James D. Murray

Bio: James D. Murray is an academic researcher from University of Washington. The author has contributed to research in topics: Pattern formation & Population. The author has an hindex of 58, co-authored 234 publications receiving 14788 citations. Previous affiliations of James D. Murray include University of Oxford & University of St Andrews.

Mechanical aspects of mesenchymal morphogenesis.

Abstract: Many embryonic cells generate substantial contractile forces as they spread and crawl.These forces mechanically deform each cell9s local environment, and the resulting distortions can alter subsequent cell movements by convection and the mechanisms of contact guidance and haptotaxis. Here we develop a model for the cumulative effects of these cell-generated forces and show how they can lead to the formation of regular large-scale patterns in cell populations. This model leads to several predictions concerning the effects of cellular and matrix properties on the resulting patterns. We apply the model to two widely studied morphogenetic processes: (a) patterns of skin-organ primordia, especially feather germ formation, and (b) the condensation of cartilagenous skeletal rudiments in the developing vertebrate limb.

A quantitative model for differential motility of gliomas in grey and white matter.

Abstract: We have extended a mathematical model of gliomas based on proliferation and diffusion rates to incorporate the effects of augmented cell motility in white matter as compared to grey matter. Using a detailed mapping of the white and grey matter in the brain developed for a MRI simulator, we have been able to simulate model tumours on an anatomically accurate brain domain. Our simulations show good agreement with clinically observed tumour geometries and suggest paths of submicroscopic tumour invasion not detectable on CT or MRI images. We expect this model to give insight into microscopic and submicroscopic invasion of the human brain by glioma cells. This method gives insight in microscopic and submicroscopic invasion of the human brain by glioma cells. Additionally, the model can be useful in defining expected pathways of invasion by glioma cells and thereby identify regions of the brain on which to focus treatments.

Pattern formation outside of equilibrium

Abstract: A comprehensive review of spatiotemporal pattern formation in systems driven away from equilibrium is presented, with emphasis on comparisons between theory and quantitative experiments. Examples include patterns in hydrodynamic systems such as thermal convection in pure fluids and binary mixtures, Taylor-Couette flow, parametric-wave instabilities, as well as patterns in solidification fronts, nonlinear optics, oscillatory chemical reactions and excitable biological media. The theoretical starting point is usually a set of deterministic equations of motion, typically in the form of nonlinear partial differential equations. These are sometimes supplemented by stochastic terms representing thermal or instrumental noise, but for macroscopic systems and carefully designed experiments the stochastic forces are often negligible. An aim of theory is to describe solutions of the deterministic equations that are likely to be reached starting from typical initial conditions and to persist at long times. A unified description is developed, based on the linear instabilities of a homogeneous state, which leads naturally to a classification of patterns in terms of the characteristic wave vector q0 and frequency ω0 of the instability. Type Is systems (ω0=0, q0≠0) are stationary in time and periodic in space; type IIIo systems (ω0≠0, q0=0) are periodic in time and uniform in space; and type Io systems (ω0≠0, q0≠0) are periodic in both space and time. Near a continuous (or supercritical) instability, the dynamics may be accurately described via "amplitude equations," whose form is universal for each type of instability. The specifics of each system enter only through the nonuniversal coefficients. Far from the instability threshold a different universal description known as the "phase equation" may be derived, but it is restricted to slow distortions of an ideal pattern. For many systems appropriate starting equations are either not known or too complicated to analyze conveniently. It is thus useful to introduce phenomenological order-parameter models, which lead to the correct amplitude equations near threshold, and which may be solved analytically or numerically in the nonlinear regime away from the instability. The above theoretical methods are useful in analyzing "real pattern effects" such as the influence of external boundaries, or the formation and dynamics of defects in ideal structures. An important element in nonequilibrium systems is the appearance of deterministic chaos. A greal deal is known about systems with a small number of degrees of freedom displaying "temporal chaos," where the structure of the phase space can be analyzed in detail. For spatially extended systems with many degrees of freedom, on the other hand, one is dealing with spatiotemporal chaos and appropriate methods of analysis need to be developed. In addition to the general features of nonequilibrium pattern formation discussed above, detailed reviews of theoretical and experimental work on many specific systems are presented. These include Rayleigh-Benard convection in a pure fluid, convection in binary-fluid mixtures, electrohydrodynamic convection in nematic liquid crystals, Taylor-Couette flow between rotating cylinders, parametric surface waves, patterns in certain open flow systems, oscillatory chemical reactions, static and dynamic patterns in biological media, crystallization fronts, and patterns in nonlinear optics. A concluding section summarizes what has and has not been accomplished, and attempts to assess the prospects for the future.

The Problem of Pattern and Scale in Ecology: The Robert H. MacArthur Award Lecture

Abstract: This book is the second of two volumes in a series on terrestrial and marine comparisons, focusing on the temporal complement of the earlier spatial analysis of patchiness and pattern (Levin et al. 1993). The issue of the relationships among pattern, scale, and patchiness has been framed forcefully in John Steele’s writings of two decades (e.g., Steele 1978). There is no pattern without an observational frame. In the words of Nietzsche, “There are no facts… only interpretations.”

The geometry of biological time , by A. T. Winfree. Pp 544. DM68. Corrected Second Printing 1990. ISBN 3-540-52528-9 (Springer)

Abstract: 1980 Preface * 1999 Preface * 1999 Acknowledgements * Introduction * 1 Circular Logic * 2 Phase Singularities (Screwy Results of Circular Logic) * 3 The Rules of the Ring * 4 Ring Populations * 5 Getting Off the Ring * 6 Attracting Cycles and Isochrons * 7 Measuring the Trajectories of a Circadian Clock * 8 Populations of Attractor Cycle Oscillators * 9 Excitable Kinetics and Excitable Media * 10 The Varieties of Phaseless Experience: In Which the Geometrical Orderliness of Rhythmic Organization Breaks Down in Diverse Ways * 11 The Firefly Machine 12 Energy Metabolism in Cells * 13 The Malonic Acid Reagent ('Sodium Geometrate') * 14 Electrical Rhythmicity and Excitability in Cell Membranes * 15 The Aggregation of Slime Mold Amoebae * 16 Numerical Organizing Centers * 17 Electrical Singular Filaments in the Heart Wall * 18 Pattern Formation in the Fungi * 19 Circadian Rhythms in General * 20 The Circadian Clocks of Insect Eclosion * 21 The Flower of Kalanchoe * 22 The Cell Mitotic Cycle * 23 The Female Cycle * References * Index of Names * Index of Subjects

Traffic and related self-driven many-particle systems

Abstract: Since the subject of traffic dynamics has captured the interest of physicists, many surprising effects have been revealed and explained. Some of the questions now understood are the following: Why are vehicles sometimes stopped by ``phantom traffic jams'' even though drivers all like to drive fast? What are the mechanisms behind stop-and-go traffic? Why are there several different kinds of congestion, and how are they related? Why do most traffic jams occur considerably before the road capacity is reached? Can a temporary reduction in the volume of traffic cause a lasting traffic jam? Under which conditions can speed limits speed up traffic? Why do pedestrians moving in opposite directions normally organize into lanes, while similar systems ``freeze by heating''? All of these questions have been answered by applying and extending methods from statistical physics and nonlinear dynamics to self-driven many-particle systems. This article considers the empirical data and then reviews the main approaches to modeling pedestrian and vehicle traffic. These include microscopic (particle-based), mesoscopic (gas-kinetic), and macroscopic (fluid-dynamic) models. Attention is also paid to the formulation of a micro-macro link, to aspects of universality, and to other unifying concepts, such as a general modeling framework for self-driven many-particle systems, including spin systems. While the primary focus is upon vehicle and pedestrian traffic, applications to biological or socio-economic systems such as bacterial colonies, flocks of birds, panics, and stock market dynamics are touched upon as well.

Biomimicry of bacterial foraging for distributed optimization and control

Abstract: We explain the biology and physics underlying the chemotactic (foraging) behavior of E. coli bacteria. We explain a variety of bacterial swarming and social foraging behaviors and discuss the control system on the E. coli that dictates how foraging should proceed. Next, a computer program that emulates the distributed optimization process represented by the activity of social bacterial foraging is presented. To illustrate its operation, we apply it to a simple multiple-extremum function minimization problem and briefly discuss its relationship to some existing optimization algorithms. The article closes with a brief discussion on the potential uses of biomimicry of social foraging to develop adaptive controllers and cooperative control strategies for autonomous vehicles. For this, we provide some basic ideas and invite the reader to explore the concepts further.