Frequency-dependent Escherichia coli chemotaxis behavior

We study Escherichia coli chemotaxis behavior in environments with spatially and temporally varying attractant sources by developing a unique microfluidic system. Our measurements reveal a frequency-dependent chemotaxis behavior. At low frequency, the E.?coli population oscillates in synchrony with the attractant. In contrast, in fast-changing environments, the population response becomes smaller and out of phase with the attractant waveform. These observations are inconsistent with the well-known Keller-Segel chemotaxis equation. A new continuum model is proposed to describe the population level behavior of E.?coli chemotaxis based on the underlying pathway dynamics. With the inclusion of a finite adaptation time and an attractant consumption rate, our model successfully explains the microfluidic experiments at different stimulus frequencies.     

Molecular and Functional Aspects of Bacterial Chemotaxis

We consider the dynamics of chemotaxis in the model bacterium Escherichia coli. We analyze both its molecular mechanisms and the functional causes governing the evolution of the observed behaviors. We review molecular models of the transduction network controlling the bacterial chemotaxis in response to chemoattractant binding to the receptors. In particular, recent progress stimulated by FRET experiments is presented for statistical physics allosteric models. The response function to a pulse of chemoattractant is expressed in terms of microscopic parameters of the allosteric models. The functional causes for the shape of the response function, as measured in experimental tethering assay, are then investigated. A hydrodynamic equation, valid for space-time scales larger than the microscopic running length and time, is derived for the position of a swimming bacterium. It is then shown how optimization over the microscopic parameters of the response function yields the curve observed experimentally. In particular, the observed property of adaptation to the background level of aspartate emerges as being produced by fluctuations in the space-time chemoattractant profiles sensed by bacteria along their trajectories. This functional cause is distinct from arguments based on the extension of the dynamical range. Future directions and experiments to probe the adaptation of E. coli chemotaxis to the environmental conditions and its response to realistic space-time chemoattractant stimuli are finally discussed.     

Nonlinear mean field Fokker-Planck equations. Application to the chemotaxis of biological populations

We study a general class of nonlinear mean field Fokker-Planck equations in relation with an effective generalized thermodynamical (E.G.T.) formalism. We show that these equations describe several physical systems such as: chemotaxis of bacterial populations, Bose-Einstein condensation in the canonical ensemble, porous media, generalized Cahn-Hilliard equations, Kuramoto model, BMF model, Burgers equation, Smoluchowski-Poisson system for self-gravitating Brownian particles, Debye-Hückel theory of electrolytes, two-dimensional turbulence... In particular, we show that nonlinear mean field Fokker-Planck equations can provide generalized Keller-Segel models for the chemotaxis of biological populations. As an example, we introduce a new model of chemotaxis incorporating both effects of anomalous diffusion and exclusion principle (volume filling). Therefore, the notion of generalized thermodynamics can have applications for concrete physical systems. We also consider nonlinear mean field Fokker-Planck equations in phase space and show the passage from the generalized Kramers equation to the generalized Smoluchowski equation in a strong friction limit. Our formalism is simple and illustrated by several explicit examples corresponding to Boltzmann, Tsallis, Fermi-Dirac and Bose-Einstein entropies among others.     

Analyse de la conduction de la chaleur aux temps ultra-courts dans un solide par la thermodynamique irréversible étendue et la dynamique moléculaire

Instantaneous heat propagation and thermodynamic local equilibrium cannot be assumed when solving space and time microscale problems. Therefore, we reconsider the thermodynamics basis of the Fourier law in order to obtain the new heat conduction models: the hyperbolic heat equation (EH) and the modified hyperbolic equation (EHM). We have performed molecular dynamics (DM) experiments which are independent of any thermodynamic model, to test the macroscopic approaches. We show that the solutions of the EH and the EHM do not agree with the numerical experiments and that the MD results are strongly dependent on the way from which the macroscopic conditions are simulated in the microscopic point of view.     

In-out intermittency in partial differential equation and ordinary differential equation models

We find concrete evidence for a recently discovered form of intermittency, referred to as in-out intermittency, in both partial differential equation (PDE) and ordinary differential equation (ODE) models of mean field dynamos. This type of intermittency [introduced in P. Ashwin, E. Covas, and R. Tavakol, Nonlinearity 9, 563 (1999)] occurs in systems with invariant submanifolds and, as opposed to on-off intermittency which can also occur in skew product systems, it requires an absence of skew product structure. By this we mean that the dynamics on the attractor intermittent to the invariant manifold cannot be expressed simply as the dynamics on the invariant subspace forcing the transverse dynamics; the transverse dynamics will alter that tangential to the invariant subspace when one is far enough away from the invariant manifold. Since general systems with invariant submanifolds are not likely to have skew product structure, this type of behavior may be of physical relevance in a variety of dynamical settings. The models employed here to demonstrate in-out intermittency are axisymmetric mean-field dynamo models which are often used to study the observed large-scale magnetic variability in the Sun and solar-type stars. The occurrence of this type of intermittency in such models may be of interest in understanding some aspects of such variabilities. (c) 2001 American Institute of Physics.     

Strong-coupling dynamics of a multicellular chemotactic system

Chemical signaling is one of the ubiquitous mechanisms by which intercellular communication takes place at the microscopic level, particularly via chemotaxis. Such multicellular systems are popularly studied using continuum, mean-field equations. In this Letter we study a stochastic model of chemotactic signaling. The Langevin formalism of the model makes it amenable to calculation via nonperturbative analysis, which enables a quantification of the effect of fluctuations on both the weak and the strongly coupled biological dynamics. In particular, we show that the (i) self-localization due to autochemotaxis is impossible. (ii) When aggregation occurs, the aggregate performs a random walk with a renormalized diffusion coefficient D(R) proportiuonal to epsilon-2N-3. (iii) The stochastic model exhibits sharp transitions in cell motile behavior for negative chemotaxis, behavior that has no parallel in the mean-field Keller-Segel equations.     

Self-organized nanostructures in surface chemical reactions: Mechanisms and mesoscopic modeling

Nanoscale patterns can form in reactive adsorbates on catalytic surfaces as a result of attractive lateral interactions. These structures can be described within a mesoscopic theory that is derived by coarse graining the microscopic master equation thus providing a link between microscopic lattice models and reaction-diffusion equations. Such mesoscopic models allow to systematically investigate mechanisms responsible for the formation of nanoscale nonequilibrium patterns in reactive condensed matter. We have found that stationary and traveling nanostructures may result from the interplay of the attractive lateral interactions and nonequilibrium reactions. Besides reviewing these results, a detailed investigation of a single reactive adsorbate in the presence of attractive lateral interactions and global coupling through the gas phase is presented. Finally, it is outlined how a mesoscopic theory should be constructed for a particular scanning tunneling microscopy experiment [the oxidation of hydrogen on a Pt(111) surface] in order to overcome the failure of a corresponding reaction-diffusion model to quantitatively reproduce the experiments. (c) 2002 American Institute of Physics.     

Brownian particles with long- and short-range interactions

We develop the kinetic theory of Brownian particles with long- and short-range interactions. Since the particles are in contact with a thermal bath fixing the temperature T, they are described by the canonical ensemble. We consider both overdamped and inertial models. In the overdamped limit, the evolution of the spatial density is governed by the generalized mean field Smoluchowski equation including a mean field potential due to long-range interactions and a generically nonlinear barotropic pressure due to short-range interactions. This equation describes various physical systems such as self-gravitating Brownian particles (Smoluchowski-Poisson system), bacterial populations experiencing chemotaxis (Keller-Segel model) and colloidal particles with capillary interactions. We also take into account the inertia of the particles and derive corresponding kinetic and hydrodynamic equations generalizing the usual Kramers, Jeans, Euler and Cattaneo equations. For each model, we provide the corresponding form of free energy and establish the H-theorem and the virial theorem. Finally, we show that the same hydrodynamic equations are obtained in the context of nonlinear mean field Fokker-Planck equations associated with generalized thermodynamics. However, in that case, the nonlinear pressure is due to the bias in the transition probabilities from one state to the other leading to non-Boltzmannian distributions while in the former case the distribution is Boltzmannian but the nonlinear pressure arises from the two-body correlation function induced by the short-range potential of interaction. As a whole, our paper develops connections between the topics of long-range interactions, short-range interactions, nonlinear mean field Fokker-Planck equations and generalized thermodynamics. It also justifies from a kinetic theory based on microscopic processes, the basic equations that were introduced phenomenologically to describe self-gravitating Brownian particles, chemotaxis and colloidal suspensions with attractive interactions.     

Microscopic information processing and communication in crowd dynamics

Due, perhaps, to the historical division of crowd dynamics research into psychological and engineering approaches, microscopic crowd models have tended toward modelling simple interchangeable particles with an emphasis on the simulation of physical factors. Despite the fact that people have complex (non-panic) behaviours in crowd disasters, important human factors in crowd dynamics such as information discovery and processing, changing goals and communication have not yet been well integrated at the microscopic level. We use our Microscopic Human Factors methodology to fuse a microscopic simulation of these human factors with a popular microscopic crowd model. By tightly integrating human factors with the existing model we can study the effects on the physical domain (movement, force and crowd safety) when human behaviour (information processing and communication) is introduced.In a large-room egress scenario with ample exits, information discovery and processing yields a crowd of non-interchangeable individuals who, despite close proximity, have different goals due to their different beliefs. This crowd heterogeneity leads to complex inter-particle interactions such as jamming transitions in open space; at high crowd energies, we found a freezing by heating effect (reminiscent of the disaster at Central Lenin Stadium in 1982) in which a barrier formation of naïve individuals trying to reach blocked exits prevented knowledgeable ones from exiting. Communication, when introduced, reduced this barrier formation, increasing both exit rates and crowd safety.     

Quenched noise in surface growth

The analytical continuous equations for the Tang and Leschhorn (Phys. Rev. A 45 (1992) R8309) and the Buldyrev et al. (Phys. Rev. A 45 (1992) R8313) models are derived from the microscopic rules using a regularization procedure. As was shown in a previous paper (Phys. Rev. E 62 (2000) 6970) the continuous equation for the Tang and Leschhorn model is formally different to the Kardar–Parisi–Zhang equation (Phys. Rev. Lett. 56 (1986) 889) with quenched noise (QKPZ). Nevertheless, after expanding the multiplicative noise, it is shown that we recover the usual QKPZ, demonstrating analytically that both equations belong to the same universality class.     

Cross-link-governed dynamics of biopolymer networks

Recent experiments show that networks of stiff biopolymers cross-linked by transient linker proteins exhibit complex stress relaxation, enabling network flow at long times. We present a model for the dynamics controlled by cross-links in such networks. We show that a single microscopic time scale for cross-linker unbinding leads to a broad spectrum of macroscopic relaxation times and a shear modulus G ～ ω(1/2) for low frequencies ω. This model quantitatively describes the measured rheology of actin networks cross-linked with α-actinin-4 over more than four decades in frequency.     

Description of far-from-equilibrium processes by mean-field lattice gas models

Mean-field kinetic equations are a valuable tool to study the atomic dynamics and spin dynamics of simple lattice gas and Ising models. They can be derived from the microscopic master equation of the system and contain analytical expressions for kinetic coefficients and thermodynamic quantities which are usually introduced phenomenologically. We review several methods to obtain such equations, and discuss applications to the dynamics of order–disorder transitions, spinodal decomposition, and dendritic growth in the isothermal or chemical model. In the case of dendritic growth we show that the mean-field kinetic equations are equivalent to standard continuum equations for this problem and derive expressions for macroscopic quantities, e.g. the surface tension and kinetic coefficients, as functions of the microscopic order parameters. In spinodal decomposition, we focus our attention on the vacancy mechanism, which is a more faithful picture of diffusion in solids than the more widely examined exchange mechanism. We study the interfaces between an unstable mixture and a stable ‘vapour’ phase, and analyse surface modes that lead to specific surface patterns. For order–disorder transitions, studied in the framework of a repulsive two-sublattice model, we derive sets of coupled equations for the mean concentration (a conserved quantity) and for the occupational difference between the two sublattices emerging from the symmetry breaking due to ordering (non-conserved order parameter). These equations are applied to transport in the presence of ordered domains. Finally, we discuss the possibilities of improving the simple mean-field approximation by density functional theories and various forms of the dynamic pair approximation, including the path-probability method.     

核多体系统输运现象的微观理论

首先回顾了描写核多体系统输运现象的一些主要模型和方法,然后介绍了输运现象微观动力学基础研究上一些新的结果,强调了单粒子运动动力学特征在建立集体输运方程和理解超重核合成机制上的重要作用。能量耗散和熵产生的数值计算结果表明,集体运动耗散过程可分为退相干、弛豫和定态等3 个阶段,弛豫过程通常表现为非常复杂的反常扩散过程。在这些理论工作的基础上,提出了一种自洽地分离核多体系统集体和单粒子变量的可能途径。In this article, I provide a simple review on conventional methods and models on the transport phenomenon of nuclear many-body systems. By exploiting the basic idea of time-dependent projection operator, I recommend a novel method to derive the transport equation for collective motion which is embedded on the microscopic dynamics of timedependent single-particle motion. It is emphasized that the microscopic dynamics of single-particle motion should play an important role for understanding the dynamics of nuclear reaction and the synthesis mechanisms of new superheavy elements. The numerical results of energy dissipation and entropy production indicate that the collective motion passes through three stages, such as dephasing/decoherence, statistical relaxation and stationary state. The statistical relaxation is a complex anomalous diffusion process in general. With the aid of above analysis and results, a possible way to define the collective and single-particle variables for the realistic nuclear many-body systems is proposed.     

Spin models as microfoundation of macroscopic market models

Macroscopic price evolution models are commonly used for investment strategies. There are first promising achievements in defining microscopic agent based models for the same purpose. Microscopic models allow a deeper understanding of mechanisms in the market than the purely phenomenological macroscopic models, and thus bear the chance for better models for market regulation. However microscopic models and macroscopic models are commonly studied separately. Here, we exemplify a unified view of a microscopic and a macroscopic market model in a case study, deducing a macroscopic Langevin equation from a microscopic spin market model closely related to the Ising model. The interplay of the microscopic and the macroscopic view allows for a better understanding and adjustment of the microscopic model, as well, and may guide the construction of agent based market models as basis of macroscopic models.