José M. Sancho

Bio: José M. Sancho is an academic researcher from University of Barcelona. The author has contributed to research in topics: Langevin equation & Brownian motion. The author has an hindex of 37, co-authored 268 publications receiving 6037 citations. Previous affiliations of José M. Sancho include University of Santiago de Compostela & University of California, San Diego.

Noise in Spatially Extended Systems

Abstract: 1 Introduction.- 1.1 Fluctuations in a Macroscopic World.- 1.1.1 Describing Stochastic Dynamics.- 1.1.2 Stochastic Partial Differential Equations.- 1.1.3 Experimental Setups.- 1.1.4 Numerical Experiments.- 1.1.5 Noise-Induced Phenomena.- 1.2 Transitions in Zero-Dimensional Systems.- 1.2.1 Internal Noise.- 1.2.2 External Noise.- 1.3 Phase Transitions in d-Dimensional Systems.- 1.3.1 Equilibrium Phase Transitions.- 1.3.2 Nonequilibrium Phase Transitions.- 1.3.3 Dynamics of Phase Transitions.- 1.4 Pattern Formation.- 1.4.1 Order-Parameter Equations.- 1.4.2 Pattern-Forming Instabilities.- 1.4.3 Amplitude Equations and Beyond.- 1.4.4 Real Patterns.- 1.5 Other Effects of Noise in Extended Media.- 1.5.1 Noise-Sustained Convective Structures.- 1.5.2 Spatial Stochastic Resonance.- 2 Fundamentals and Tools.- 2.1 Introduction to Stochastic Partial Differential Equations.- 2.1.1 Generalities and Modeling.- 2.1.2 Stochastic Calculus in SPDEs.- 2.1.3 Fokker-Planck Equation for Spatially Extended Systems.- 2.1.4 Statistical Moments and Correlations.- 2.2 Analytical Techniques.- 2.2.1 Mean-Field Analysis and Beyond.- 2.2.2 Small Noise Expansions.- 2.2.3 Linear Stability Analysis.- 2.2.4 Dynamic Renormalization Group Analysis.- 2.3 Numerical Techniques.- 2.3.1 Algorithms for Solving SPDEs.- 2.3.2 Generation of Correlated Noises.- 3 Noise-Induced Phase Transitions.- 3.1 Additive Noise.- 3.1.1 Ginzburg-Landau Model with Colored Noise.- 3.1.2 Noise-Induced Shift of the Transition Point.- 3.1.3 Fokker-Planck Analysis.- 3.1.4 Dynamic Renormalization Group Analysis.- 3.2 Additive and Multiplicative Noise.- 3.2.1 Ginzburg-Landau Model with Multiplicative Noise.- 3.2.2 Pure Noise-Induced Phase Transitions.- 3.2.3 Noise-Induced First-Order Phase Transitions.- 3.3 Multiplicative Noise.- 3.3.1 Multiplicative Noise Universality Class.- 3.3.2 Disordering Transitions Induced by Pure Multiplicative Noise.- 3.3.3 Numerical Simulation Results.- 4 Dynamics of Phase Transitions with Fluctuations.- 4.1 Internal Multiplicative Noise.- 4.1.1 Mesoscopic Derivation.- 4.1.2 Application to Phase Separation Dynamics.- 4.1.3 Extension to Nonconserved Order Parameter.- 4.2 Noise-Induced Phase Separation.- 4.2.1 External Fluctuations in Phase Separation.- 4.2.2 Stability Analysis.- 4.2.3 Phase Diagram.- 5 Pattern Formation Under Multiplicative Noise.- 5.1 Multiplicative Noise in the Swift-Hohenberg Model.- 5.1.1 A Model Equation for Rayleigh-Benard Convection.- 5.1.2 Fluctuations in the Control Parameter.- 5.1.3 Effect of a Spatially Correlated Noise.- 5.2 Pure Noise-Induced Patterns.- 6 Front Dynamics and External Fluctuations.- 6.1 External Fluctuations in Deterministic Fronts.- 6.1.1 Front Propagation in Fluctuating Media.- 6.1.2 Theoretical Approach and Predictions.- 6.1.3 Noise Effects on the Front Selection Problem.- 6.1.4 Profile Shape and Velocity Shift.- 6.1.5 Front Diffusive Spreading.- 6.2 Noise-Induced Fronts.- 6.2.1 Modeling and Analytical Results.- 6.2.2 Numerical Results.- 6.3 Reactive Fronts under Turbulent Advection.- 6.3.1 Modeling.- 6.3.2 A Gaussian Turbulence?.- 6.3.3 Theoretical Analysis and Numerical Results.- 6.3.4 The Role of Different Spectra.- 7 Conclusions.- 7.1 What Has Been Done.- 7.2 What Needs to Be Done.- A Continuum and Discrete Space Descriptions.- A.1 Coarse Graining.- A.2 Continuum Limit and Functional Analysis.- B Fourier Transforms.- B.1 Continuum Fourier Transforms.- B.2 Discrete Fourier Transforms.- B.3 Discrete Fourier Transform of a Real Uncorrelated Field.- C Fokker-Planck Equation for an Additive Colored Noise.- D Colored Noise in a Linear Model.- E Fokker-Planck Equation for a Multiplicative Noise.- References.

Spatiotemporal order out of noise

Abstract: Natural systems are undeniably subject to random fluctuations, arising from either environmental variability or thermal effects. The consideration of those fluctuations supposes to deal with noisy quantities whose variance might at times be a sizable fraction of their mean levels. It is known that, under these conditions, noisy fluctuations can interact with the system's nonlinearities to render counterintuitive behavior, in which an increase in the noise level produces a more regular behavior. In systems with spatial degrees of freedom, this regularity takes the form of spatiotemporal order. An overview is presented of the mechanisms through which noise induces, enhances, and sustains ordered behavior in passive and active nonlinear media, and different spatiotemporal phenomena are described resulting from these effects. The general theoretical framework used in the analysis of these effects is reviewed, encompassing the theory of stochastic partial differential equations and coupled sets of ordinary stochastic differential equations. Experimental observations of self-organized behavior arising out of noise are also described, and details on the numerical algorithms needed in the computer simulation of these problems are given.

Adiabatic elimination for systems of Brownian particles with nonconstant damping coefficients

Abstract: We discuss the problem of eliminating the momentum variable in the phase space Langevin equations for a system of Brownian particles in two related situations: (i) position-dependent damping and (ii) existence of hydrodynamic interactions. We discuss the problems associated with the conventional elimination and we develop an alternative elimination procedure, in the Lagevin framework, which leads to the correct Smoluchowski equation. We give a heuristic argument on the basis of stochastic differential equations for the Smoluchowski limit and establish rigorously the limit for the general case of position-dependent friction and diffusion coefficents.

Diffusion on a Solid Surface: Anomalous is Normal

Abstract: We present a numerical study of classical particles diffusing on a solid surface. The particles' motion is modeled by an underdamped Langevin equation with ordinary thermal noise. The particle-surface interaction is described by a periodic or a random two-dimensional potential. The model leads to a rich variety of different transport regimes, some of which correspond to anomalous diffusion such as has recently been observed in experiments and Monte Carlo simulations. We show that this anomalous behavior is controlled by the friction coefficient and stress that it emerges naturally in a system described by ordinary canonical Maxwell-Boltzmann statistics.

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。

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

Reaction-rate theory: fifty years after Kramers

Abstract: The calculation of rate coefficients is a discipline of nonlinear science of importance to much of physics, chemistry, engineering, and biology. Fifty years after Kramers' seminal paper on thermally activated barrier crossing, the authors report, extend, and interpret much of our current understanding relating to theories of noise-activated escape, for which many of the notable contributions are originating from the communities both of physics and of physical chemistry. Theoretical as well as numerical approaches are discussed for single- and many-dimensional metastable systems (including fields) in gases and condensed phases. The role of many-dimensional transition-state theory is contrasted with Kramers' reaction-rate theory for moderate-to-strong friction; the authors emphasize the physical situation and the close connection between unimolecular rate theory and Kramers' work for weakly damped systems. The rate theory accounting for memory friction is presented, together with a unifying theoretical approach which covers the whole regime of weak-to-moderate-to-strong friction on the same basis (turnover theory). The peculiarities of noise-activated escape in a variety of physically different metastable potential configurations is elucidated in terms of the mean-first-passage-time technique. Moreover, the role and the complexity of escape in driven systems exhibiting possibly multiple, metastable stationary nonequilibrium states is identified. At lower temperatures, quantum tunneling effects start to dominate the rate mechanism. The early quantum approaches as well as the latest quantum versions of Kramers' theory are discussed, thereby providing a description of dissipative escape events at all temperatures. In addition, an attempt is made to discuss prominent experimental work as it relates to Kramers' reaction-rate theory and to indicate the most important areas for future research in theory and experiment.

Stochastic Processes in Physics and Chemistry

Abstract: N G van Kampen 1981 Amsterdam: North-Holland xiv + 419 pp price Dfl 180 This is a book which, at a lower price, could be expected to become an essential part of the library of every physical scientist concerned with problems involving fluctuations and stochastic processes, as well as those who just enjoy a beautifully written book. It provides an extensive graduate-level introduction which is clear, cautious, interesting and readable.

Stochastic thermodynamics, fluctuation theorems and molecular machines

Abstract: Stochastic thermodynamics as reviewed here systematically provides a framework for extending the notions of classical thermodynamics such as work, heat and entropy production to the level of individual trajectories of well-defined non-equilibrium ensembles. It applies whenever a non-equilibrium process is still coupled to one (or several) heat bath(s) of constant temperature. Paradigmatic systems are single colloidal particles in time-dependent laser traps, polymers in external flow, enzymes and molecular motors in single molecule assays, small biochemical networks and thermoelectric devices involving single electron transport. For such systems, a first-law like energy balance can be identified along fluctuating trajectories. For a basic Markovian dynamics implemented either on the continuum level with Langevin equations or on a discrete set of states as a master equation, thermodynamic consistency imposes a local-detailed balance constraint on noise and rates, respectively. Various integral and detailed fluctuation theorems, which are derived here in a unifying approach from one master theorem, constrain the probability distributions for work, heat and entropy production depending on the nature of the system and the choice of non-equilibrium conditions. For non-equilibrium steady states, particularly strong results hold like a generalized fluctuation–dissipation theorem involving entropy production. Ramifications and applications of these concepts include optimal driving between specified states in finite time, the role of measurement-based feedback processes and the relation between dissipation and irreversibility. Efficiency and, in particular, efficiency at maximum power can be discussed systematically beyond the linear response regime for two classes of molecular machines, isothermal ones such as molecular motors, and heat engines such as thermoelectric devices, using a common framework based on a cycle decomposition of entropy production. (Some figures may appear in colour only in the online journal) This article was invited by Erwin Frey.