interface*, 2012

DOI:10.1098/rsif.2012.0205

**Voliotis M, Cohen N, Molina-París C, Liverpool TB** Proofreading of misincorporated nucleotides in DNA transcription *Physical Biology*, **9**, 2012

DOI:10.1088/1478-3975/9/3/036007

View abstract

**Voliotis M, Cohen N, Molina-París C, Liverpool TB** Proofreading of misincorporated nucleotides in DNA transcription *Physical Biology*, **9**, 2012

DOI:10.1088/1478-3975/9/3/036002

View abstract

**Alemeida ARM, Amado IF, Reynolds J, Berges J, Lythe G, Molina-Paris C, Freitas AA** Quorum-Sensing in CD4+ T Cell Homeostasis: A Hypothesis and a Model *Frontiers in Immunology*, **3**, 2012

DOI:10.3389/fimmu.2012.00125

View abstract

**van den Berg HA, Molina-ParíS C, Sewel AK** Specific T-cell activation in an unspecific T-cell repertoire *Science Progress*, **94**, 245-264, 2011

DOI:10.3184/003685011X13139280383942

View abstract

**Molina-París C ** *Mathematical Models and Immune Cell Biology*. Springer Verlag 2011

View abstract

**Van Den Berg HA, Molina-París C, Sewell AK** Specific T-cell activation in an unspecific T-cell repertoire. *Sci Prog*, **94**, 245-264, 2011

View abstract

**Visser M, Molina-Paris C** Acoustic geometry for general relativistic barotropic irrotational fluid flow *NEW J PHYS*, **12**, 2010

DOI:10.1088/1367-2630/12/9/095014

**Latham AM, Molina-París C, Homer-Vanniasinkam S, Ponnambalam S** An integrative model for vascular endothelial growth factor A as a tumour biomarker. *Integr Biol (Camb)*, **2**, 397-407, 2010

DOI:10.1039/c0ib00008f

View abstract

**Stirk ER, Lythe G, van den Berg HA, Molina-París C** Stochastic competitive exclusion in the maintenance of the naïve T cell repertoire. *J Theor Biol*, **265**, 396-410, 2010

DOI:10.1016/j.jtbi.2010.05.004

View abstract

**Stirk ER, Lythe G, van den Berg HA, Hurst GA, Molina-París C** The limiting conditional probability distribution in a stochastic model of T cell repertoire maintenance. *Math Biosci*, **224**, 74-86, 2010

DOI:10.1016/j.mbs.2009.12.004

View abstract

**Anderson PR, Molina-Paris C, Mottola E** Cosmological horizon modes and linear response in de Sitter spacetime *PHYS REV D*, **80**, 2009

DOI:10.1103/PhysRevD.80.084005

**Voliotis M, Cohen N, Molina-Paris C, Liverpool TB** Backtracking and Proofreading in DNA Transcription *PHYS REV LETT*, **102**, 2009

DOI:10.1103/PhysRevLett.102.258101

**Stirk ER, Molina-París C, van den Berg HA** Stochastic niche structure and diversity maintenance in the T cell repertoire. *J Theor Biol*, **255**, 237-249, 2008

DOI:10.1016/j.jtbi.2008.07.017

View abstract

**Anderson PR, Molina-Paris C, Evanich D, Cook GB** Study of the preheating phase of chaotic inflation *PHYS REV D*, **78**, 2008

DOI:10.1103/PhysRevD.78.083514

**Dunn S, Morrison EE, Liverpool TB, Molina-París C, Cross RA, Alonso MC, Peckham M** Differential trafficking of Kif5c on tyrosinated and detyrosinated microtubules in live cells. *J Cell Sci*, **121**, 1085-1095, 2008

DOI:10.1242/jcs.026492

View abstract

**Voliotis M, Cohen N, Molina-Paris C, Liverpool TB** Fluctuations, pauses, and backtracking in DNA transcription *BIOPHYS J*, **94**, 334-348, 2008

DOI:10.1529/biophysj.107.105767

**Voliotis M, Molina-Paris C, Cohen N, Liverpool T** Fluctuations, pauses and backtracking in DNA transcription *Biophysical Journal*, **94**, 334-348, 2008

**Briones C, de Vicente A, Molina-París C, Domingo E** Minority memory genomes can influence the evolution of HIV-1 quasispecies in vivo. *Gene*, **384**, 129-138, 2006

DOI:10.1016/j.gene.2006.07.037

View abstract

**Voliotis M; Molina-Paris C; Liverpool TB; Cohen N ** *Noise R Us: from gene regulatory networks to WWW*Proceedings of AISB'06: Adaptation in Artificial and Biological Systems, 167-175 2006

**Briones C, Molina-Paris C, Domingo E** Minority
memory genomes can influence the evolution of HIV-1 quasispecies in
vivo'
memory genomes can influence the evolution of HIV-1 quasispecies in
vivo'. *Gene*, 2006

**Castro M, Molina-París C, Deisboeck TS** Tumor growth instability and the onset of invasion. *Phys Rev E Stat Nonlin Soft Matter Phys*, **72**, 041907, 2005

DOI:10.1103/PhysRevE.72.041907

View abstract

**Anderson PR, Molina-Paris C, Mottola E** Short distance and initial state effects in inflation: Stress tensor and decoherence *PHYS REV D*, **72**, 2005

DOI:10.1103/PhysRevD.72.043515

**Habib S, Heinen A, Heitmann K, Jungman G, Molina-Paris C** Characterizing inflationary perturbations: The uniform approximation *PHYS REV D*, **70**, 2004

DOI:10.1103/PhysRevD.70.083507

**Briones C, Domingo E, Molina-Paris C** Memory in retroviral quasispecies: experimental evidence and theoretical model for human immunodeficiency virus *Journal of Molecular Biology*, **331**, 213-229, 2003

DOI:10.1016/S0022-2836(03)00661-2

**Gaite J, Hochberg D, Molina-París C** Large-scale features of rotating forced turbulence *Physical Review E - Statistical, Nonlinear, and Soft Matter Physics*, **67**, 263041-2630410, 2003

View abstract

**Gaite J, Hochberg D, Molina-París C** Large-scale features of rotating forced turbulence. *Phys Rev E Stat Nonlin Soft Matter Phys*, **67**, 026304, 2003

DOI:10.1103/PhysRevE.67.026304

View abstract

**Van den Berg H, Molina-Paris C** Thymic Presentation of Autoantigens and the Efficency of Negative Selection *Journal of Theoretical Medicine*, **5**, 1-22, 2003

DOI:10.1080/102736620310001604910

**Anderson PR, Molina-Paris C, Mottola E** Linear response, validity of semiclassical gravity, and the stability of flat space *Physical Review D (Particles and Fields)*, **67**, pp.024026, 2003

DOI:10.1103/PhysRevD.67.024026

**Domingo E, Ruiz-Jarabo CM, Arias A, Molina-Paris C, Briones C, Baranowski E, Escarmis C** Detection and biological implications of genetic memory in viral quasispecies *None*, 2003

**Habib S, Molina-Paris C, Deisboeck TS** Complex Dynamics of Tumors: Modeling an Emerging Brain Tumour System with Coupled Reaction-Diffusion Equations *Physica A - Statistical and Theoretical Physics*, **327**, 501-524, 2003

**Habib S, Heitmann K, Jungman G, Molina-París C** The inflationary perturbation spectrum *Physical Review Letters*, **89**, 2002

View abstract

**Habib S, Heitmann K, Jungman G, Molina-Paris C** The Inflationary Perturbation Spectrum *Physical Review Letters*, **89**, pp.281301, 2002

DOI:10.1103/PhysRevLett.89.281301

**Ruíz-Jarabo CM, Arias A, Molina-París C, Briones C, Baranowski E, Escarmís C, Domingo E** Duration and fitness dependence of quasispecies memory. *J Mol Biol*, **315**, 285-296, 2002

DOI:10.1006/jmbi.2001.5232

View abstract

**Molina-Paris C; Gaite J; Hochberg D; Perez-Mercader J ** *Magnetohydrodynamic turbulence in protostars*ASTR SOC P, 307-312 2002

View abstract

**Habib S, Lindenberg K, Lythe GD, Molina-Paris C** Diffusion-limited reaction in one dimension: Paired and unpaired nucleation *Journal of Chemical Physics*, **115**, 73-89, 2001

DOI:10.1063/1.1372763

**Dalvit DAR, Mazzitelli FD, Molina-Paris C** One-loop graviton corrections to Maxwell's equations *PHYS REV D*, **6308**, 2001

**Hochberg D, Molina-París C, Visser M** Heat kernel regularization of the effective action for stochastic reaction-diffusion equations *Physical Review E - Statistical, Nonlinear, and Soft Matter Physics*, **63**, 361321-3613217, 2001

View abstract

**Hochberg D, Molina-Paris C, Visser M** Heat kernel regularization of the effective action for stochastic reaction-diffusion equations *PHYS REV E*, **6303**, 2001

**Habib S; Heitmann K; Jungman G; Molina-Paris C; Singh A ** *A Methodology for Analzing Predictions from Slow-roll Inflation: Preliminary Results* 2001

**Hochberg D, Molina-Paris C, Mercader JP, Visser M** SmalL-scale Properties of the KPZ Equation and Dynamical Symmetry Breaking *Physics Letters. Section A: General, Atomic and Solid State Physics*, **278**, 177-183, 2001

**Anderson PR, Eaker W, Habib S, Molina-Paris C** Attractor States and Quantum Instabilities in de Sitter Space *International Journal of Theoretical Physics*, **40**, 2217-2229, 2001

DOI:10.1023/A:1012934204432

**Molina-Paris C, Anderson PR, Ramsey S** Interacting Field Theories in Robertson-Walker Spacetimes: Analytic Approximations *International Journal of Theoretical Physics*, **40**, 2231-2258, 2001

DOI:10.1023/A:1012938321270

**Anderson PR, Eaker W, Habib S, Molina-Paris C, Mottola E** Attractor states and infrared scaling in de Sitter space *PHYS REV D*, **6212**, 2000

**Molina-Paris C** Deterministic and stochastic naive T cell population dynamics: symmetric and asymmetric cell division *An international journal of Dynamical Systems*

**Lythe GD** A stochastic T cell response criterion *Journal of the Royal Society Interface*

Molina-Paris C; Higuera Luis,de la; Lopez-Garcia,Martin; Lythe,G *IL-2 stimulation of regulatory T cells: a stochastic and algorithmic approach*

**Molina-Paris C, Ferrarini M, Lythe G** Sampling from T cell receptor repertoires In *Contributions in Mathematical and Computational Sciences*

View abstract

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