Professor JOHN KING's Outputs (75)

An optogenetic method for interrogating YAP1 and TAZ nuclear-cytoplasmic shuttling (2021)
Journal Article
Dowbaj, A. M., Jenkins, R. P., Williamson, D., Heddleston, J. M., Ciccarelli, A., Fallesen, T., Hahn, K. M., O'Dea, R. D., King, J. R., Montagner, M., & Sahai, E. (2021). An optogenetic method for interrogating YAP1 and TAZ nuclear-cytoplasmic shuttling. Journal of Cell Science, 134(13), Article 5520657. https://doi.org/10.1242/jcs.253484

The shuttling of transcription factors and transcriptional regulators into and out of the nucleus is central to the regulation of many biological processes. Here we describe a new method for studying the rates of nuclear entry and exit of transcripti... Read More about An optogenetic method for interrogating YAP1 and TAZ nuclear-cytoplasmic shuttling.

Time dependent asymptotic analysis of the gene regulatory network of the AcrAB-TolC efflux pump system in gram-negative bacteria (2021)
Journal Article
Youlden, G. H., Ricci, V., Wang-Kan, X., Piddock, L. J., Jabbari, S., & King, J. R. (2021). Time dependent asymptotic analysis of the gene regulatory network of the AcrAB-TolC efflux pump system in gram-negative bacteria. Journal of Mathematical Biology, 82, Article 31. https://doi.org/10.1007/s00285-021-01576-4

Efflux pumps are a mechanism of intrinsic and evolved resistance in bacteria. If an efflux pump can expel an antibiotic so that its concentration within the cell is below a killing threshold the bacteria are resistant to the antibiotic. Efflux pumps... Read More about Time dependent asymptotic analysis of the gene regulatory network of the AcrAB-TolC efflux pump system in gram-negative bacteria.

A Model to Investigate the Impact of Farm Practice on Antimicrobial Resistance in UK Dairy Farms (2021)
Journal Article
Lanyon, C. W., King, J. R., Stekel, D. J., & Gomes, R. L. (2021). A Model to Investigate the Impact of Farm Practice on Antimicrobial Resistance in UK Dairy Farms. Bulletin of Mathematical Biology, 83(4), Article 36. https://doi.org/10.1007/s11538-021-00865-9

© 2021, The Author(s). The ecological and human health impact of antibiotic use and the related antimicrobial resistance (AMR) in animal husbandry is poorly understood. In many countries, there has been considerable pressure to reduce overall antibio... Read More about A Model to Investigate the Impact of Farm Practice on Antimicrobial Resistance in UK Dairy Farms.

Physicochemical and metabolic constraints for thermodynamics-based stoichiometric modelling under mesophilic growth conditions (2021)
Journal Article
Tomi-Andrino, C., Norman, R., Millat, T., Soucaille, P., Winzer, K., Barrett, D. A., King, J., & Kim, D.-H. (2021). Physicochemical and metabolic constraints for thermodynamics-based stoichiometric modelling under mesophilic growth conditions. PLoS Computational Biology, 17(1), Article e1007694. https://doi.org/10.1371/journal.pcbi.1007694

© 2021 Tomi-Andrino et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source a... Read More about Physicochemical and metabolic constraints for thermodynamics-based stoichiometric modelling under mesophilic growth conditions.

Termination points and homoclinic glueing for a class of inhomogeneous nonlinear ordinary differential equations (2021)
Journal Article
Keeler, J., Blyth, M., & King, J. (2021). Termination points and homoclinic glueing for a class of inhomogeneous nonlinear ordinary differential equations. Nonlinearity, 34(1), 532-561. https://doi.org/10.1088/1361-6544/abb18f

Solutions u(x) to the class of inhomogeneous nonlinear ordinary differential equations taking the form u + u 2 = αf (x) for parameter α are studied. The problem is defined on the x line with decay of both the solution u(x) and the imposed forcing f (... Read More about Termination points and homoclinic glueing for a class of inhomogeneous nonlinear ordinary differential equations.

Assessing the impact of physicochemical parameters in the predictive capabilities of thermodynamics-based stoichiometric approaches under mesophilic and thermophilic conditions (2020)
Preprint / Working Paper
Tomi-Andrino, C., Norman, R., Millat, T., Soucaille, P., Winzer, K., Barrett, D. A., King, J., & Kim, D.-H. Assessing the impact of physicochemical parameters in the predictive capabilities of thermodynamics-based stoichiometric approaches under mesophilic and thermophilic conditions

Metabolic engineering in the post-genomic era is characterised by the development of new methods for metabolomics and fluxomics, supported by the integration of genetic engineering tools and mathematical modelling. Particularly, constraint-based stoi... Read More about Assessing the impact of physicochemical parameters in the predictive capabilities of thermodynamics-based stoichiometric approaches under mesophilic and thermophilic conditions.

Type II singularities on complete non-compact Yamabe flow (2020)
Journal Article
Choi, B., Daskalopoulos, P., & King, J. (2021). Type II singularities on complete non-compact Yamabe flow. Journal für die reine und angewandte Mathematik, 2021(772), 83-119. https://doi.org/10.1515/crelle-2020-0032

This work concerns with the existence and detailed asymptotic analysis of Type II singularities for solutions to complete non-compact confor-mally flat Yamabe flow with cylindrical behavior at infinity. We provide the specific blow-up rate of the max... Read More about Type II singularities on complete non-compact Yamabe flow.

Type II Singularities on complete non-compact Yamabe flow (2020)
Journal Article
Choi, B., Daskalopoulos, P., & King, J. (2021). Type II Singularities on complete non-compact Yamabe flow. Journal für die reine und angewandte Mathematik, 2021(772), 83-119. https://doi.org/10.1515/crelle-2020-0032

This work concerns with the existence and detailed asymptotic analysis of Type II singularities for solutions to complete non-compact confor-mally flat Yamabe flow with cylindrical behavior at infinity. We provide the specific blow-up rate of the max... Read More about Type II Singularities on complete non-compact Yamabe flow.

Using singular perturbation theory to determine kinetic parameters in a non-standard coupled enzyme assay (2020)
Journal Article
Dalwadi, M. P., Orol, D., Walter, F., Minton, N. P., King, J. R., & Kovács, K. (2020). Using singular perturbation theory to determine kinetic parameters in a non-standard coupled enzyme assay. Journal of Mathematical Biology, 81(2), 649-690. https://doi.org/10.1007/s00285-020-01524-8

We investigate how to characterize the kinetic parameters of an aminotransaminase using a non-standard coupled (or auxiliary) enzyme assay, where the peculiarity arises for two reasons. First, one of the products of the auxiliary enzyme is a substrat... Read More about Using singular perturbation theory to determine kinetic parameters in a non-standard coupled enzyme assay.

A Systematic Upscaling of Nonlinear Chemical Uptake Within a Biofilm (2020)
Journal Article
Dalwadi, M. P., & King, J. R. (2020). A Systematic Upscaling of Nonlinear Chemical Uptake Within a Biofilm. SIAM Journal on Applied Mathematics, 80(4), 1723-1750. https://doi.org/10.1137/19m130220x

When modelling transport of a chemical species to a colony of bacteria in a biofilm, it is computationally expensive 4 to treat each bacterium even as a point sink, let alone to capture the finite nature of each bacterium. Instead, models tend to 5 t... Read More about A Systematic Upscaling of Nonlinear Chemical Uptake Within a Biofilm.

Development of a Corynebacterium glutamicum bio-factory for self-sufficient transaminase reactions (2020)
Journal Article
Grigoriou, S., Kugler, P., Kulcinskaja, E., Walter, F., King, J., Hill, P., Wendisch, V. F., & O'Reilly, E. (2020). Development of a Corynebacterium glutamicum bio-factory for self-sufficient transaminase reactions. Green Chemistry, 22(13), 4128-4132. https://doi.org/10.1039/d0gc01432j

The development of biocatalytic routes for the synthesis of chiral amines starting from achiral building blocks is highly desirable. Here, we report a self-sufficient whole-cell system for the conversion of a model ketone to the corresponding cyclic... Read More about Development of a Corynebacterium glutamicum bio-factory for self-sufficient transaminase reactions.

Mathematical model to determine the effect of a sub-glycocalyx space (2020)
Journal Article
Dalwadi, M. P., Dalwadi, M. P., King, J. R., Dyson, R. J., & Arkill, K. P. (2020). Mathematical model to determine the effect of a sub-glycocalyx space. Physical Review Fluids, 5(4), Article 043103. https://doi.org/10.1103/physrevfluids.5.043103

We consider the drainage of blood plasma across the capillary wall, focusing on the flow through the endothelial glycocalyx layer that coats the luminal surface of vascular endothelial cells. We investigate how the presence of a sub-glycocalyx space... Read More about Mathematical model to determine the effect of a sub-glycocalyx space.

An asymptotic analysis of the malonyl-CoA route to 3-hydroxypropionic acid in genetically engineered microbes (2020)
Journal Article
Dalwadi, M. P., & King, J. R. (2020). An asymptotic analysis of the malonyl-CoA route to 3-hydroxypropionic acid in genetically engineered microbes. Bulletin of Mathematical Biology, 82, Article 36. https://doi.org/10.1007/s11538-020-00714-1

There has been recent interest in creating an efficient microbial production route for 3-hydroxypropionic acid, an important platform chemical. We develop and solve a mathematical model for the time-dependent metabolite concentrations in the malonyl-... Read More about An asymptotic analysis of the malonyl-CoA route to 3-hydroxypropionic acid in genetically engineered microbes.

Moving boundary problems for quasi-steady conduction limited melting (2019)
Journal Article
Morrow, L. C., King, J. R., Moroney, T. J., & Mccue, S. (2019). Moving boundary problems for quasi-steady conduction limited melting. SIAM Journal on Applied Mathematics, 79(5), 2107-2131. https://doi.org/10.1137/18M123445X

The problem of melting a crystal dendrite is modelled as a quasi-steady Stefan 5 problem. By employing the Baiocchi transform, asymptotic results are derived in the limit that 6 the crystal melts completely, extending previous results that hold for a... Read More about Moving boundary problems for quasi-steady conduction limited melting.

Mathematical modelling of contact dermatitis from nickel and chromium (2019)
Journal Article
Ward, J. P., Franks, S. J., Tindall, M. J., King, J. R., Curtis, A., & Evans, G. S. (2019). Mathematical modelling of contact dermatitis from nickel and chromium. Journal of Mathematical Biology, 79(2), 595-630. https://doi.org/10.1007/s00285-019-01371-2

Dermal exposure to metal allergens can lead to irritant and allergic contact dermatitis (ACD). In this paper we present a mathematical model of the absorption of metal ions, hexavalent chromium and nickel, into the viable epidermis and compare the lo... Read More about Mathematical modelling of contact dermatitis from nickel and chromium.

A core mechanism for specifying root vascular pattern can replicate the anatomical variation seen in diverse plant species (2019)
Journal Article
Mellor, N., Vaughan-Hirsch, J., Kümpers, B. M., Help-Rinta-Rahko, H., Miyashima, S., Pekka Mähönen, A., Campilho, A., King, J. R., & Bishopp, A. (2019). A core mechanism for specifying root vascular pattern can replicate the anatomical variation seen in diverse plant species. Development, 146(6), Article dev172411. https://doi.org/10.1242/dev.172411

Pattern formation is typically controlled through the interaction between molecular signals within a given tissue. During early embryonic development, roots of the model plant Arabidopsis thaliana have a radially symmetric pattern, but a heterogeneou... Read More about A core mechanism for specifying root vascular pattern can replicate the anatomical variation seen in diverse plant species.

Gsmodutils: a python based framework for test-driven genome scale metabolic model development (2019)
Journal Article
Gilbert, J., Pearcy, N., Norman, R., Millat, T., Winzer, K., King, J., Hodgman, C., Minton, N., & Twycross, J. (2019). Gsmodutils: a python based framework for test-driven genome scale metabolic model development. Bioinformatics, 35(18), 3397-3403. https://doi.org/10.1093/bioinformatics/btz088

© 2019 The Author(s) 2019. Published by Oxford University Press. Motivation: Genome scale metabolic models (GSMMs) are increasingly important for systems biology and metabolic engineering research as they are capable of simulating complex steady-stat... Read More about Gsmodutils: a python based framework for test-driven genome scale metabolic model development.

A tractable mathematical model for tissue growth (2019)
Journal Article
Eyles, J., King, J. R., & Styles, V. (2019). A tractable mathematical model for tissue growth. Interfaces and Free Boundaries, 21(4), 463-493. https://doi.org/10.4171/IFB/428

© European Mathematical Society 2019 Using formal asymptotic methods we derive a free boundary problem representing one of the simplest mathematical descriptions of the growth and death of a tumour or other biological tissue. The mathematical model t... Read More about A tractable mathematical model for tissue growth.

Gsmodutils: A python based framework for test-driven genome scale metabolic model development (2018)
Other
Gilbert, J. P., Pearcy, N., Norman, R., Millat, T., Winzer, K., King, J., Hodgman, C., Minton, N., & Twycross, J. (2018). Gsmodutils: A python based framework for test-driven genome scale metabolic model development

Motivation Genome scale metabolic models (GSMMs) are increasingly important for systems biology and metabolic engineering research as they are capable of simulating complex steady-state behaviour. Constraints based models of this form can include tho... Read More about Gsmodutils: A python based framework for test-driven genome scale metabolic model development.

The structure of a dewetting rim with strong slip: the long-time evolution (2018)
Journal Article
Evans, P., King, J., & Münch, A. (2018). The structure of a dewetting rim with strong slip: the long-time evolution. Multiscale Modeling and Simulation: A SIAM Interdisciplinary Journal, 16(3), 1365-1391. https://doi.org/10.1137/15M1051221

When a thin viscous film dewets from a solid substrate, the liquid forms a characteristic rim near the contact line as the contact line retracts. The shape of the rim and also the retraction rate vary strongly with the amount of slip that occurs at t... Read More about The structure of a dewetting rim with strong slip: the long-time evolution.