ORCID Profile
0000-0001-6981-4350
Current Organisation
University of Queensland
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In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Biological Mathematics | Theoretical and Applied Mechanics | Applied Mathematics |
Expanding Knowledge in the Physical Sciences | Expanding Knowledge in the Biological Sciences | Expanding Knowledge in the Mathematical Sciences
Publisher: Informa UK Limited
Date: 04-2008
DOI: 10.4161/CAM.2.2.6373
Publisher: Springer Science and Business Media LLC
Date: 17-03-2010
Publisher: Elsevier BV
Date: 04-2016
Publisher: Public Library of Science (PLoS)
Date: 16-03-2022
DOI: 10.1371/JOURNAL.PONE.0264521
Abstract: Through the integration of results from an imaging analysis of intracellular trafficking of labelled neurosecretory vesicles in chromaffin cells, we develop a Markov state model to describe their transport and binding kinetics. Our simulation results indicate that a spatial redistribution of neurosecretory vesicles occurs upon secretagogue stimulation leading vesicles to the plasma membrane where they undergo fusion thereby releasing adrenaline and noradrenaline. Furthermore, we find that this redistribution alone can explain the observed up-regulation of vesicle transport upon stimulation and its directional bias towards the plasma membrane. Parameter fitting indicates that in the deeper compartment within the cell, vesicle transport is asymmetric and characterised by a bias towards the plasma membrane.
Publisher: Springer Science and Business Media LLC
Date: 04-2011
DOI: 10.1007/BF03322585
Publisher: World Scientific Pub Co Pte Lt
Date: 07-2006
DOI: 10.1142/S0218202506001509
Abstract: We present partial differential equation (PDE) model hierarchies for the chemotactically driven motion of biological cells. Starting from stochastic differential models, we derive a kinetic formulation of cell motion coupled to diffusion equations for the chemoattractants. We also derive a fluid dynamic (macroscopic) Keller–Segel type chemotaxis model by scaling limit procedures. We review rigorous convergence results and discuss finite-time blow-up of Keller–Segel type systems. Finally, recently developed PDE-models for the motion of leukocytes in the presence of multiple chemoattractants and of the slime mold Dictyostelium Discoideum are reviewed.
Publisher: Vilnius Gediminas Technical University
Date: 15-04-2014
DOI: 10.3846/13926292.2014.910279
Abstract: This paper is devoted to the analysis of a relaxation-type numerical scheme for a nonlinear Schrödinger equation arising in plasma physics. The scheme is shown to be preservative in the sense that it preserves mass and energy. We prove the well-posedness of the semidiscretized system and prove convergence to the solution of the time-continuous model.
Publisher: Oxford University Press (OUP)
Date: 12-2005
Abstract: We present a model for the chemotactically directed migration of neutrophil leukocytes. It reproduces the multistep navigation by memory effects investigated experimentally by E. F. Foxman, J. J. C bell and E. C. Butcher in 1997. The model consists of a system of stochastic differential equations. The long time behaviour of the corresponding deterministic system is analysed and two approaches for the numerical solution of the full stochastic system are compared. One of them consists in performing direct simulations, the other one is based on a moment approximation of the Fokker-Planck equation and numerical methods for convection-dominated partial differential equations.
Publisher: Elsevier BV
Date: 09-2021
Publisher: Springer Science and Business Media LLC
Date: 23-08-2007
Publisher: Springer Science and Business Media LLC
Date: 19-04-2011
DOI: 10.1007/S00285-011-0421-9
Abstract: A steepest descent approximation scheme is derived for a recently developed model for the dynamics of the actin cytoskeleton in the lamellipodia of living cells. The scheme is used as a numerical method for the simulation of thought experiments, where a lamellipodial fragment is pushed by a pipette, and subsequently changes its shape and position.
Publisher: American Institute of Mathematical Sciences (AIMS)
Date: 05-2016
DOI: 10.3934/DCDS.2016014
Publisher: Elsevier BV
Date: 2009
DOI: 10.1016/J.MBS.2008.10.007
Abstract: We consider a model for the polymerization (fragmentation) process involved in infectious prion self-replication and study both its dynamics and non-zero steady state. We address several issues. Firstly, we extend a previous study of the nucleated polymerization model [M.L. Greer, L. Pujo-Menjouet, G.F. Webb, A mathematical analysis of the dynamics of prion proliferation, J. Theoret. Biol. 242 (2006) 598 H. Engler, J. Pruss, G.F. Webb, Analysis of a model for the dynamics of prions II, J. Math. Anal. Appl. 324 (2006) 98] to take into account size dependent replicative properties of prion aggregates. This is achieved by a choice of coefficients in the model that are not constant. Secondly, we show stability results for this steady state for general coefficients where reduction to a system of differential equations is not possible. We use a duality method based on recent ideas developed for population models. These results confirm the potential influence of the amyloid precursor production rate in promoting amyloidogenic diseases. Finally, we investigate how the converting factor may depend upon the aggregate size. Besides the confirmation that size-independent parameters are unlikely to occur, the present study suggests that the PrPsc aggregate size repartition is amongst the most relevant experimental data in order to investigate this dependence. In terms of prion strain, our results indicate that the PrPsc aggregate repartition could be a constraint during the adaptation mechanism of the species barrier overcoming, that opens experimental perspectives for prion amyloid polymerization and prion strain investigation.
Publisher: Springer Science and Business Media LLC
Date: 14-05-2013
DOI: 10.1007/S00285-013-0682-6
Abstract: A mathematical model in one dimension for a non-sarcomeric actomyosin bundle featuring anti-parallel flows of anti-parallel F-actin is introduced. The model is able to relate these flows to the effect of cross-linking and bundling proteins, to the forces due to myosin-II filaments and to external forces at the extreme tips of the bundle. The modeling is based on a coarse graining approach starting with a microscopic model which includes the description of chemical bonds as elastic springs and the force contribution of myosin filaments. In a second step we consider the asymptotic regime where the filament lengths are small compared to the overall bundle length and restrict to the lowest order contributions. There it becomes apparent that myosin filaments generate forces which are partly compensated by drag forces due to cross-linking proteins. The remaining local contractile forces are then propagated to the tips of the bundle by the viscosity effect of bundling proteins in the filament gel. The model is able to explain how a disordered bundle of comparatively short actin filaments interspersed with myosin filaments can effectively contract the two tips of the actomyosin bundle. It gives a quantitative description of these forces and of the anti-parallel flows of the two phases of anti-parallel F-actin. An asymptotic version of the model with infinite viscosity can be solved explicitly and yields an upper bound to the contractile force of the bundle.
Publisher: American Physical Society (APS)
Date: 05-09-2019
Publisher: Elsevier BV
Date: 11-2015
Publisher: Elsevier BV
Date: 11-2011
Publisher: Springer Science and Business Media LLC
Date: 07-2022
DOI: 10.1007/S00285-022-01737-Z
Abstract: Contraction of actomyosin networks underpins important cellular processes including motility and ision. The mechanical origin of actomyosin contraction is not fully-understood. We investigate whether contraction arises on the scale of in idual filaments, without needing to invoke network-scale interactions. We derive discrete force-balance and continuum partial differential equations for two symmetric, semi-flexible actin filaments with an attached myosin motor. Assuming the system exists within a homogeneous background material, our method enables computation of the stress tensor, providing a measure of contractility. After deriving the model, we use a combination of asymptotic analysis and numerical solutions to show how F-actin bending facilitates contraction on the scale of two filaments. Rigid filaments exhibit polarity-reversal symmetry as the motor travels from the minus to plus-ends, such that contractile and expansive components cancel. Filament bending induces a geometric asymmetry that brings the filaments closer to parallel as a myosin motor approaches their plus-ends, decreasing the effective spring force opposing motor motion. The reduced spring force enables the motor to move faster close to filament plus-ends, which reduces expansive stress and gives rise to net contraction. Bending-induced geometric asymmetry provides both new understanding of actomyosin contraction mechanics, and a hypothesis that can be tested in experiments.
Publisher: Springer Science and Business Media LLC
Date: 25-07-2023
Publisher: Elsevier BV
Date: 05-2022
Publisher: Elsevier BV
Date: 10-2018
Publisher: Elsevier BV
Date: 12-2018
Publisher: Springer Science and Business Media LLC
Date: 03-2021
Publisher: Society for Industrial & Applied Mathematics (SIAM)
Date: 2015
DOI: 10.1137/130947052
Publisher: Springer International Publishing
Date: 2017
Publisher: Springer Science and Business Media LLC
Date: 08-06-2023
DOI: 10.1038/S41467-023-38866-Y
Abstract: Single-molecule localization microscopy techniques are emerging as vital tools to unravel the nanoscale world of living cells by understanding the spatiotemporal organization of protein clusters at the nanometer scale. Current analyses define spatial nanoclusters based on detections but neglect important temporal information such as cluster lifetime and recurrence in “hotspots” on the plasma membrane. Spatial indexing is widely used in video games to detect interactions between moving geometric objects. Here, we use the R-tree spatial indexing algorithm to determine the overlap of the bounding boxes of in idual molecular trajectories to establish membership in nanoclusters. Extending the spatial indexing into the time dimension allows the resolution of spatial nanoclusters into multiple spatiotemporal clusters. Using spatiotemporal indexing, we found that syntaxin1a and Munc18-1 molecules transiently cluster in hotspots, offering insights into the dynamics of neuroexocytosis. Nanoscale spatiotemporal indexing clustering (NASTIC) has been implemented as a free and open-source Python graphic user interface.
Publisher: Springer Science and Business Media LLC
Date: 23-04-2019
DOI: 10.1007/S00285-019-01369-W
Abstract: It is often assumed in biophysical studies that when multiple identical molecular motors interact with two parallel microtubules, the microtubules will be crosslinked and locked together. The aim of this study is to examine this assumption mathematically. We model the forces and movements generated by motors with a time-continuous Markov process and find that, counter-intuitively, a tug-of-war results from opposing actions of identical motors bound to different microtubules. The model shows that many motors bound to the same microtubule generate a great force applied to a smaller number of motors bound to another microtubule, which increases detachment rate for the motors in minority, stabilizing the directional sliding. However, stochastic effects cause occasional changes of the sliding direction, which has a profound effect on the character of the long-term microtubule motility, making it effectively diffusion-like. Here, we estimate the time between the rare events of switching direction and use them to estimate the effective diffusion coefficient for the microtubule pair. Our main result is that parallel microtubules interacting with multiple identical motors are not locked together, but rather slide bidirectionally. We find explicit formulae for the time between directional switching for various motor numbers.
Publisher: Elsevier BV
Date: 10-2015
DOI: 10.1016/J.JTBI.2015.06.044
Abstract: The Filament Based Lamellipodium Model (FBLM) is a two-phase two-dimensional continuum model, describing the dynamics of two interacting families of locally parallel actin filaments (Oelz and Schmeiser, 2010b). It contains accounts of the filaments' bending stiffness, of adhesion to the substrate, and of cross-links connecting the two families. An extension of the model is presented with contributions from nucleation of filaments by branching, from capping, from contraction by actin-myosin interaction, and from a pressure-like repulsion between parallel filaments due to Coulomb interaction. The effect of a chemoattractant is described by a simple signal transduction model influencing the polymerization speed. Simulations with the extended model show its potential for describing various moving cell shapes, depending on the signal transduction procedure, and for predicting transients between non-moving and moving states as well as changes of direction.
Publisher: International Press of Boston
Date: 2016
Publisher: European Mathematical Society - EMS - Publishing House GmbH
Date: 2008
DOI: 10.4171/IFB/197
Publisher: American Institute of Mathematical Sciences (AIMS)
Date: 03-2016
Publisher: International Press of Boston
Date: 2014
Publisher: American Institute of Mathematical Sciences (AIMS)
Date: 05-2015
Start Date: 03-2018
End Date: 03-2024
Amount: $300,083.00
Funder: Australian Research Council
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