All Outputs (67)

Assessing the impact of physicochemical parameters in the predictive capabilities of thermodynamics-based stoichiometric approaches under mesophilic and thermophilic conditions (2020)
Working Paper

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

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

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.

A Systematic Upscaling of Nonlinear Chemical Uptake Within a Biofilm (2020)
Journal Article

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

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

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

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

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

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

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

© 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

© 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

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

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.

Bifurcations of self-similar solutions for reversing interfaces in the slow diffusion equation with strong absorption (2018)
Journal Article

Bifurcations of self-similar solutions for reversing interfaces are studied in the slow diffusion equation with strong absorption. The self-similar solutions bifurcate from the time-independent solutions for standing interfaces. We show that such bif... Read More about Bifurcations of self-similar solutions for reversing interfaces in the slow diffusion equation with strong absorption.

Lie symmetries of nonlinear parabolic-elliptic systems and their application to a tumour growth model (2018)
Journal Article

A generalisation of the Lie symmetry method is applied to classify a coupled system of reaction-diffusion equations wherein the nonlinearities involve arbitrary functions in the limit case in which one equation of the pair is quasi-steady but the oth... Read More about Lie symmetries of nonlinear parabolic-elliptic systems and their application to a tumour growth model.

Limit-cycle oscillatory coexpression of cross-inhibitory transcription factors: a model mechanism for lineage promiscuity (2018)
Journal Article

Lineage switches are genetic regulatory motifs that govern and maintain the commitment of a developing cell to a particular cell fate. A canonical example of a lineage switch is the pair of transcription factors PU.1 and GATA-1, of which the former i... Read More about Limit-cycle oscillatory coexpression of cross-inhibitory transcription factors: a model mechanism for lineage promiscuity.

Upscaling Diffusion Through First-Order Volumetric Sinks: A Homogenization of Bacterial Nutrient Uptake (2018)
Journal Article

In mathematical models that include nutrient delivery to bacteria, it is prohibitively expensive to include a pointwise nutrient uptake within small bacterial regions over bioreactor length-scales, and so such models often impose an effective uptake... Read More about Upscaling Diffusion Through First-Order Volumetric Sinks: A Homogenization of Bacterial Nutrient Uptake.

Finite indentation of highly curved elastic shells (2018)
Journal Article

Experimentally measuring the elastic properties of thin biological surfaces is non-trivial, particularly when they are curved. One technique that may be used is the indentation of a thin sheet of material by a rigid indenter, whilst measuring the app... Read More about Finite indentation of highly curved elastic shells.

Applying asymptotic methods to synthetic biology: modelling the reaction kinetics of the mevalonate pathway (2017)
Journal Article

The mevalonate pathway is normally found in eukaryotes, and allows for the production of isoprenoids, a useful class of organic compounds. This pathway has been successfully introduced to Escherichia coli, enabling a biosynthetic production route for... Read More about Applying asymptotic methods to synthetic biology: modelling the reaction kinetics of the mevalonate pathway.