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Cooperative behavior, the costly provision of benefits to others, is common across all domains of life. This review article discusses cooperative behavior in the microbial world, mediated by the exchange of extracellular products called public goods. We focus on model species for which the production of a public good and the related growth disadvantage for the producing cells are well described. To unveil the biological and ecological factors promoting the emergence and stability of cooperative traits we take an interdisciplinary perspective and review insights gained from both mathematical models and well-controlled experimental model systems. Ecologically, we include crucial aspects of the microbial life cycle into our analysis and particularly consider population structures where an ensemble of local communities (sub populations) continuously emerge, grow, and disappear again. Biologically, we explicitly consider the synthesis and regulation of public good production. The discussion of the theoretical approaches includes general evolutionary concepts, population dynamics, and evolutionary game theory. As a specific but generic biological example we consider populations of Pseudomonas putida and its regulation and utilization of pyoverdines, iron scavenging molecules. The review closes with an overview on cooperation in spatially extended systems and also provides a critical assessment of the insights gained from the experimental and theoretical studies discussed. Current challenges and important new research opportunities are discussed, including the biochemical regulation of public goods, more realistic ecological scenarios resembling native environments, cell to cell signalling, and multi-species communities., Comment: Review article, 88 pages, 14 figures

Vibrated polar disks have been used experimentally to investigate collective motion of driven particles, where fully-ordered asymptotic regimes could not be reached. Here we present a model reproducing quantitatively the single, binary and collective properties of this granular system. Using system sizes not accessible in the laboratory, we show in silico that true long-range order is possible in the experimental system. Exploring the model's parameter space, we find a phase diagram qualitatively different from that of dilute or point-like particle systems., Comment: 5 pages, 4 figures

Self-organized monolayers of highly flexible \Frechet dendrons were deposited on graphite surfaces by solution casting. Scanning tunneling microscopy (STM) reveals an unprecedented variety of patterns with up to seven stable hierarchical ordering motifs serving as a versatile model system. The essential molecular properties determined by molecular mechanics simulations are condensed to a coarse grained interaction site model of various chain configurations. In a Monte Carlo approach with random starting configurations the experimental pattern diversity can be reproduced in all facets of the local and global ordering. Based on an energy analysis of the Monte Carlo and molecular mechanics modeling the thermodynamically most stable pattern is predicted coinciding with the pattern, which dominates in the STM images after several hours or upon moderate heating., Comment: 6 pages, 7 figures

Species extinction occurs regularly and unavoidably in ecological systems. The time scales for extinction can broadly vary and inform on the ecosystem's stability. We study the spatio-temporal extinction dynamics of a paradigmatic population model where three species exhibit cyclic competition. The cyclic dynamics reflects the non-equilibrium nature of the species interactions. While previous work focusses on the coarsening process as a mechanism that drives the system to extinction, we found that unexpectedly the dynamics to extinction is much richer. We observed three different types of dynamics. In addition to coarsening, in the evolutionary relevant limit of large times, oscillating traveling waves and heteroclinic orbits play a dominant role. The weight of the different processes depends on the degree of mixing and the system size. By analytical arguments and extensive numerical simulations we provide the full characteristics of scenarios leading to extinction in one of the most surprising models of ecology.

The constraints imposed by nano- and microscale confinement on the conformational degrees of freedom of thermally fluctuating biopolymers are utilized in contemporary nano-devices to specifically elongate and manipulate single chains. A thorough theoretical understanding and quantification of the statistical conformations of confined polymer chains is thus a central concern in polymer physics. We present an analytical calculation of the radial distribution function of harmonically confined semiflexible polymers in the weakly bending limit. Special emphasis has been put on a proper treatment of global modes, i.e. the possibility of the chain to perform global movements within the channel. We show that the effect of these global modes significantly impacts the chain statistics in cases of weak and intermediate confinement. Comparing our analytical model to numerical data from Monte Carlo simulations we find excellent agreement over a broad range of parameters., Comment: 6 pages, 3 figures typo corrected, slightly revised line of reasoning, results unchanged

Populations of competing biological species exhibit a fascinating interplay between the nonlinear dynamics of evolutionary selection forces and random fluctuations arising from the stochastic nature of the interactions. The processes leading to extinction of species, whose understanding is a key component in the study of evolution and biodiversity, are influenced by both of these factors. In this paper, we investigate a class of stochastic population dynamics models based on generalized Lotka-Volterra systems. In the case of neutral stability of the underlying deterministic model, the impact of intrinsic noise on the survival of species is dramatic: it destroys coexistence of interacting species on a time scale proportional to the population size. We introduce a new method based on stochastic averaging which allows one to understand this extinction process quantitatively by reduction to a lower-dimensional effective dynamics. This is performed analytically for two highly symmetrical models and can be generalized numerically to more complex situations. The extinction probability distributions and other quantities of interest we obtain show excellent agreement with simulations., Comment: 14 pages, 7 figures

It is a long-standing question in origin-of-life research whether the information content of replicating molecules can be maintained in the presence of replication errors. Extending standard quasispecies models of non-enzymatic replication, we analyze highly specific enzymatic self-replication mediated through an otherwise neutral recognition region, which leads to frequency-dependent replication rates. We find a significant reduction of the maximally tolerable error rate, because the replication rate of the fittest molecules decreases with the fraction of functional enzymes. Our analysis is extended to hypercyclic couplings as an example for catalytic networks., Comment: 6 pages, 4 figures; accepted at Europhys. Lett

The dynamic response of prestressed semiflexible biopolymers is characterized by the propagation and relaxation of tension, which arises due to the near inextensibility of a stiff backbone. It is coupled to the dynamics of contour length stored in thermal undulations, but also to the local relaxation of elongational strain. We present a systematic theory of tension dynamics for stiff yet extensible wormlike chains. Our results show that even moderate prestress gives rise to distinct Rouse-like extensibility signatures in the high-frequency viscoelastic response., Comment: 4 pages, 1 figure; corrected typos

Mutual uncrossability of polymers generates topological constraints on their conformations and dynamics, which are generally described using the tube model. We imaged confinement tubes for individual polymers within a F-actin solution by sampling over many successive micrographs of fluorescently labeled probe filaments. The resulting average tube width shows the predicted scaling behavior. Unexpectedly, we found an exponential distribution of tube curvatures which is attributed to transient entropic trapping in network void spaces., Comment: 6 pages, 4 figures

The relaxation of initially straight semiflexible polymers has been discussed mainly with respect to the longest relaxation time. The biologically relevant non-equilibrium dynamics on shorter times is comparatively poorly understood, partly because "initially straight" can be realized in manifold ways. Combining Brownian dynamics simulations and systematic theory, we demonstrate how different experimental preparations give rise to specific short-time and universal long-time dynamics. We also discuss boundary effects and the onset of the stretch--coil transition., Comment: 14 pages, 5 figures, 3 tables

We present a theory for the elasticity of cross-linked stiff polymer networks. Stiff polymers, unlike their flexible counterparts, are highly anisotropic elastic objects. Similar to mechanical beams stiff polymers easily deform in bending, while they are much stiffer with respect to tensile forces (``stretching''). Unlike in previous approaches, where network elasticity is derived from the stretching mode, our theory properly accounts for the soft bending response. A self-consistent effective medium approach is used to calculate the macroscopic elastic moduli starting from a microscopic characterization of the deformation field in terms of ``floppy modes'' -- low-energy bending excitations that retain a high degree of non-affinity. The length-scale characterizing the emergent non-affinity is given by the ``fiber length'' $l_f$, defined as the scale over which the polymers remain straight. The calculated scaling properties for the shear modulus are in excellent agreement with the results of recent simulations obtained in two-dimensional model networks. Furthermore, our theory can be applied to rationalize bulk rheological data in reconstituted actin networks., Comment: 12 pages, 10 figures, revised Section III

While actin bundles are used by living cells for structural fortification, the microscopic origin of the elasticity of bundled networks is not understood. Here, we show that above a critical concentration of the actin binding protein fascin, a solution of actin filaments organizes into a pure network of bundles. While the elasticity of weakly crosslinked networks is dominated by the affine deformation of tubes, the network of bundles can be fully understood in terms of non-affine bending undulations., Comment: 5 pages, 3 figures, final version as published

We consider the influence of disorder on the non-equilibrium steady state of a minimal model for intracellular transport. In this model particles move unidirectionally according to the \emph{totally asymmetric exclusion process} (TASEP) and are coupled to a bulk reservoir by \emph{Langmuir kinetics}. Our discussion focuses on localized point defects acting as a bottleneck for the particle transport. Combining analytic methods and numerical simulations, we identify a rich phase behavior as a function of the defect strength. Our analytical approach relies on an effective mean-field theory obtained by splitting the lattice into two subsystems, which are effectively connected exploiting the local current conservation. Introducing the key concept of a carrying capacity, the maximal current which can flow through the bulk of the system (including the defect), we discriminate between the cases where the defect is irrelevant and those where it acts as a bottleneck and induces various novel phases (called {\it bottleneck phases}). Contrary to the simple TASEP in the presence of inhomogeneities, many scenarios emerge and translate into rich underlying phase-diagrams, the topological properties of which are discussed., Comment: 14 pages, 15 figures, 1 table

We analyze the nonequilibrium dynamics of single inextensible semiflexible biopolymers as stretching forces are applied at the ends. Based on different (contradicting) heuristic arguments, various scaling laws have been proposed for the propagation speed of the backbone tension which is induced in response to stretching. Here, we employ a newly developed unified theory to systematically substantiate, restrict, and extend these approaches. Introducing the practically relevant scenario of a chain equilibrated under some prestretching force $f_\text{pre}$ that is suddenly exposed to a different external force $f_\text{ext}$ at the ends, we give a concise physical explanation of the underlying relaxation processes by means of an intuitive blob picture. We discuss the corresponding intermediate asymptotics, derive results for experimentally relevant observables, and support our conclusions by numerical solutions of the coarse-grained equations of motion for the tension., Comment: 14 pages, 8 figures; final version as published

We investigate the non-equilibrium steady state of a one-dimensional (1D) lattice gas of dimers. The dynamics is described by a totally asymmetric exclusion process (TASEP) supplemented by attachment and detachment processes, mimicking chemical equilibrium of the 1D driven transport with the bulk reservoir. The steady-state phase diagram, current and density profiles are calculated using both a refined mean-field theory and extensive stochastic simulations. As a consequence of the on-off kinetics, a new phase coexistence region arises intervening between low and high density phases such that the discontinuous transition line of the TASEP splits into two continuous ones. The results of the mean-field theory and simulations are found to coincide. We show that the physical picture obtained in the corresponding lattice gas model with monomers is robust, in the sense that the phase diagram changes quantitatively, but the topology remains unaltered. The mechanism for phase separation is identified as generic for a wide class of driven 1D lattice gases., Comment: 15 pages, 10 figures, 1table

We study the dynamics of the totally asymmetric exclusion process with open boundaries by phenomenological theories complemented by extensive Monte-Carlo simulations. Upon combining domain wall theory with a kinetic approach known as Boltzmann-Langevin theory we are able to give a complete qualitative picture of the dynamics in the low and high density regime and at the corresponding phase boundary. At the coexistence line between high and low density phases we observe a time scale separation between local density fluctuations and collective domain wall motion, which are well accounted for by the Boltzmann-Langevin and domain wall theory, respectively. We present Monte-Carlo data for the correlation functions and power spectra in the full parameter range of the model., Comment: 10 pages, 9 figures

The phase behavior of a two-dimensional colloidal system subject to a commensurate triangular potential is investigated. We consider the integer number of colloids in each potential minimum as rigid composite objects with effective discrete degrees of freedom. It is shown that there is a rich variety of phases including ``herring bone'' and ``Japanese 6 in 1'' phases. The ensuing phase diagram and phase transitions are analyzed analytically within variational mean-field theory and supplemented by Monte Carlo simulations. Consequences for experiments are discussed., Comment: 10 pages, 4 figures

Recent Monte Carlo simulations of a grafted semiflexible polymer in 1+1 dimensions have revealed a pronounced bimodal structure in the probability distribution of the transverse (bending) fluctuations of the free end, when the total contour length is of the order of the persistence length [G. Lattanzi et al., Phys. Rev E 69, 021801 (2004)]. In this paper, we show that the emergence of bimodality is related to a similar behavior observed when a random walker is driven in the transverse direction by a certain type of shear flow. We adapt an effective-medium argument, which was first introduced in the context of the sheared random-walk problem [E. Ben-Naim et al., Phys. Rev. A 45, 7207 (1992)], in order to obtain a simple analytic approximation of the probability distribution of the free-end fluctuations. We show that this approximation captures the bimodality and most of the qualitative features of the free-end fluctuations. We also predict that relaxing the local inextensibility constraint of the wormlike chain could lead to the disappearence of bimodality., Comment: 5 pages, 4 figures

We discuss a new class of driven lattice gas obtained by coupling the one-dimensional totally asymmetric simple exclusion process to Langmuir kinetics. In the limit where these dynamics are competing, the resulting non-conserved flow of particles on the lattice leads to stationary regimes for large but finite systems. We observe unexpected properties such as localized boundaries (domain walls) that separate coexisting regions of low and high density of particles (phase coexistence). A rich phase diagram, with high an low density phases, two and three phase coexistence regions and a boundary independent ``Meissner'' phase is found. We rationalize the average density and current profiles obtained from simulations within a mean-field approach in the continuum limit. The ensuing analytic solution is expressed in terms of Lambert $W$-functions. It allows to fully describe the phase diagram and extract unusual mean-field exponents that characterize critical properties of the domain wall. Based on the same approach, we provide an explanation of the localization phenomenon. Finally, we elucidate phenomena that go beyond mean-field such as the scaling properties of the domain wall., Comment: 22 pages, 23 figures. Accepted for publication on Phys. Rev. E

Motivated by the phenomenologies of dynamic roughening of strings in random media and magnetohydrodynamics, we examine the universal properties of driven diffusive system with coupled fields. We demonstrate that cross-correlations between the fields lead to amplitude-ratios and scaling exponents varying continuosly with the strength of these cross-correlations. The implications of these results for experimentally relevant systems are discussed., Comment: To appear in Phys. Rev. E (Rapid Comm.) (2003)

We study a one-dimensional totally asymmetric exclusion process with random particle attachments and detachments in the bulk. The resulting dynamics leads to unexpected stationary regimes for large but finite systems. Such regimes are characterized by a phase coexistence of low and high density regions separated by domain walls. We use a mean-field approach to interpret the numerical results obtained by Monte-Carlo simulations and we predict the phase diagram of this non-conserved dynamics in the thermodynamic limit., Comment: 4 pages, 3 figures. Accepted for publication on Phys. Rev. Lett

We study the effect of generic spatial anisotropies on the scaling behavior in the Kardar-Parisi-Zhang equation. In contrast to its "conserved" variants, anisotropic perturbations are found to be relevant in d > 2 dimensions, leading to rich phenomena that include novel universality classes and the possibility of first-order phase transitions and multicritical behavior. These results question the presumed scaling universality in the strong-coupling rough phase, and shed further light on the connection with generalized driven diffusive systems., Comment: 4 pages, revtex, 2 figures (eps files enclosed)

We study the critical dynamics of three-dimensional ferromagnets with uniaxial anisotropy by taking into account exchange and dipole-dipole interaction. The dynamic spin correlation functions and the transport coefficients are calculated within a mode coupling theory. It is found that the crossover scenario is determined by the subtle interplay between three length scales: the correlation length, the dipolar and uniaxial wave vector. We compare our theoretical findings with hyperfine interaction experiments on Gd and find quantitative agreement. This analysis allows us to identify the universality class for Gd. It also turns out that the $\mu$SR relaxation rate can be best fitted if it is assumed that muons occupy octahedral interstitials sites within the Gd lattice., Comment: 21 pages, 23 figures

We investigate the Kardar--Parisi--Zhang (KPZ) equation in $d$ spatial dimensions with Gaussian spatially long--range correlated noise --- characterized by its second moment $R(\vec{x}-\vec{x}') \propto |\vec{x}-\vec{x}'|^{2\rho-d}$ --- by means of dynamic field theory and the renormalization group. Using a stochastic Cole--Hopf transformation we derive {\em exact} exponents and scaling functions for the roughening transition and the smooth phase above the lower critical dimension $d_c = 2 (1+\rho)$. Below the lower critical dimension, there is a line $\rho_*(d)$ marking the stability boundary between the short-range and long-range noise fixed points. For $\rho \geq \rho_*(d)$, the general structure of the renormalization-group equations fixes the values of the dynamic and roughness exponents exactly, whereas above $\rho_*(d)$, one has to rely on some perturbational techniques. We discuss the location of this stability boundary $\rho_* (d)$ in light of the exact results derived in this paper, and from results known in the literature. In particular, we conjecture that there might be two qualitatively different strong-coupling phases above and below the lower critical dimension, respectively., Comment: 21 pages, 15 figures

We have investigated the viscosity and the plateau modulus of actin solutions with a magnetically driven rotating disc rheometer. For entangled solutions we observed a scaling of the plateau modulus versus concentration with a power of 7/5. The measured terminal relaxation time increases with a power 3/2 as a function of polymer length. We interpret the entanglement transition and the scaling of the plateau modulus in terms of the tube model for semiflexible polymers., Comment: 5 pages, 4 figures, published version

We determine the zero-temperature phase diagram of the hard-core Bose-Hubbard model on a square lattice by mean-field theory supplemented by a linear spin-wave analysis. Due to the interplay between nearest and next-nearest neighbor interaction and cubic anisotropy several supersolid phases with checkerboard, stripe domain or intermediate symmetry are stabilized. The phase diagrams show three different topologies depending on the relative strength of nearest and next-nearest neighbor interaction. We also find a rich variety of new quantum critical behavior and multicritical points and discuss the corresponding effective actions and universality classes., Comment: 19 pages, ReVTeX, 18 figures included, submitted to PRB

We resolve a longstanding puzzle for the static and dynamic critical behavior of Gadolinium by a combined theoretical and experimental investigation. It is shown that the spin dynamics of a three dimensional ferromagnet with hcp lattice structure and a spin-spin interaction given by both exchange and dipole-dipole interaction belongs to a new dynamic universality class, model J$^*$. Comparing results from mode coupling theory with results from three different hyperfine interaction probes we find quantitative agreement. The crossover scenario for the wavevector dependence of the hyperfine relaxation rate is determined by a subtle interplay between three length scales: the correlation length, the dipolar and the uniaxial wave vector., Comment: 5 pages, 3 figures, REVTeX, also available at http://WWW.Physik.TU-Muenchen.DE:81/~frey/

Quasi-elastic light scattering (QELS) is applied to investigate the effect of the tropomyosin/troponin complex (Tm/Tn) on the stiffness of actin filaments. The importance of hydrodynamic screening in semidilute solutions is demonstrated. A new concentration dependent expression for the dynamic structure factor $g(\bm k,t)$ of semiflexible polymers in semidilute solutions is used to analyze the experimental QELS data. A concentration independent value for the bending modulus $\kappa$ is thus obtained. It increases by 50\% as a consequence of Tm/Tn binding in a 7:1:1 molar ratio of actin/Tm/Tn. In addition a new expression for the initial slope of the dynamic structure factor of a semiflexible polymer is used to determine the effective hydrodynamic diameter of the actin filament. Our results confirm the general relevance of the concept of (intrinsic) semiflexibility to polymer dynamics., Comment: 9 pages, RevTeX, 9 figures, all uuencoded gziped

Percolation clusters are probably the simplest example for scale--invariant structures which either are governed by isotropic scaling--laws (``self--similarity'') or --- as in the case of directed percolation --- may display anisotropic scaling behavior (``self--affinity''). Taking advantage of the fact that both isotropic and directed bond percolation (with one preferred direction) may be mapped onto corresponding variants of (Reggeon) field theory, we discuss the crossover between self--similar and self--affine scaling. This has been a long--standing and yet unsolved problem because it is accompanied by different upper critical dimensions: $d_c^{\rm I} = 6$ for isotropic, and $d_c^{\rm D} = 5$ for directed percolation, respectively. Using a generalized subtraction scheme we show that this crossover may nevertheless be treated consistently within the framework of renormalization group theory. We identify the corresponding crossover exponent, and calculate effective exponents for different length scales and the pair correlation function to one--loop order. Thus we are able to predict at which characteristic anisotropy scale the crossover should occur. The results are subject to direct tests by both computer simulations and experiment. We emphasize the broad range of applicability of the proposed method., Comment: 19 pages, written in RevTeX, 12 figures available upon request (from tauber@cmt.harvard.edu or frey@physik.tu-muenchen.de), EF/UCT--94/2, to be published in Phys. Rev. E (May 1994)

A three-dimensional weak coupling BCS model with an {\it anisotropic} pairing interaction in momentum space is reported. It exhibits an anisotropic gap in accord with recent experimental observations for high-$T_c$ oxides. The gap ratio ${2 \Delta / k_B T_c }$ is calculated as function of the anisotropy ratio of the electron pairing. It is found that the mean gap ratio decreases with increasing anisotropy of the electron pairing, whereas the maximum gap ratio increases. Assuming a unique strength of the effective electron interaction the transition temperature turns out to be always larger than in the isotropic case. The temperature dependence of the gap in the Cu-O plane and along the c-axis of YBaCuO is presented., Comment: 13 LaTex pages using RevTex (3 figures available on request), UNITUE-THEP-6-1993