We have experimentally realized unidirectional or one-way coupling in a mechanical array by powering the coupling with flowing water. In cyclic arrays with an even number of elements, solitonlike waves spontaneously form but eventually annihilate in pairs, leaving a spatially alternating static attractor. In cyclic arrays with an odd number of elements, this alternating attractor is topologically impossible, and a single soliton always remains to propagate indefinitely. Our experiments with 14- and 15-element arrays highlight the dynamical importance of both noise and disorder and are further elucidated by our computer simulations.

We report on the realization of a rewritable and local source inside a Si-based photonic crystal microcavity by infiltrating a solution of colloidal PbS quantum dots inside a single pore of the structure. We show that the resulting spontaneous emission from the source is both spatially and spectrally redistributed due to the mode structure of the photonic crystal cavity. The coupling of the quantum dot emission to the cavity mode is analyzed by mapping the luminescence signal of the infiltrated solution with a scanning near-field optical microscope at room temperature. Spectral characterization and the mode profile are in good agreement with a three-dimensional numerical calculation of the system.

Virus capsids are highly specific assemblies that are formed from a large number of often chemically identical capsid subunits. In the present paper we ask to what extent these structures can be viewed as mathematically tilable objects using a single two-dimensional tile. We find that spherical viruses from a large number of families—eight out of the twelve studied—qualitatively possess properties that allow their representation as two-dimensional monohedral tilings of a bound surface, where each tile represents a subunit. This we did by characterizing the extent to which individual spherical capsids display subunit-subunit (1) holes, (2) overlaps, and (3) gross structural variability. All capsids with $T$ numbers greater than 1 from the Protein Data Bank, with homogeneous protein composition, were used in the study. These monohedral tilings, called canonical capsids due to their platonic (mathematical) form, offer a mathematical segue into the structural and dynamical understanding of not one, but a large number of virus capsids. From our data, it appears as though one may only break the long-standing rules of quasiequivalence by the introduction of subunit-subunit structural variability, holes, and gross overlaps into the shell. To explore the utility of canonical capsids in understanding structural aspects of such assemblies, we used graph theory and discrete geometry to enumerate the types of shapes that the tiles (and hence the subunits) must possess. We show that topology restricts the shape of the face to a limited number of five-sided prototiles, one of which is the “bisected trapezoid” that is a platonic representation of the most ubiquitous capsid subunit shape seen in nature (the trapezoidal jelly-roll motif). This motif is found in a majority of seemingly unrelated virus families that share little to no host, size, or amino acid sequence similarity. This suggests that topological constraints may exhibit dominant roles in the natural design of biological assemblies, while having little effect on amino acid sequence similarity.

We develop two simplified dynamical models with which to explore the conditions under which temporal differentiation leads to increased system output. By temporal differentiation, we mean a division of labor whereby different subtasks associated with performing a given task are done at different times. The idea is that, by focusing on one particular set of subtasks at a time, it is possible to increase the efficiency with which each subtask is performed, thereby allowing for faster completion of the overall task. In the first model, we consider the filling and emptying of a tank in the presence of a time-varying resource profile. If a given resource is available, the tank may be filled at some rate $r_f$. As long as the tank contains a resource, it may be emptied at a rate $r_e$, corresponding to processing into some product, which is either the final product of a process or an intermediate that is transported for further processing. Given a resource-availability profile over some time interval $T$, we develop an algorithm for determining the fill-empty profile that produces the maximum quantity of processed resource at the end of the time interval. We rigorously prove that the basic algorithm is one where the tank is filled when a resource is available and emptied when a resource is not available. In the second model, we consider a process whereby some resource is converted into some final product in a series of three agent-mediated steps. Temporal differentiation is incorporated by allowing the agents to oscillate between performing the first two steps and performing the last step. We find that temporal differentiation is favored when the number of agents is at intermediate values and when there are process intermediates that have long lifetimes compared to other characteristic time scales in the system. Based on these results, we speculate that temporal differentiation may provide an evolutionary basis for the emergence of phenomena such as sleep, distinct REM and non-REM sleep states, and circadian rhythms in general. The essential argument is that in sufficiently complex biological systems, a maximal amount of information and tasks can be processed and completed if the system follows a temporally differentiated “work plan,” whereby the system focuses on one or a few tasks at a time.

By considering the structure of holococcoliths (calcite plates that cover holococcolithophores, a haploid phase of the coccolithophore life cycle) as a photonic structure, we apply a discrete dipolar approximation to study the light backscattering properties of these algae. We show that some holococcolith structures have the ability to scatter the ultraviolet radiation. This property may represent an advantage for holococcolithophores possessing it, by allowing them to live higher in the water column than other coccolithophores.

We propose a very simple one-dimensional swimmer consisting of three spheres that are linked by rigid rods whose lengths can change between two values. With a periodic motion in a nonreciprocal fashion, which breaks the time-reversal symmetry as well as the translational symmetry, we show that the model device can swim at low Reynolds number. This model system could be used in constructing molecular-sized machines.

Phase objects can become visible by slightly defocusing an optical microscope, a technique seldom used as a useful tool. We revisited the theory of defocusing and apply it to our optical microscope with optics corrected at infinity. In our approximation, we obtain that the image contrast is proportional to the two-dimensional (2D) Laplacian of the phase difference introduced by the phase object. If the index of refraction of the phase object is uniform the image obtained from defocusing microscopy is the image of curvature (Laplacian of the local thickness) of the phase object, while standard phase-contrast microscopy gives information about the thickness of the object. We made artificial phase objects and measured image contrasts with defocusing microscopy. Measured contrasts are in excellent agreement with our theoretical model. We use defocusing microscopy to study curvature fluctuations (ruffles) on the surface of macrophages (cell of the innate immune system), and try to correlate mechanical properties of macrophage surface and phagocytosis. We observe large coherent propagating structures: Their shape, speed, density are measured and curvature energy estimated. Inhomogeneities of cytoskeleton refractive index, curvature modulations due to thermal fluctuations and/or periodic changes in cytoskeleton-membrane interactions cause random fluctuations in image contrast. From the temporal and spatial contrast correlation functions, we obtain the decay time and correlation length of such fluctuations that are related to their size and the viscoelastic properties of the cytoskeleton. In order to associate the dynamics of cytoskeleton with the process of phagocytosis, we use an optical tweezers to grab a zymosan particle and put it into contact with the macrophage. We then measure the time for a single phagocytosis event. We add the drug cytochalasin D that depolymerizes the cytoskeleton F-actin network: It inhibits the large propagating coherent fluctuations on the cell surface, increases the relaxation time of cytoskeleton fluctuations, and increases the phagocytosis time. Our results suggest that the methods developed in this work can be of utility to assess the importance of cytoskeleton motility in the dynamics of cellular processes such as phagocytosis exhibited by macrophages.

The Ikeda, Parker, and Sawai river meandering model is reexamined using a physical approach employing an explicit equation of motion. For periodic river shapes as seen from above, a cross-stream surface elevation gradient creates a velocity shear that is responsible for the decay of small-wavelength meander bends, whereas secondary currents in the plane perpendicular to the downstream direction are responsible for the growth of large-wavelength bends. A decay length ${D=H/2C}_f$ involving the river depth H and the friction coefficient $C_f$ sets the scale for meandering, giving the downstream distance required for the fluid velocity profile to recover from changes in the channel curvature. Using this length scale and a time scale T, we explicitly trace the observed length scale invariance to the equations of motion, and predict similar time and velocity scale invariances. A general time-dependent nonlinear modal analysis for periodic rivers reveals that modes higher than the third mode are needed to describe upstream migration of bend apexes just before oxbow cutoff, and are important to accurate calculations of the time and sinuosity at cutoff.

In living cells, cytoskeletal filaments interact with the plasma membrane to form structures that play a key role in cell shape and mechanical properties. To study the interaction between these basic components, we designed an in vitro self-assembled network of actin filaments attached to the outer surface of giant unilamellar vesicles. Optical tweezers and single-particle tracking experiments are used to study the rich dynamics of these actin-coated membranes (ACM). We show that microrheology studies can be carried out on such an individual microscopic object. The principle of the experiment consists in measuring the thermally excited position fluctuations of a probe bead attached biochemically to the membrane. We propose a model that relates the power spectrum of these thermal fluctuations to the viscoelastic properties of the membrane. The presence of the actin network modifies strongly the membrane dynamics with respect to a fluid, lipid bilayer one. It induces first a finite (ω=0) two-dimensional (2D) shear modulus $G_{2\mathrm{D}}^0\sim 0.5$ to 5 μN/m in the membrane plane. Moreover, the frequency dependence at high frequency of the shear modulus $\left[G_{2\mathrm{D}}^{\prime }\right(f\left)\sim f^{0.85\pm 0.07}\right]$ and of the bending modulus $\left({\kappa }_{\mathrm{ACM}}\mathrm{}\right(f\left)\mathrm{}\sim f^{0.55\pm 0.21}\right)$ demonstrate the viscoelastic behavior of the composite membrane. These results are consistent with a common exponent of 0.75 for both moduli as expected from our model and from prior measurements on actin solutions.

We report on a series of measurements aimed to characterize the development and the dynamics of the rhythmic applause in concert halls. Our results demonstrate that while this process shares many characteristics of other systems that are known to synchronize, it also has features that are unexpected and unaccounted for in many other systems. In particular, we find that the mechanism lying at the heart of the synchronization process is the period doubling of the clapping rhythm. The characteristic interplay between synchronized and unsynchronized regimes during the applause is the result of a frustration in the system. All results are understandable in the framework of the Kuramoto model.

Application of time correlated single photon counting to pulsed Mie scattering enables one to resolve changes in light scattering to better than 50 ps. This technique is applied to the highly nonlinear motion of a sonoluminescing bubble. Physical processes, such as outgoing shock wave emission, that limit the interpretation of the data are measured with a streak camera and microscopy. Shock speeds about 6 km/s have been observed.

We present a model for the dynamics of a cerebral cortex in which inputs to neuronal assemblies are treated as random Gaussian fluctuations about a mean value. We incorporate the effect of general anesthetic agents on the cortex as a modulation of the inhibitory neurotransmitter rate constant. Stochastic differential equations are derived for the state variable $h_e,$ the average excitatory soma potential, coherent fluctuations of which are believed to be the source of scalp-measured electroencephalogram (EEG) signals. Using this stochastic approach we derive a stationary (long-time limit) fluctuation spectrum for $h_e.$ The model predicts that there will be three distinct stationary (equilibrium) regimes for cortical activity. In region I (“coma”), corresponding to a strong inhibitory anesthetic effect, $h_e$ is single valued, large, and negative, so that neuronal firing rates are suppressed. In region II for a zero or small anesthetic effect, $h_e$ can take on three values, two of which are stable; we label the stable solutions as “active” (enhanced firing) and “quiescent” (suppressed firing). For region III, corresponding to negative anesthetic (i.e., analeptic) effect, $h_e$ again becomes single valued, but is now small and negative, resulting in strongly elevated firing rates (“seizure”). If we identify region II as associated with the conscious state of the cortex, then the model predicts that there will be a rapid transit between the active-conscious and comatose unconscious states at a critical value of anesthetic concentration, suggesting the existence of phase transitions in the cortex. The low-frequency spectral power in the $h_e$ signal should increase strongly during the initial stage of anesthesia induction, before collapsing to much lower values after the transition into comatose-unconsciousness. These qualitative predictions are consistent with clinical measurements by Bührer et al. [Anaesthesiology 77, 226 (1992)], MacIver et al. [ibid. 84, 1411 (1996)], and Kuizenga et al. [Br. J. Anaesthesia 80, 725 (1998)]. This strong increase in EEG spectral power in the vicinity of the critical point is similar to the divergences observed during thermodynamic phase transitions. We show that the divergence in low-frequency power in our model is a natural consequence of the existence of turning points in the trajectory of stationary states for the cortex.