A wide range of experimental systems including gliding, swarming and swimming bacteria, in vitro motility assays, and shaken granular media are commonly described as self-propelled rods. Large ...ensembles of those entities display a large variety of self-organized, collective phenomena, including the formation of moving polar clusters, polar and nematic dynamic bands, mobility-induced phase separation, topological defects, and mesoscale turbulence, among others. Here, we give a brief survey of experimental observations and review the theoretical description of self-propelled rods. Our focus is on the emergent pattern formation of ensembles of dry self-propelled rods governed by short-ranged, contact mediated interactions and their wet counterparts that are also subject to long-ranged hydrodynamic flows. Altogether, self-propelled rods provide an overarching theme covering many aspects of active matter containing well-explored limiting cases. Their collective behavior not only bridges the well-studied regimes of polar self-propelled particles and active nematics, and includes active phase separation, but also reveals a rich variety of new patterns.
F
1
-ATPase is a nanosized biological energy transducer working as part of F
o
F
1
-ATP synthase. Its rotary machinery transduces energy between chemical free energy and mechanical work and plays a ...central role in the cellular energy transduction by synthesizing most ATP in virtually all organisms. However, information about its energetics is limited compared to that of the reaction scheme. Actually, fundamental questions such as how efficiently F
1
-ATPase transduces free energy remain unanswered. Here, we demonstrated reversible rotations of isolated F
1
-ATPase in discrete 120° steps by precisely controlling both the external torque and the chemical potential of ATP hydrolysis as a model system of F
o
F
1
-ATP synthase. We found that the maximum work performed by F
1
-ATPase per 120° step is nearly equal to the thermodynamical maximum work that can be extracted from a single ATP hydrolysis under a broad range of conditions. Our results suggested a 100% free-energy transduction efficiency and a tight mechanochemical coupling of F
1
-ATPase.
The Mpemba effect occurs when a hot system cools faster than an initially colder one, when both are refrigerated in the same thermal reservoir. Using the custom-built supercomputer Janus II, we study ...the Mpemba effect in spin glasses and show that it is a nonequilibrium process, governed by the coherence length ξ of the system. The effect occurs when the bath temperature lies in the glassy phase, but it is not necessary for the thermal protocol to cross the critical temperature. In fact, the Mpemba effect follows from a strong relationship between the internal energy and ξ that turns out to be a sure-tell sign of being in the glassy phase. Thus, the Mpemba effect presents itself as an intriguing avenue for the experimental study of the coherence length in supercooled liquids and other glass formers.
Fibonacci family of dynamical universality classes Popkov, Vladislav; Schadschneider, Andreas; Schmidt, Johannes ...
Proceedings of the National Academy of Sciences - PNAS,
10/2015, Volume:
112, Issue:
41
Journal Article
Peer reviewed
Open access
Universality is a well-established central concept of equilibrium physics. However, in systems far away from equilibrium, a deeper understanding of its underlying principles is still lacking. Up to ...now, a few classes have been identified. Besides the diffusive universality class with dynamical exponentz= 2, another prominent example is the superdiffusive Kardar–Parisi–Zhang (KPZ) class withz= 3/2. It appears, e.g., in low-dimensional dynamical phenomena far from thermal equilibrium that exhibit some conservation law. Here we show that both classes are only part of an infinite discrete family of nonequilibrium universality classes. Remarkably, their dynamical exponentszα
are given by ratios of neighboring Fibonacci numbers, starting with eitherz₁ = 3/2 (if a KPZ mode exist) orz₁ = 2 (if a diffusive mode is present). If neither a diffusive nor a KPZ mode is present, all dynamical modes have the Golden Meanz= (1 + √5)/2 as dynamical exponent. The universal scaling functions of these Fibonacci modes are asymmetric Lévy distributions that are completely fixed by the macroscopic current density relation and compressibility matrix of the system and hence accessible to experimental measurement.
Actin is the main protein used by biological cells to adapt their structure and mechanics to their needs. Cellular adaptation is made possible by molecular processes that strongly depend on ...mechanics. The actin cytoskeleton is also an active material that continuously consumes energy. This allows for dynamical processes that are possible only out of equilibrium and opens up the possibility for multiple layers of control that have evolved around this single protein. Here we discuss the actin cytoskeleton from the viewpoint of physics as an active adaptive material that can build structures superior to man-made soft matter systems. Not only can actin be used to build different network architectures on demand and in an adaptive manner, but it also exhibits the dynamical properties of feedback systems, like excitability, bistability, or oscillations. Therefore, it is a prime example of how biology couples physical structure and information flow and a role model for biology-inspired metamaterials.
In these notes we provide an introductory description of the physics of active matter, focusing on theoretical aspects, and on some methods which are often used in the field. We discuss a selection ...of active systems, where activity comes from different microscopic sources (mainly self-replication, self-propulsion, non-thermal forces), and in all cases we focus on their statistical physics and emergent collective behaviour, which is often linked to underlying nonequilibrium phase transitions. We hope to convey the idea that this field is a fascinating growing area of research at the interphase between statistical, soft matter and biological physics, and that active matter systems can possess, in general, a much richer physics than their passive counterparts.
•We review some introductory features of active matter physics.•We show how to model growing microbial colonies.•We discuss the physics of self-motile systems.•We provide an introduction to the physics of active gels.
We propose a two-dimensional cellular automaton model to simulate pedestrian traffic. It is a
v
max=1 model with exclusion statistics and parallel dynamics. Long-range interactions between the ...pedestrians are mediated by a so-called
floor field which modifies the transition rates to neighbouring cells. This field, which can be discrete or continuous, is subject to diffusion and decay. Furthermore it can be modified by the motion of the pedestrians. Therefore, the model uses an idea similar to chemotaxis, but with pedestrians following a virtual rather than a chemical trace. Our main goal is to show that the introduction of such a floor field is sufficient to model collective effects and self-organization encountered in pedestrian dynamics, e.g. lane formation in counterflow through a large corridor. As an application we also present simulations of the evacuation of a large room with reduced visibility, e.g. due to failure of lights or smoke.
In the so-called “microscopic” models of vehicular traffic, attention is paid explicitly to each individual vehicle each of which is represented by a “particle”; the nature of the “interactions” ...among these particles is determined by the way the vehicles influence each others’ movement. Therefore, vehicular traffic, modeled as a system of
interacting “particles”
driven far from equilibrium, offers the possibility to study various fundamental aspects of truly nonequilibrium systems which are of current interest in statistical physics. Analytical as well as numerical techniques of statistical physics are being used to study these models to understand rich variety of physical phenomena exhibited by vehicular traffic. Some of these phenomena, observed in vehicular traffic under different circumstances, include transitions from one dynamical phase to another, criticality and self-organized criticality, metastability and hysteresis, phase-segregation, etc. In this critical review, written from the
perspective of statistical physics, we explain the guiding principles behind all the main theoretical approaches. But we present detailed discussions on the results obtained mainly from the so-called “particle-hopping” models, particularly emphasizing those which have been formulated in recent years using the language of cellular automata.
We consider the non-equilibrium steady-state conversion of chemical to mechanical energy in motor protein systems with protein–protein interactions. Our approach combines a two-dimensional ...chemomechanical coupling model with a simple exclusion process. The chemomechanical model explicitly includes both chemical and mechanical degrees of freedom to describe not only coupled chemomechanical transitions but also uncoupled transitions, such as futile chemical cycles, that lead to energy loss. The simple exclusion process describes strong repulsive protein–protein interactions in the mechanical degree of freedom and these interactions have implications for the chemical degree of freedom via the chemomechanical coupling. Using the combined chemomechanical exclusion model, we determine the efficiency of energy conversion as a function of motor density and chemical driving force. We show that as motor density increases, mechanical motion is blocked, losses due to futile chemical cycles increase, and the efficiency of chemical-to-mechanical energy conversion is reduced.
•Analytic expression of bulk reaction velocity of a periodic 2-dimensional ASEP model.•Efficiency of energy conversion and mass transport for interacting Brownian motors.•Analysis of the chemical-to-motion efficacy of interacting Brownian motors.•Dissipation futile chemical cycles induced by intracellular transport jamming.
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