Philip Holmes

Bio: Philip Holmes is an academic researcher from Princeton University. The author has contributed to research in topics: Homoclinic orbit & Dynamical systems theory. The author has an hindex of 70, co-authored 259 publications receiving 37715 citations. Previous affiliations of Philip Holmes include Cornell University & University of Stuttgart.

Nonlinear Oscillations, Dynamical Systems, and Bifurcations of Vector Fields

Abstract: Contents: Introduction: Differential Equations and Dynamical Systems.- An Introduction to Chaos: Four Examples.- Local Bifurcations.- Averaging and Perturbation from a Geometric Viewpoint.- Hyperbolic Sets, Sympolic Dynamics, and Strange Attractors.- Global Bifurcations.- Local Codimension Two Bifurcations of Flows.- Appendix: Suggestions for Further Reading. Postscript Added at Second Printing. Glossary. References. Index.

The Proper Orthogonal Decomposition in the Analysis of Turbulent Flows

Abstract: It has often been remarked that turbulence is a subject of great scientific and technological importance, and yet one of the least understood (e.g. McComb 1990). To an outsider this may seem strange, since the basic physical laws of fluid mechanics are well established, an excellent mathematical model is available in the Navier-Stokes equations, and the results of well over a century of increasingly sophisticated experiments are at our disposal. One major difficulty, of course, is that the governing equations are nonlinear and little is known about their solutions at high Reynolds number, even in simple geometries. Even mathematical questions as basic as existence and uniqueness are unsettled in three spatial dimensions (cf Temam 1988). A second problem, more important from the physical viewpoint, is that experiments and the available mathematical evidence all indicate that turbulence involves the interaction of many degrees of freedom over broad ranges of spatial and temporal scales. One of the problems of turbulence is to derive this complex picture from the simple laws of mass and momentum balance enshrined in the NavierStokes equations. It was to this that Ruelle & Takens (1971) contributed with their suggestion that turbulence might be a manifestation in physical

Turbulence, Coherent Structures, Dynamical Systems and Symmetry

Abstract: Preface Part I. Turbulence: 1. Introduction 2. Coherent structures 3. Proper orthogonal decomposition 4. Galerkin projection Part II. Dynamical Systems: 5. Qualitative theory 6. Symmetry 7. One-dimensional 'turbulence' 8. Randomly perturbed systems Part III. 9. Low-dimensional Models: 10. Behaviour of the models Part IV. Other Applications and Related Work: 11. Some other fluid problems 12. Review: prospects for rigor Bibliography.

The physics of optimal decision making: a formal analysis of models of performance in two-alternative forced-choice tasks.

Abstract: In this article, the authors consider optimal decision making in two-alternative forced-choice (TAFC) tasks. They begin by analyzing 6 models of TAFC decision making and show that all but one can be reduced to the drift diffusion model, implementing the statistically optimal algorithm (most accurate for a given speed or fastest for a given accuracy). They prove further that there is always an optimal trade-off between speed and accuracy that maximizes various reward functions, including reward rate (percentage of correct responses per unit time), as well as several other objective functions, including ones weighted for accuracy. They use these findings to address empirical data and make novel predictions about performance under optimality.

Book Review: Nonlinear Oscillations, Dynamical Systems, and Bifurcations of Vector Fields

Abstract: One important aspect of dynamical systems is the study of the long-term behavior of a set of ordinary differential equations (ODEs) In recent years many systems that are simple to write down have been discovered whose solutions are chaotic They oscillate irregularly, never settling down to a regular pattern Two trajectories which start close together will separate quickly Systems whose time evolution is governed by a parameter p can undergo intriguing variations in the behavior of trajectories In many cases, there are values p* such that the long-term behavior of typical trajectories of p p* For example, the system may go from stable periodic behavior for p p* Such sudden, discontinuous changes or "bifurcations" are quite common Research in chaos and bifurcations in dynamical processes has advanced at a rapid pace during the past decade, acquiring an extraordinary breadth of applications in fields as diverse as fluid mechanics, electrical engineering and neurophysiology The new results interest a wide spectrum of the scientific community, many of whose members, however, lack the mathematical background necessary to decipher the literature Accordingly, Guckenheimer and Holmes have written their book as a "user's guide" to an extensive and rapidly growing field The book surveys the theory and techniques needed to understand chaotic behavior of ODEs The first chapter contains a brief introduction of the theory of ODEs; it is a review of topics usually found in a standard text like Hirsch and Smale (1) The second chapter considers four examples of chaotic systems: the forced van der Pol oscillator, Duffing's equation, the celebrated Lorenz equations, and Holmes' "bouncing ball map" (perhaps more familiar as the map which describes the motion of a periodically forced, damped planar pendulum in the absence of gravity) These examples

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

A Reflection on Nonlinear Oscillations, Dynamical Systems, and Bifurcations of Vector Fields

Abstract: Contents: Introduction: Differential Equations and Dynamical Systems.- An Introduction to Chaos: Four Examples.- Local Bifurcations.- Averaging and Perturbation from a Geometric Viewpoint.- Hyperbolic Sets, Sympolic Dynamics, and Strange Attractors.- Global Bifurcations.- Local Codimension Two Bifurcations of Flows.- Appendix: Suggestions for Further Reading. Postscript Added at Second Printing. Glossary. References. Index.

Synchronization in chaotic systems

Abstract: Certain subsystems of nonlinear, chaotic systems can be made to synchronize by linking them with common signals. The criterion for this is the sign of the sub-Lyapunov exponents. We apply these ideas to a real set of synchronizing chaotic circuits.

Principles of Neural Science

Abstract: I have developed "tennis elbow" from lugging this book around the past four weeks, but it is worth the pain, the effort, and the aspirin. It is also worth the (relatively speaking) bargain price. Including appendixes, this book contains 894 pages of text. The entire panorama of the neural sciences is surveyed and examined, and it is comprehensive in its scope, from genomes to social behaviors. The editors explicitly state that the book is designed as "an introductory text for students of biology, behavior, and medicine," but it is hard to imagine any audience, interested in any fragment of neuroscience at any level of sophistication, that would not enjoy this book. The editors have done a masterful job of weaving together the biologic, the behavioral, and the clinical sciences into a single tapestry in which everyone from the molecular biologist to the practicing psychiatrist can find and appreciate his or

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.