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Dr David Richards

Dr David Richards

MRC Career Development Fellow, Senior Lecturer

 7483

 Living Systems Institute T02.13

 

Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD

Overview

Personal webpage

http://www.exeter.ac.uk/davidrichards/

Research

I am currently an MRC Career Development Fellow and a Turing Fellow based in the Living Systems Institute at the University of Exeter. My research uses a combination of mathematical modelling, computer simulation and experimental work to study various biological and medical processes. This typically involves using a combination of dynamical systems, reaction-diffusion equations, spatio-temporal modelling, numerical simulation, machine learning and image analysis. Currently my group is working on the following projects:

  • Target shape dependence during phagocytosis
  • The multistage nature of phagocytic engulfment
  • Computer simulations of early embryogenesis
  • Machine learning of microglial state
  • Understanding the growth of filamentous fungi
  • The dynamics of peroxisome shape
  • The role of noise in pituitary cells
  • Plant response to phytopathogens

One of the main areas of my research is phagocytosis (the way that our immune cells engulf and destroy relatively large target particles such as bacteria and dead cells). In particular, my group studies how phagocytosis depends on properties of both the immune cell (such as membrane tension) and the target (such as size and shape). This work uses an integrated modelling-experimental approach that couples computational models of membrane shape with dual-micropipette experiments. This has applications to both the design of microparticle drug delivery systems and various medical conditions such as lupus and Wiskott-Aldrich syndrome.

Background

After an undergraduate in physics, I studied for a masters in mathematics (both at the University of Cambridge). My PhD was in string theory and was based at DAMTP in Cambridge. I then spent a year teaching at the African Institute for Mathematical Sciences (AIMS) in Cape Town, before switching fields to mathematical and computational biology. This included post-docs at the John Innes Centre in Norwich and Imperial College London, before my current position at the University of Exeter.

Possible PhD projects

Some examples of possible PhD project ideas:

  • Simulations of early embryogenesis
  • Mathematical modelling of cell shape across organisms
  • Models of engulfment during phagocytosis
  • Simulations of the dynamics of peroxisome shape
  • Quantitative understanding of the plant response to fungal attack
  • Machine learning to identify microglial state
  • Image analysis of filamentous fungi

Group

My group currently includes:

  • Jim Lees - MRC-funded Postdoctoral Research Fellow - working on "The Fundamentals of Phagocytosis: Integrating
  • Jordan Hembrow - PhD student - working on "Mathematical modelling of phytopathogen-targeted secretion pathways"
  • Peyman Shadmani - PhD student - working on "Models of cell shape during phagocytosis"
  • Alaina Cockerell - PhD student - working on "Simulation of human blastocyst development"
  • Sophie Nye - PhD student - working on understanding and modelling fungal growth
  • Amber Connerton - PhD student - working on "The role of Rho GTPases in plant immunity"
  • Victoria Armer - PhD student - working on "Exploring communication mechanisms between fungal pathogens and plant cells"
  • Ifeoma Nwabufo - Master's student - working on a machine learning approach to identifying microglial state

Funding

I am funded by the MRC as a Career Development Fellow. My group is also supported by BBSRC and the Wellcome Trust.

Research

Publications

Key publications | Publications by category | Publications by year

Publications by category


Journal articles

Richards D, Cockerell A, Wright L, Dattani A, Guo G, Smith A, Tsaneva K (2023). Biophysical models of early mammalian embryogenesis. Stem Cell Reports, 18, 26-46.
Richards DM, Walker JJ, Tabak J (2020). Ion channel noise shapes the electrical activity of endocrine cells. PLoS Comput Biol, 16(4). Abstract.  Author URL.
Passmore JB, Carmichael RE, Schrader TA, Godinho LF, Ferdinandusse S, Lismont C, Wang Y, Hacker C, Islinger M, Fransen M, et al (2020). Mitochondrial fission factor (MFF) is a critical regulator of peroxisome maturation. Biochim Biophys Acta Mol Cell Res, 1867(7). Abstract.  Author URL.
Richards DM (2020). Receptor Models of Phagocytosis: the Effect of Target Shape. Adv Exp Med Biol, 1246, 55-70. Abstract.  Author URL.
Castro IG, Richards DM, Metz J, Costello JL, Passmore JB, Schrader TA, Gouveia A, Ribeiro D, Schrader M (2018). A role for Mitochondrial Rho GTPase 1 (MIRO1) in motility and membrane dynamics of peroxisomes. Traffic, 19(3), 229-242.
Richards DM, Endres RG (2017). How cells engulf: a review of theoretical approaches to phagocytosis. Reports on Progress in Physics, 80(12), 126601-126601.
Richards DM, Endres RG (2016). Target shape dependence in a simple model of receptor-mediated endocytosis and phagocytosis. Proceedings of the National Academy of Sciences of the United States of America, 113, 6113-6118. Abstract.
Micali G, Aquino G, Richards DM, Endres RG (2015). Accurate Encoding and Decoding by Single Cells: Amplitude Versus Frequency Modulation. PLOS Computational Biology, 11(6), e1004222-e1004222.
Richards DM, Saunders TE (2015). Spatiotemporal Analysis of Different Mechanisms for Interpreting Morphogen Gradients. Biophysical Journal, 108(8), 2061-2073.
Richards DM, Endres RG (2014). The Mechanism of Phagocytosis: Two Stages of Engulfment. Biophysical Journal, 107(7), 1542-1553.
Richards D, Berry S, Howard M (2013). Illustrations of Mathematical Modeling in Biology: Epigenetics, Meiosis, and an Outlook. Cold Spring Harbor Symposia on Quantitative Biology, 77(0), 175-181.
Richards DM, Hempel AM, Flärdh K, Buttner MJ, Howard M (2012). Mechanistic basis of branch-site selection in filamentous bacteria. PLoS Computational Biology, 8(3). Abstract.
Richards DM, Greer E, Martin AC, Moore G, Shaw PJ, Howard M (2012). Quantitative Dynamics of Telomere Bouquet Formation. PLoS Computational Biology, 8(12), e1002812-e1002812.
Flardh K, Richards DM, Hempel AM, Howard M, Buttner MJ (2012). Regulation of apical growth and hyphal branching in Streptomyces. CURRENT OPINION IN MICROBIOLOGY, 15(6), 737-743. Author URL.
Hempel AM, Cantlay S, Molle V, Wang S-B, Naldrett MJ, Parker JL, Richards DM, Jung Y-G, Buttner MJ, Flärdh K, et al (2012). The Ser/Thr protein kinase AfsK regulates polar growth and hyphal branching in the filamentous bacteria. <i>Streptomyces</i>. Proceedings of the National Academy of Sciences, 109(35). Abstract.
Richards DM (2008). The one-loop five-graviton amplitude and the effective action. Journal of High Energy Physics, 2008(10), 042-042.
Richards DM (2008). The one-loop<i>H</i><sup>2</sup><i>R</i><sup>3</sup>and<i>H</i><sup>2</sup>(∇<i>H</i>)<sup>2</sup><i>R</i>terms in the effective action. Journal of High Energy Physics, 2008(10), 043-043.

Publications by year


In Press

Valente F, Mansfield J, Herring D, Romana G, Rodrigues C, Metz J, Craze M, Bowden S, Greenland A, Moger J, et al (In Press). Wheat cells show positional responses to invasive <i>Zymoseptoria tritici</i>.  Abstract.

2023

Richards D, Cockerell A, Wright L, Dattani A, Guo G, Smith A, Tsaneva K (2023). Biophysical models of early mammalian embryogenesis. Stem Cell Reports, 18, 26-46.

2020

Richards DM, Walker JJ, Tabak J (2020). Ion channel noise shapes the electrical activity of endocrine cells. PLoS Comput Biol, 16(4). Abstract.  Author URL.
Passmore JB, Carmichael RE, Schrader TA, Godinho LF, Ferdinandusse S, Lismont C, Wang Y, Hacker C, Islinger M, Fransen M, et al (2020). Mitochondrial fission factor (MFF) is a critical regulator of peroxisome maturation. Biochim Biophys Acta Mol Cell Res, 1867(7). Abstract.  Author URL.
Richards DM (2020). Receptor Models of Phagocytosis: the Effect of Target Shape. Adv Exp Med Biol, 1246, 55-70. Abstract.  Author URL.

2018

Castro IG, Richards DM, Metz J, Costello JL, Passmore JB, Schrader TA, Gouveia A, Ribeiro D, Schrader M (2018). A role for Mitochondrial Rho GTPase 1 (MIRO1) in motility and membrane dynamics of peroxisomes. Traffic, 19(3), 229-242.

2017

Richards DM, Endres RG (2017). How cells engulf: a review of theoretical approaches to phagocytosis. Reports on Progress in Physics, 80(12), 126601-126601.

2016

Richards DM, Endres RG (2016). Target shape dependence in a simple model of receptor-mediated endocytosis and phagocytosis. Proceedings of the National Academy of Sciences of the United States of America, 113, 6113-6118. Abstract.

2015

Micali G, Aquino G, Richards DM, Endres RG (2015). Accurate Encoding and Decoding by Single Cells: Amplitude Versus Frequency Modulation. PLOS Computational Biology, 11(6), e1004222-e1004222.
Richards DM, Saunders TE (2015). Spatiotemporal Analysis of Different Mechanisms for Interpreting Morphogen Gradients. Biophysical Journal, 108(8), 2061-2073.

2014

Richards DM, Endres RG (2014). The Mechanism of Phagocytosis: Two Stages of Engulfment. Biophysical Journal, 107(7), 1542-1553.

2013

Richards D, Berry S, Howard M (2013). Illustrations of Mathematical Modeling in Biology: Epigenetics, Meiosis, and an Outlook. Cold Spring Harbor Symposia on Quantitative Biology, 77(0), 175-181.

2012

Richards DM, Hempel AM, Flärdh K, Buttner MJ, Howard M (2012). Mechanistic basis of branch-site selection in filamentous bacteria. PLoS Computational Biology, 8(3). Abstract.
Richards DM, Greer E, Martin AC, Moore G, Shaw PJ, Howard M (2012). Quantitative Dynamics of Telomere Bouquet Formation. PLoS Computational Biology, 8(12), e1002812-e1002812.
Flardh K, Richards DM, Hempel AM, Howard M, Buttner MJ (2012). Regulation of apical growth and hyphal branching in Streptomyces. CURRENT OPINION IN MICROBIOLOGY, 15(6), 737-743. Author URL.
Hempel AM, Cantlay S, Molle V, Wang S-B, Naldrett MJ, Parker JL, Richards DM, Jung Y-G, Buttner MJ, Flärdh K, et al (2012). The Ser/Thr protein kinase AfsK regulates polar growth and hyphal branching in the filamentous bacteria. <i>Streptomyces</i>. Proceedings of the National Academy of Sciences, 109(35). Abstract.

2008

Richards DM (2008). The one-loop five-graviton amplitude and the effective action. Journal of High Energy Physics, 2008(10), 042-042.
Richards DM (2008). The one-loop<i>H</i><sup>2</sup><i>R</i><sup>3</sup>and<i>H</i><sup>2</sup>(∇<i>H</i>)<sup>2</sup><i>R</i>terms in the effective action. Journal of High Energy Physics, 2008(10), 043-043.

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Teaching

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