Collective dynamics of two-dimensional coupled Brownian motors

The transport properties of coupled Brownian particles in a two-dimensional rocking ratchet are investigated via Langevin simulation. The results show that the average center-of-mass velocity is multi-peaks function of the frequency of the driving force. Furthermore, in the 2D coupled Brownian motor system there are the collective effect and ratchet behavior, which can switch depending on the frequency of driving force. It turns out that the cooperative effect between the interaction of coupled particles and external rocking driving force facilitates collective directional motion and energy conversion.     

Enhanced ordering of interacting filaments by molecular motors

We theoretically study the cooperative behavior of cytoskeletal filaments in motility assays in which immobilized motor proteins bind the filaments to substrate surfaces and actively pull them along these surfaces. Because of the mutual exclusion of the filaments, the coupled dynamics of filaments, motor heads, and motor tails leads to a nonequilibrium phase transition which generalizes the isotropic-nematic phase transition of the corresponding equilibrium system, the hard-rod fluid. Langevin dynamics simulations show that the motor activity enhances the tendency for nematic ordering. We develop a quantitative theory for the location of the phase boundary as a function of motor density. At high detachment forces of motors, we also observe filament clusters arising from blocking effects.     

Collective alignment of polar filaments by molecular motors

We study the alignment of polar biofilaments, such as microtubules and actin, subject to the action of multiple molecular motors attached simultaneously to more than one filament. Focusing on a paradigm model of only two filaments interacting with multiple motors, we were able to investigate in detail the alignment dynamics. While almost no alignment occurs in the case of a single motor, the filaments become rapidly aligned due to the collective action of the motors. Our analysis shows that the alignment time is governed by the number of bound motors and the magnitude of the motors’ stepping fluctuations. We predict that the time scale of alignment is in the order of seconds, much faster than that reported for passive crosslink-induced bundling. In vitro experiments on the alignment of microtubules by multiple-motor covered beads are in qualitative agreement. We also discuss another mode of fast alignment of filaments, namely the cooperation between motors and passive crosslinks.     

Collective phase chaos in the dynamics of interacting oscillator ensembles

We study the chaotic behavior of order parameters in two coupled ensembles of self-sustained oscillators. Coupling within each of these ensembles is switched on and off alternately, while the mutual interaction between these two subsystems is arranged through quadratic nonlinear coupling. We show numerically that in the course of alternating Kuramoto transitions to synchrony and back to asynchrony, the exchange of excitations between two subpopulations proceeds in such a way that their collective phases are governed by an expanding circle map similar to the Bernoulli map. We perform the Lyapunov analysis of the dynamics and discuss finite-size effects.     

Evolution of cooperation among interacting individuals through molecular dynamics simulations

Using molecular dynamics (MD) simulation and evolutionary game theory, we incorporate the spacial structure of individuals into the study of the behaviors of cooperation, by adopting the prisoner's dilemma and snowdrift game as metaphors of cooperation between unrelated individuals. The results show that the introduction of spacial structure enhances cooperation using the strategy of prisoner's dilemma while does not make much changes to the cooperation if the strategy of snowdrift game is used. It is also found that our model is a meta-phase between regular ring graph model and complex network model. And the “activity of players” T^* we introduced makes our simulation much more closer to real world problems.     

Collective states of interacting ferromagnetic nanoparticles

Discontinuous magnetic multilayers [CoFe/Al₂O₃] are studied by use of magnetometry, susceptometry and numeric simulations. Soft ferromagnetic Co₈₀Fe₂₀ nanoparticles are embedded in a diamagnetic insulating a-Al₂O₃ matrix and can be considered as homogeneously magnetized superspins exhibiting randomness of size (viz. moment), position and anisotropy. Lacking intra-particle core-surface ordering, generic freezing processes into collective states rather than individual particle blocking are encountered. With increasing particle density one observes first superspin glass and then superferromagnetic domain state behavior. The phase diagram resembles that of a dilute disordered ferromagnet. Criteria for the identification of the individual phases are given.     

生物分子马达

生物分子马达处在生命与纳米两学科的交叉点上,注定会成为本世纪基础研究的主角之一。生物分子马达的研究尽管经历了150多年,但突破性进展出现在最近二十年,这既得益于单分子技术的发展,更要归功于物理学家、生物化学家、医学家及计算学家等的联合交叉研究。文章回顾了分子马达研究的历程,展示了主要成果,也提出了面临的问题。     

DNA based molecular motors

Most of the essential cellular processes such as polymerisation reactions, gene expression and regulation are governed by mechanical processes. Controlled mechanical investigations of these processes are therefore required in order to take our understanding of molecular biology to the next level. Single-molecule manipulation and force spectroscopy have over the last 15 years been developed into extremely powerful techniques. Applying these techniques to the investigation of proteins and DNA molecules has led to a mechanistic understanding of protein function on the level of single molecules. As examples for DNA based molecular machines we will describe single-molecule experiments on RNA polymerases as well as on the packaging of DNA into a viral capsid—a process that is driven by one of the most powerful molecular motors.     

Elastically coupled molecular motors

We study the influence of filament elasticity on the motion of collective molecular motors. It is found that for a backbone flexibility exceeding a characteristic value (motor stiffness divided through the mean displacement between attached motors), the ability of motors to produce force reduces as compared to rigidly coupled motors, while the maximum velocity remains unchanged. The force-velocity-relation in two different analytic approximations is calculated and compared with Monte-Carlo simulations. Finally, we extend our model by introducing motors with a strain-dependent detachment rate. A remarkable crossover from the nearly hyperbolic shape of the Hill curve for stiff backbones to a linear force-velocity relation for very elastic backbones is found. With realistic model parameters we show that the backbone flexibility plays no role under physiological conditions in muscles, but it should be observable in certain in vitro assays. Received: 27 November 1997 / Revised: 20 February 1998 / Accepted: 27 March 1998     

Effect of varying load in moving period of a step on dynamics of molecular motors

The European Physical Journal E -     

Light-driven molecular switches and motors

Technology is omnipresent in our modern-day society and it is hard to imagine a world without machines, computers or robots. One of the main current scientific challenges is the bottom-up construction of systems that represent nanosize analogues of switches, devices and motors. Our efforts in this area have focussed on the construction of devices based on sterically overcrowded alkenes. In this paper, we present our ongoing research on the construction of binary molecular switches, which has recently led to genuine molecular motors. The control of chirality in a molecular switching system allows interconversion between molecules of opposite helicity using different wavelengths of light. Such bistable chiral switches are of potential use in optical data storage and processing at the molecular level. The control of molecular chirality is even more subtle in the case of molecular motor systems. The exquisite control of chirality using light as an energy source has resulted in a controlled, repetitive 360° unidirectional rotation in two generations of molecular motor systems. Received: 21 January 2002 / Accepted: 11 February 2002 / Published online: 22 April 2002     

Controlling transport in mixtures of interacting particles using Brownian motors

An outstanding open problem in nanoscience is how to control the motion of tiny particles. Ratchetlike devices, inspired by biological motors, have been proposed as a way to achieve this goal. However, the net directed transport is almost suppressed if the diffusing particles are weakly coupled to the underlying spatially asymmetric substrate. Here we show how adding particles of an auxiliary species, that interact with both the primary particles of interest and the substrate, provides a controlled enhancement of the flow for both species. These can move either together or in opposite directions, depending upon the strength of the interaction, and whether it is attractive or repulsive.     

Deformation in cooperative molecular motors

We implement a model to represent the effect of the deformation of the backbone of a system of motor proteins while sliding on a track filament. This model incorporates a nearest neighbor interaction term among the motors for the deformation energy. Correlations induced by this term result in increased motor force for inter-particle distances small compared to the ratchet period. Received 20 February 2001 and Received in final form 31 May 2001     

Collective dynamics at RHIC

We discuss the strong collective flow effects, 〈v ₂〉 and 〈β _t 〉, observed at RHIC (√ ^s NN=130 GeV). We argue that part of the collectivity could have already developed at partonic stage. To ‘see’ the partonic effects directly, measurements of multi-strange baryons like Ξ, Ω and charmed particles like J/ψ transverse momentum distributions are important. They provide one of the possible keys to the discovery of collective modes with the partonic (quarks and gluons) degrees of freedom.     

Collective behaviour of a two-dimensional array of interacting lines

A statistical two-dimensional interacting line model is defined in terms of three parameters describing the line stiffness, the line-line interaction and an external restoring force. It describes the collective properties of various physical systems like reconstructing surfaces, disordering stepped surfaces and adsorbed interacting polymers. The statistical properties are calculated by a Monte-Carlo method. The resulting phase diagram is presented for various parameters and an Ising critical behaviour at the phase boundaries is established. For the case of competing interactions a disorder line is found.     

Collective dynamics of multicellular systems

We have studied the collective behaviour of a one-dimensional ring of cells for conditions when the individual uncoupled cells show stable, bistable and oscillatory dynamics. We show that the global dynamics of this model multicellular system depends on the system size, coupling strength and the intrinsic dynamics of the cells. The intrinsic variability in dynamics of the constituent cells are suppressed to stable dynamics, or modified to intermittency under different conditions. This simple model study reveals that cell–cell communication, system size and intrinsic cellular dynamics can lead to evolution of collective dynamics in structured multicellular biological systems that is significantly different from its constituent single-cell behaviour.