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      Rapid calculation of maximum particle lifetime for diffusion in complex geometries

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      The Journal of Chemical Physics
      AIP Publishing

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          Random walk models in biology.

          Mathematical modelling of the movement of animals, micro-organisms and cells is of great relevance in the fields of biology, ecology and medicine. Movement models can take many different forms, but the most widely used are based on the extensions of simple random walk processes. In this review paper, our aim is twofold: to introduce the mathematics behind random walks in a straightforward manner and to explain how such models can be used to aid our understanding of biological processes. We introduce the mathematical theory behind the simple random walk and explain how this relates to Brownian motion and diffusive processes in general. We demonstrate how these simple models can be extended to include drift and waiting times or be used to calculate first passage times. We discuss biased random walks and show how hyperbolic models can be used to generate correlated random walks. We cover two main applications of the random walk model. Firstly, we review models and results relating to the movement, dispersal and population redistribution of animals and micro-organisms. This includes direct calculation of mean squared displacement, mean dispersal distance, tortuosity measures, as well as possible limitations of these model approaches. Secondly, oriented movement and chemotaxis models are reviewed. General hyperbolic models based on the linear transport equation are introduced and we show how a reinforced random walk can be used to model movement where the individual changes its environment. We discuss the applications of these models in the context of cell migration leading to blood vessel growth (angiogenesis). Finally, we discuss how the various random walk models and approaches are related and the connections that underpin many of the key processes involved.
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            Reaction kinetics in intracellular environments with macromolecular crowding: simulations and rate laws.

            We review recent evidence illustrating the fundamental difference between cytoplasmic and test tube biochemical kinetics and thermodynamics, and showing the breakdown of the law of mass action and power-law approximation in in vivo conditions. Simulations of biochemical reactions in non-homogeneous media show that as a result of anomalous diffusion and mixing of the biochemical species, reactions follow a fractal-like kinetics. Consequently, the conventional equations for biochemical pathways fail to describe the reactions in in vivo conditions. We present a modification to fractal-like kinetics following the Zipf-Mandelbrot distribution which will enable the modelling and analysis of biochemical reactions occurring in crowded intracellular environments. Copyright 2004 Elsevier Ltd.
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              Incorporating Diffusion in Complex Geometries into Stochastic Chemical Kinetics Simulations

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                Author and article information

                Journal
                The Journal of Chemical Physics
                The Journal of Chemical Physics
                AIP Publishing
                0021-9606
                1089-7690
                March 07 2018
                March 07 2018
                : 148
                : 9
                : 094113
                Affiliations
                [1 ]School of Mathematical Sciences, Queensland University of Technology (QUT), Brisbane, Australia
                Article
                10.1063/1.5019180
                7bf83148-2fc3-470f-9db6-f745fcf8492e
                © 2018
                History

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