Can self-propelled objects escape from compression stimulation?

We studied circular papers impregnated with camphor (CPs) and CPs with magnets (MCPs) as self-propelled objects floating on water under the compression of the water surface as an inanimate system for evacuation in an emergency. Two water chambers-Cin and Cout-were connected via a plastic gate, and eight CPs or eight MCPs were placed on Cin. We monitored the movement of the CPs or MCPs from Cin to Cout when the gate was opened and the area of Cin (Ain) was decreased using a barrier. When Ain was large, CPs moved stochastically from Cin to Cout while exhibiting random motion. The escape probability from Cin to Cout (P) at time t = 20 s increased with a decrease in Ain, and the rate of increase in P increased depending on the width of the gate (Wg). By contrast, clustering was observed for MCPs. Consequently, P of MCPs was lower than that of CPs. The difference in the surface tension between Cin and Cout (Δγ) increased with a decrease in Ain. P is discussed in relation to Δγ as the driving force for emergencies and the repulsive forces between CPs or attractive forces between MCPs. These results suggest that the repulsive force enhances the self-propulsion of objects towards the gate, that is, as a result, higher values of P are obtained.

Inversion probability of three-bladed self-propelled rotors after forced stops of different durations.

We investigated self-propelled rotation of a symmetric three-bladed rotor on water under periodic halt and release operations. The rotation was driven by the difference in the surface tension around the blades of the rotor because camphor molecules developed from three camphor disks glued at the blade ends. Spontaneous inversion of rotation direction was observed after a forced stop of the rotor and the subsequent release. The probability of such inversion decreased with an increase in the halting time. The asymmetric distribution of camphor molecules around the blades was also inverted after the forced stop and the degree of asymmetry increased with an increase in the angular velocity characterizing the stationary rotation of the rotor. Our experimental results for rotors with different shapes indicate that there is a strong correlation between the stationary angular velocity of the rotor and the maximum time duration of the forced stop for which a high probability of inversion is observed.

Diverse stochasticity leads a colony of ants to optimal foraging.

A mathematical model of garden ants (Lasius japonicus) is introduced herein to investigate the relationship between the distribution of the degree of stochasticity in following pheromone trails and the group foraging efficiency. Numerical simulations of the model indicate that depending on the systematic change of the feeding environment, the optimal distribution of stochasticity shifts from a mixture of almost deterministic and mildly stochastic ants to a contrasted mixture of almost deterministic ants and highly stochastic ants. In addition, the interaction between the stochasticity and the pheromone path regulates the dynamics of the foraging efficiency optimization. Stochasticity could strengthen the collective efficiency when the variance in the sensitivity to pheromone for ants is introduced in the model.

Synchronization of self-propelled soft pendulums.

We investigated self-propelled motions of thin filaments atop water, where we focused on understanding pendulum-type oscillations and synchronization. The filaments were produced from a commercial adhesive (consisting mainly of nitrocellulose and acetone), and exhibited deformable motions. One end of each filament was held on the edge of a quadrangular water chamber while the other was left free. Acetone and other organic molecules from the nitrocellulose filament develop on the water surface and decrease the surface tension. The difference in the surface tension around the filament becomes the driving force of the self-propelled motions. When a single filament was placed in the water chamber, a pendulum-type oscillation in the deformation of the filament was observed. When two filaments were placed in parallel in the chamber, in-phase, out-of-phase, and no-synchronization motions were observed. It was found that the class of motions depends on the distance between the two fixed points of the filaments. Mathematical modeling and numerical simulations were also used in order to further understand the dynamics of the surface active molecules and the filament motions. We propose a mathematical model equation and reproduce various behaviors exhibited by soft self-propelled matters through numerical simulation.

Characteristics of daily foraging activity of Camponotus japonicus via time series analysis.

Social insects often share tasks among individuals. In this study, we analyzed the foraging activity of ants (Camponotus japonicus) and recorded the daily passage event counts of individual workers between a nest chamber and a foraging arena in five monodomous colonies. We proposed two hypotheses on the time series of foraging frequency by individual worker ants as follows: (i) for the time series of foraging frequency by individual worker ants, the foraging frequency on a certain day could be expressed by the product of the foraging frequency on the previous day and the exponential of a random number. (ii) The random numbers are correlated between some pairs of worker ants. The results for the five tested ant colonies showed that the probability of total daily passage counts (the sum of an individual's passage count) followed a log-normal distribution. The worker ants behaved differently in terms of active days and foraging frequency. However, for > 54% of the worker ants, the probability of the daily passage count was characterized by a log-normal distribution, and these worker ants performed > 72% of the tasks in each colony. Furthermore, for > 73% of the worker ants, the time development of the passage count was mathematically modeled; the logarithmic first difference between the passage counts on a certain day and those on the previous day was a random normal variable. These results support hypothesis (i). Additionally, the random numbers that were equivalent to the logarithmic first difference were correlated for some pairs of worker ants. These results support hypothesis (ii).

Bifurcation analysis of the transition of dune shapes under a unidirectional wind.

A bifurcation analysis of dune shape transition is made. By use of a reduced model of dune morphodynamics, the Dune Skeleton model, we elucidate the transition mechanism between different shapes of dunes under unidirectional wind. It was found that the decrease in the total amount of sand in the system and/or the lateral sand flow shifts the stable state from a straight transverse dune to a wavy transverse dune through a pitchfork bifurcation. A further decrease causes wavy transverse dunes to shift into barchans through a Hopf bifurcation. These bifurcation structures reveal the transition mechanism of dune shapes under unidirectional wind.

Stabilization of a straight longitudinal dune under bimodal wind with large directional variation.

It has been observed that the direction in which a sand dune extends its crest line depends on seasonal variation of wind direction; when the variation is small, the crest line develops more or less perpendicularly to the mean wind direction to form a transverse dune with some undulation. In the case of bimodal wind with a large relative angle, however, the dune extends its crest along the mean wind direction and evolves into an almost straight longitudinal dune. Motivated by these observations, we investigate the dynamical stability of isolated dunes using the crest line model, where the dune dynamics is represented by its crest line motion. First, we extend the previous linear stability analysis under the unidirectional wind to the case with nonzero slant angle between the wind direction and the normal direction of the crest line, and show that the stability diagram does not depend on the slant angle. Second, we examine how the linear stability is affected by the seasonal changes of wind direction in the case of bimodal wind with equal strength and duration. For the transverse dune, we find that the stability is virtually the same with that for the unidirectional wind as long as the dune evolution during a season is small. On the other hand, in the case of the longitudinal dune, the dispersions of the growth rates for the perturbation are drastically different from those of the unidirectional wind, and we find that the largest growth rate is always located at k=0. This is because the growth of the perturbation with k≠0 is canceled by the alternating wind from opposite sides of the crest line even though it grows during each duration period of the bimodal wind. For a realistic parameter set, the system is in the wavy unstable regime of the stability diagram for the unidirectional wind, thus the straight transverse dune is unstable to develop undulation and eventually evolves into a string of barchans when the seasonal variation of wind direction is small, but the straight longitudinal dune is stabilized under the large variation of bimodal wind direction. We also perform numerical simulations on the crest line model, and find that the results are consistent with our linear analysis and the previous reports that show that the longitudinal dunes tend to have a straight ridge elongating over time.

Verification of mathematical models of response threshold through statistical characterisation of the foraging activity in ant societies.

The concept of response threshold (RT) has been developed to explain task allocation in social insect colonies, wherein individual workers engage in tasks depending on their responsiveness to the task-related stimulus. Moreover, a mathematical model of RT has been proposed to explain data obtained from task allocation experiments; however, its applicability range warrants clarification through adequate quantitative analysis. Hence, we used an automatic measuring system to count passage events between a nest chamber and a foraging arena in five colonies of ants, Camponotus japonicus. The events were measured using radio-frequency identification tags attached to all workers of each colony. Here, we examined the detailed forms of i) labour distribution during foraging among workers in each colony and ii) the persistence of rank-order of foraging among workers. We found that labour distribution was characterized by a generalized gamma-distribution, indicating that only few workers carried out a large part of the workload. The rank-order of foraging activity among workers in each colony was maintained for a month and collapsed within a few months. We compared the obtained data with testable predictions of the RT model. The comparison indicated that proper evaluation of the mathematical model is required based on the obtained data.

Splash detail due to a single grain incident on a granular bed.

Using the discrete element method, we study the splash processes induced by the impact of a grain on a randomly packed bed. Good correspondence is obtained between our numerical results and the findings of previous experiments for the movement of ejected grains. Furthermore, the distributions of the ejection angle and ejection speed for individual grains vary depending on the relative timing at which the grains are ejected after the initial impact. Obvious differences are observed between the distributions of grains ejected during the earlier and later splash periods: the form of the vertical ejection-speed distribution varies from a power-law form to a lognormal form with time; this difference may determine grain trajectory after ejection.

The 1-Particle-per-k-Nucleotides (1PkN) Elastic Network Model of DNA Dynamics with Sequence-Dependent Geometry.

Coarse-grained models of DNA have made important contributions to the determination of the physical properties of genomic DNA, working as a molecular machine for gene regulation. In this study, to analyze the global dynamics of long DNA sequences with consideration of sequence-dependent geometry, we propose elastic network models of DNA where each particle represents k nucleotides (1-particle-per-k-nucleotides, 1PkN). The models were adjusted according to profiles of the anisotropic fluctuations obtained from our previous 1-particle-per-1-nucleotide (1P1N) model, which was proven to reproduce such profiles of all-atom models. We confirmed that the 1P3N and 1P4N models are suitable for the analysis of detailed dynamics such as local twisting motion. The models are intended for the analysis of large structures, e.g., 10-nm fibers in the nucleus, and nucleoids of mitochondrial or phage DNA at low computational costs. As an example, we surveyed the physical characteristics of the whole mitochondrial human and Plasmodium falciparum genomes.

The Flux of Euglena gracilis Cells Depends on the Gradient of Light Intensity.

We have quantified the photomovement behavior of a suspension of Euglena gracilis representing a behavioral response to a light gradient. Despite recent measurements of phototaxis and photophobicity, the details of macroscopic behavior of cell photomovements under conditions of light intensity gradients, which are critical to understand recent experiments on spatially localized bioconvection patterns, have not been fully understood. In this paper, the flux of cell number density under a light intensity gradient was measured by the following two experiments. In the first experiment, a capillary containing the cell suspension was illuminated with different light intensities in two regions. In the steady state, the differences of the cell numbers in the two regions normalized by the total number were proportional to the light difference, where the light intensity difference ranged from 0.5-2.0 µmol m-2 s-1. The proportional coefficient was positive (i.e., the bright region contained many microorganisms) when the mean light intensity was weak (1.25 µmol m-2 s-1), whereas it was negative when the mean intensity was strong (13.75 µmol m-2 s-1). In the second experiment, a shallow rectangular container of the suspension was illuminated with stepwise light intensities. The cell number density distribution exhibited a single peak at the position where the light intensity was about Ic ≃ 3.8 µmol m-2 s-1. These results suggest that the suspension of E. gracilis responded to the light gradient and that the favorable light intensity was Ic.

Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence.

Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of temperature factors for several crystal structures of DNA. Second, we propose a coarse-grained elastic network model of DNA, where each nucleotide is described only by one node. This model could effectively reproduce the detailed dynamics obtained with the all-atom elastic network model according to the sequence-dependent geometry. Through normal-mode analysis for the coarse-grained elastic network model, we exhaustively analyzed the dynamic features of a large number of long DNA sequences, approximately ∼150 bp in length. These analyses revealed positive correlations between the nucleosome-forming abilities and the inter-strand fluctuation strength of double-stranded DNA for several DNA sequences.

Bifurcation phenomena of two self-propelled camphor disks on an annular field depending on system length.

Mode selection and bifurcation of a synchronized motion involving two symmetric self-propelled objects in a periodic one-dimensional domain were investigated numerically and experimentally by using camphor disks placed on an annular water channel. Newton's equation of motion for each camphor disk, whose driving force was the difference in surface tension, and a reaction-diffusion equation for camphor molecules on water were used in the numerical calculations. Among various dynamical behaviors found numerically, four kinds of synchronized motions (reversal oscillation, stop-and-move rotation, equally spaced rotation, and clustered rotation) were also observed in experiments by changing the diameter of the water channel. The mode bifurcation of these motions, including their coexistence, were clarified numerically and analytically in terms of the number density of the disk. These results suggest that the present mathematical model and the analysis of the equations can be worthwhile in understanding the characteristic features of motion, e.g., synchronization, collective motion, and their mode bifurcation.

Influences of excluded volume of molecules on signaling processes on the biomembrane.

We investigate the influences of the excluded volume of molecules on biochemical reaction processes on 2-dimensional surfaces using a model of signal transduction processes on biomembranes. We perform simulations of the 2-dimensional cell-based model, which describes the reactions and diffusion of the receptors, signaling proteins, target proteins, and crowders on the cell membrane. The signaling proteins are activated by receptors, and these activated signaling proteins activate target proteins that bind autonomously from the cytoplasm to the membrane, and unbind from the membrane if activated. If the target proteins bind frequently, the volume fraction of molecules on the membrane becomes so large that the excluded volume of the molecules for the reaction and diffusion dynamics cannot be negligible. We find that such excluded volume effects of the molecules induce non-trivial variations of the signal flow, defined as the activation frequency of target proteins, as follows. With an increase in the binding rate of target proteins, the signal flow varies by i) monotonically increasing; ii) increasing then decreasing in a bell-shaped curve; or iii) increasing, decreasing, then increasing in an S-shaped curve. We further demonstrate that the excluded volume of molecules influences the hierarchical molecular distributions throughout the reaction processes. In particular, when the system exhibits a large signal flow, the signaling proteins tend to surround the receptors to form receptor-signaling protein clusters, and the target proteins tend to become distributed around such clusters. To explain these phenomena, we analyze the stochastic model of the local motions of molecules around the receptor.

Collective motion of symmetric camphor papers in an annular water channel.

We investigate the collective motion of symmetric self-propelled objects that are driven by a difference in the surface tension. The objects move around an annular water channel spontaneously and interact through the camphor layer that develops on the water surface. We found that two collective motion modes, discrete and continuous density waves, are generated depending on the number of self-propelled objects. The two modes are characterized by examining the local and global dynamics, and the collective motion mechanism is discussed in relation to the distribution of camphor concentration in the annular water channel. We conclude that the difference between these two modes originates from that of the driving mechanism that pushes a camphor paper away from a cluster, through which mechanism density waves are generated and maintained.

Segregation-pattern reorientation of a granular mixture on a horizontally oscillating tray.

Reorientation of the segregation pattern of a binary granular mixture on a two-dimensional horizontally oscillating tray is numerically realized. The mixture consists of large and heavy particles and small and light particles, and the segregation pattern shows a transition between a striped pattern perpendicular to the oscillation and one parallel to the oscillating direction according to the change of area fractions of the two types of particle. The transition mechanism is discussed on the basis of a simplified one-dimensional dynamics.

Swarming of self-propelled camphor boats.

When an ensemble of self-propelled camphor boats move in a one-dimensional channel, they exhibit a variety of collective behaviors. Under certain conditions, the boats tend to cluster together and move in a relatively tight formation. This type of behavior, referred to as clustering or swarming here, is one of three types recently observed in experiment. Similar clustering behavior is also reproduced in simulations based on a simple theoretical model. Here we examine this model to determine the clustering mechanism and the conditions under which clustering occurs. We also propose a method of quantifying the behavior that may be used in future experimental work.

Effective stochastic resonance of coupled excitable elements under noise of unequal amplitude.

Effective stochastic resonance (SR) is numerically studied using a model of two coupled excitable FitzHugh-Nagumo elements exposed to noise of unequal amplitude. Compared to previous SR models of a single excitable element and of two coupled excitable elements exposed to noise of equal amplitude, the present model exhibits a more intense resonance to the external signal. To extract the key dynamics of this effective SR, the idea of triggered excitation is introduced. Triggered excitation means a process in which the noise-free element is excited synchronously to the external signal with the triggering action of another element that randomly fluctuates asynchronously to the external signal. A deterministic simulation simply proving the triggered excitation process supports our idea.

Saddle-node bifurcation to jammed state for quasi-one-dimensional counter-chemotactic flow.

The transition of a counter-chemotactic particle flow from a free-flow state to a jammed state in a quasi-one-dimensional path is investigated. One of the characteristic features of such a flow is that the constituent particles spontaneously form a cluster that blocks the path, called a path-blocking cluster (PBC), and causes a jammed state when the particle density is greater than a threshold value. Near the threshold value, the PBC occasionally collapses on itself to recover the free flow. In other words, the time evolution of the size of the PBC governs the flux of a counter-chemotactic flow. In this Rapid Communication, on the basis of numerical results of a stochastic cellular automata (SCA) model, we introduce a Langevin equation model for the size evolution of the PBC that reproduces the qualitative characteristics of the SCA model. The results suggest that the emergence of the jammed state in a quasi-one-dimensional counterflow is caused by a saddle-node bifurcation.

Collective behavior of inanimate boats.

We propose an inanimate system composed of camphor boats in an annular water channel in order to understand the collective motions. The boats move on the water surface spontaneously and interact with one another through the concentration of the camphor molecules on the water. We observed several modes of collective motion, e.g., behaviors analogous to traffic flow or an ant trail. Our system provides a convenient experimental setup for the investigation of a variety of collective motions.