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Jörn Dunkel

Publications and source records attributed to Jörn Dunkel.

At least 73 records · Page 4Linked to original sources

Meaning of temperature in different thermostatistical ensembles

Depending on the exact experimental conditions, the thermodynamic properties of physical systems can be related to one or more thermostatistical ensembles. Here, we survey the notion of thermodynamic temperature in different statistical ensembles, focusing in particular on subtleties that arise when ensembles become non-equivalent. The 'mother' of all ensembles, the microcanonical ensemble, uses entropy and internal energy (the most fundamental, dynamically conserved quantity) to derive temperature as a secondary thermodynamic variable. Over the past century, some confusion has been caused by the fact that several competing microcanonical entropy definitions are used in the literature, most commonly the volume and surface entropies introduced by Gibbs. It can be proved, however, that only the volume entropy satisfies exactly the traditional form of the laws of thermodynamics for a broad class of physical systems, including all standard classical Hamiltonian systems, regardless of their size. This mathematically rigorous fact implies that negative 'absolute' temperatures and Carnot efficiencies $>1$ are not achievable within a standard thermodynamical framework. As an important offspring of microcanonical thermostatistics, we shall briefly consider the canonical ensemble and comment on the validity of the Boltzmann weight factor. We conclude by addressing open mathematical problems that arise for systems with discrete energy spectrum.

cond-mat.stat-mech↗

Generalized Navier-Stokes equations for active suspensions

We discuss a minimal generalization of the incompressible Navier-Stokes equations to describe the solvent flow in an active suspension. To account phenomenologically for the presence of an active component driving the ambient fluid flow, we postulate a generic nonlocal extension of the stress-tensor, conceptually similar to those recently introduced in granular media flows. Stability and spectral properties of the resulting hydrodynamic model are studied both analytically and numerically for the two-dimensional (2D) case with periodic boundary conditions. Future generalizations of this momentum-conserving theory could be useful for quantifying the shear properties of active suspensions.

cond-mat.soft↗

Thermodynamic laws in isolated systems

The recent experimental realization of exotic matter states in isolated quantum systems and the ensuing controversy about the existence of negative absolute temperatures demand a careful analysis of the conceptual foundations underlying microcanonical thermostatistics. Here, we provide a detailed comparison of the most commonly considered microcanonical entropy definitions, focussing specifically on whether they satisfy or violate the zeroth, first and second law of thermodynamics. Our analysis shows that, for a broad class of systems that includes all standard classical Hamiltonian systems, only the Gibbs volume entropy fulfills all three laws simultaneously. To avoid ambiguities, the discussion is restricted to exact results and analytically tractable examples.

cond-mat.stat-mech↗

Rheotaxis facilitates upstream navigation of mammalian sperm cells

A major puzzle in biology is how mammalian sperm determine and maintain the correct swimming direction during the various phases of the sexual reproduction process. Whilst chemotaxis is assumed to dominate in the immediate vicinity of the ovum, it is unclear which biochemical or physical cues guide spermatozoa on their long journey towards the egg cell. Currently debated mechanisms range from peristaltic pumping to temperature sensing (thermotaxis) and direct response to fluid flow variations (rheotaxis), but little is known quantitatively about their relative importance. Here, we report the first quantitative experimental study of mammalian sperm rheotaxis. Using microfluidic devices, we investigate systematically the swimming behavior of human and bull sperm over the whole range of physiologically relevant shear rates and viscosities. Our measurements show that the interplay of fluid shear, steric surface-interactions and chirality of the flagellar beat leads to a stable upstream spiraling motion of sperm cells, thus providing a generic and robust rectification mechanism to support mammalian fertilisation. To rationalise these findings, we identify a minimal mathematical model that is capable of describing quantitatively the experimental observations. The combined experimental and theoretical evidence supports the hypothesis that the shape and beat patterns of mammalian sperm cells have evolved to optimally exploit rheotaxis for long-distance navigation.

physics.bio-ph↗

Reply to Frenkel and Warren [arXiv:1403.4299v1]

In their paper [arXiv:1403.4299v1], Frenkel and Warren claim that the Gibbs temperature does not characterize thermal equilibrium correctly. We point out the main logical errors in their argument.

cond-mat.stat-mech↗

Confinement Stabilizes a Bacterial Suspension into a Spiral Vortex

Confining surfaces play crucial roles in dynamics, transport and order in many physical systems, but their effects on active matter, a broad class of dynamically self-organizing systems, are poorly understood. We investigate here the influence of global confinement and surface curvature on collective motion by studying the flow and orientational order within small droplets of a dense bacterial suspension. The competition between radial confinement, self-propulsion, steric interactions and hydrodynamics robustly induces an intriguing steady single-vortex state, in which cells align in inwardly-spiralling patterns accompanied by a thin counterrotating boundary layer. A minimal continuum model is shown to be in good agreement with these observations.

cond-mat.soft↗

Inconsistent thermostatistics and negative absolute temperatures

A considerable body of experimental and theoretical work claims the existence of negative absolute temperatures in spin systems and ultra-cold quantum gases. Here, we clarify that such findings can be attributed to the use of a popular yet inconsistent entropy definition, which violates fundamental thermodynamic relations and fails to produce sensible results for simple analytically tractable classical and quantum systems. Within a mathematically consistent thermodynamic formalism, based on an entropy concept originally derived by Gibbs, absolute temperature remains positive even for systems with bounded spectrum. We address spurious arguments against the Gibbs formalism and comment briefly on heat engines with efficiencies greater than one.

cond-mat.stat-mech↗

Fluid dynamics of bacterial turbulence

Self-sustained turbulent structures have been observed in a wide range of living fluids, yet no quantitative theory exists to explain their properties. We report experiments on active turbulence in highly concentrated 3D suspensions of Bacillus subtilis and compare them with a minimal fourth-order vector-field theory for incompressible bacterial dynamics. Velocimetry of bacteria and surrounding fluid, determined by imaging cells and tracking colloidal tracers, yields consistent results for velocity statistics and correlations over two orders of magnitude in kinetic energy, revealing a decrease of fluid memory with increasing swimming activity and linear scaling between energy and enstrophy. The best-fit model parameters allow for quantitative agreement with experimental data.

cond-mat.soft↗

Ciliary contact interactions dominate surface scattering of swimming eukaryotes

Interactions between swimming cells and surfaces are essential to many microbiological processes, from bacterial biofilm formation to human fertilization. However, in spite of their fundamental importance, relatively little is known about the physical mechanisms that govern the scattering of flagellated or ciliated cells from solid surfaces. A more detailed understanding of these interactions promises not only new biological insights into structure and dynamics of flagella and cilia, but may also lead to new microfluidic techniques for controlling cell motility and microbial locomotion, with potential applications ranging from diagnostic tools to therapeutic protein synthesis and photosynthetic biofuel production. Due to fundamental differences in physiology and swimming strategies, it is an open question whether microfluidic transport and rectification schemes that have recently been demonstrated for pusher-type microswimmers such as bacteria and sperm cells, can be transferred to puller-type algae and other motile eukaryotes, as it is not known whether long-range hydrodynamic or short-range mechanical forces dominate the surface interactions of these microorganisms. Here, using high-speed microscopic imaging, we present direct experimental evidence that the surface scattering of both mammalian sperm cells and unicellular green algae is primarily governed by direct ciliary contact interactions. Building on this insight, we predict and verify experimentally the existence of optimal microfluidic ratchets that maximize rectification of initially uniform Chlamydomonas reinhardtii suspensions. Since mechano-elastic properties of cilia are conserved across eukaryotic species, we expect that our results apply to a wide range of swimming microorganisms.

physics.bio-ph↗

Minimal continuum theories of structure formation in dense active fluids

Self-sustained dynamical phases of living matter can exhibit remarkable similarities over a wide range of scales, from mesoscopic vortex structures in microbial suspensions and motility assays of biopolymers to turbulent large-scale instabilities in flocks of birds or schools of fish. Here, we argue that, in many cases, the phenomenology of such active states can be efficiently described in terms of fourth- and higher-order partial differential equations. Structural transitions in these models can be interpreted as Landau-type kinematic transitions in Fourier (wavenumber) space, suggesting that microscopically different biological systems can share universal long-wavelength features. This general idea is illustrated through numerical simulations for two classes of continuum models for incompressible active fluids: a Swift-Hohenberg-type scalar field theory, and a minimal vector model that extends the classical Toner-Tu theory and appears to be a promising candidate for the quantitive description of dense bacterial suspensions. We also discuss briefly how microscopic symmetry-breaking mechanisms can enter macroscopic continuum descriptions of collective microbial motion near surfaces and conclude by outlining future applications.

cond-mat.soft↗

Meso-scale turbulence in living fluids

Turbulence is ubiquitous, from oceanic currents to small-scale biological and quantum systems. Self-sustained turbulent motion in microbial suspensions presents an intriguing example of collective dynamical behavior amongst the simplest forms of life, and is important for fluid mixing and molecular transport on the microscale. The mathematical characterization of turbulence phenomena in active non-equilibrium fluids proves even more difficult than for conventional liquids or gases. It is not known which features of turbulent phases in living matter are universal or system-specific, or which generalizations of the Navier-Stokes equations are able to describe them adequately. Here, we combine experiments, particle simulations, and continuum theory to identify the statistical properties of self-sustained meso-scale turbulence in active systems. To study how dimensionality and boundary conditions affect collective bacterial dynamics, we measured energy spectra and structure functions in dense Bacillus subtilis suspensions in quasi-2D and 3D geometries. Our experimental results for the bacterial flow statistics agree well with predictions from a minimal model for self-propelled rods, suggesting that at high concentrations the collective motion of the bacteria is dominated by short-range interactions. To provide a basis for future theoretical studies, we propose a minimal continuum model for incompressible bacterial flow. A detailed numerical analysis of the 2D case shows that this theory can reproduce many of the experimentally observed features of self-sustained active turbulence.

cond-mat.soft↗

Fluid dynamics and noise in bacterial cell-cell and cell-surface scattering

Bacterial processes ranging from gene expression to motility and biofilm formation are constantly challenged by internal and external noise. While the importance of stochastic fluctuations has been appreciated for chemotaxis, it is currently believed that deterministic long-range fluid dynamical effects govern cell-cell and cell-surface scattering - the elementary events that lead to swarming and collective swimming in active suspensions and to the formation of biofilms. Here, we report the first direct measurements of the bacterial flow field generated by individual swimming Escherichia coli both far from and near to a solid surface. These experiments allowed us to examine the relative importance of fluid dynamics and rotational diffusion for bacteria. For cell-cell interactions it is shown that thermal and intrinsic stochasticity drown the effects of long-range fluid dynamics, implying that physical interactions between bacteria are determined by steric collisions and near-field lubrication forces. This dominance of short-range forces closely links collective motion in bacterial suspensions to self-organization in driven granular systems, assemblages of biofilaments, and animal flocks. For the scattering of bacteria with surfaces, long-range fluid dynamical interactions are also shown to be negligible before collisions; however, once the bacterium swims along the surface within a few microns after an aligning collision, hydrodynamic effects can contribute to the experimentally observed, long residence times. As these results are based on purely mechanical properties, they apply to a wide range of microorganisms.

physics.bio-ph↗

Lévy Fluctuations and Tracer Diffusion in Dilute Suspensions of Algae and Bacteria

Swimming microorganisms rely on effective mixing strategies to achieve efficient nutrient influx. Recent experiments, probing the mixing capability of unicellular biflagellates, revealed that passive tracer particles exhibit anomalous non-Gaussian diffusion when immersed in a dilute suspension of self-motile Chlamydomonas reinhardtii algae. Qualitatively, this observation can be explained by the fact that the algae induce a fluid flow that may occasionally accelerate the colloidal tracers to relatively large velocities. A satisfactory quantitative theory of enhanced mixing in dilute active suspensions, however, is lacking at present. In particular, it is unclear how non-Gaussian signatures in the tracers' position distribution are linked to the self-propulsion mechanism of a microorganism. Here, we develop a systematic theoretical description of anomalous tracer diffusion in active suspensions, based on a simplified tracer-swimmer interaction model that captures the typical distance scaling of a microswimmer's flow field. We show that the experimentally observed non-Gaussian tails are generic and arise due to a combination of truncated Lévy statistics for the velocity field and algebraically decaying time correlations in the fluid. Our analytical considerations are illustrated through extensive simulations, implemented on graphics processing units to achieve the large sample sizes required for analyzing the tails of the tracer distributions.

cond-mat.soft↗

Swimmer-tracer scattering at low Reynolds number

Understanding the stochastic dynamics of tracer particles in active fluids is important for identifying the physical properties of flow generating objects such as colloids, bacteria or algae. Here, we study both analytically and numerically the scattering of a tracer particle in different types of time-dependent, hydrodynamic flow fields. Specifically, we compare the tracer motion induced by an externally driven colloid with the one generated by various self-motile, multi-sphere swimmers. Our results suggest that force-free swimmers generically induce loop-shaped tracer trajectories. The specific topological structure of these loops is determined by the hydrodynamic properties of the microswimmer. Quantitative estimates for typical experimental conditions imply that the loops survive on average even if Brownian motion effects are taken into account.

cond-mat.soft↗

Low Reynolds number hydrodynamics of asymmetric, oscillating dumbbell pairs

Active dumbbell suspensions constitute one of the simplest model system for collective swimming at low Reynolds number. Generalizing recent work, we derive and analyze stroke-averaged equations of motion that capture the effective hydrodynamic far-field interaction between two oscillating, asymmetric dumbbells in three space dimensions. Time-averaged equations of motion, as those presented in this paper, not only yield a considerable speed-up in numerical simulations, they may also serve as a starting point when deriving continuum equations for the macroscopic dynamics of multi-swimmer suspensions. The specific model discussed here appears to be particularly useful in this context, since it allows one to investigate how the collective macroscopic behavior is affected by changes in the microscopic symmetry of individual swimmers.

cond-mat.soft↗

Noisy swimming at low Reynolds numbers

Small organisms (e.g., bacteria) and artificial microswimmers move due to a combination of active swimming and passive Brownian motion. Considering a simplified linear three-sphere swimmer, we study how the swimmer size regulates the interplay between self-driven and diffusive behavior at low Reynolds number. Starting from the Kirkwood-Smoluchowski equation and its corresponding Langevin equation, we derive formulas for the orientation correlation time, the mean velocity and the mean square displacement in three space dimensions. The validity of the analytical results is illustrated through numerical simulations. Tuning the swimmer parameters to values that are typical of bacteria, we find three characteristic regimes: (i) Brownian motion at small times, (ii) quasi-ballistic behavior at intermediate time scales, and (iii) quasi-diffusive behavior at large times due to noise-induced orientation flipping. Our analytical results can be useful for a better quantitative understanding of optimal foraging strategies in bacterial systems, and they can help to construct more efficient artificial microswimmers in fluctuating fluids.

cond-mat.soft↗

Nonlocal observables and lightcone-averaging in relativistic thermodynamics

The unification of relativity and thermodynamics has been a subject of considerable debate over the last 100 years. The reasons for this are twofold: (i) Thermodynamic variables are nonlocal quantities and, thus, single out a preferred class of hyperplanes in spacetime. (ii) There exist different, seemingly equally plausible ways of defining heat and work in relativistic systems. These ambiguities led, for example, to various proposals for the Lorentz transformation law of temperature. Traditional 'isochronous' formulations of relativistic thermodynamics are neither theoretically satisfactory nor experimentally feasible. Here, we demonstrate how these deficiencies can be resolved by defining thermodynamic quantities with respect to the backward-lightcone of an observation event. This approach yields novel, testable predictions and allows for a straightforward-extension of thermodynamics to General Relativity. Our theoretical considerations are illustrated through three-dimensional relativistic many-body simulations.

cond-mat.stat-mech↗