To investigate the effect of quantum coherence on electronic energy transfer, which is the subject of current interest in photosynthesis, we solve the problem of transport for the simplest model of an aggregate of monomers interacting through dipole-dipole forces using both quantum and classical dynamics. We conclude that for realistic coupling strengths quantum and classical coherent transport are identical. This is demonstrated by numerical calculations for a linear chain and for the photosynthetic Fenna-Matthews-Olson complex.

Inspired by recent laboratory observations, we propose a mechanical model for eccentrically weighted motors coupled through a vibrating plate. The equations are found to generalize those of Kuramoto to frequency- and position-dependent coupling. The behavior of the model, as determined analytically for no disorder and numerically for systems with and without quenched disorder, shows the key features observed in the laboratory, including hysteresis, bistability, and a spectral gap. The model exhibits stimulated emission and discontinuous lasinglike transitions.

We consider control of reaction and population systems by imposing transitions between states with different numbers of particles or individuals. The transitions take place at predetermined instants of time. Even where they are significantly less frequent than spontaneous transitions, they can exponentially strongly modify the rates of rare events, including switching between metastable states or population extinction. We also study optimal control of rare events. Specifically, we are interested in the optimal control of disease extinction for a limited vaccine supply. A comparison is made with control of rare events by modulating the rates of elementary transitions rather than imposing transitions deterministically. It is found that, unexpectedly, for the same mean control parameters, controlling the transitions rates can be more efficient.

Human DNA shows a complex structure with compositional features at many scales; the isochores—long DNA segments ($~{10}^5$ bp) of relatively homogeneous guanine-cytosine (G + C) content—are the largest well-documented and well-analyzed compositional structures. However, we report here on the existence of a high-level compositional organization of isochores in the human genome. By using a segmentation algorithm incorporating the long-range correlations existing in human DNA, we find that every chromosome is composed of a few huge segments ($~$ ${10}^7$ bp) of relatively homogeneous G + C content, which become the largest compositional organization of the genome. Finally, we show evidence of the biological relevance of these superstructures, pointing to a large-scale functional organization of the human genome.

We report experiments on soap film configurations in a triangular prism for which the shape factor can be changed continuously. Two stable configurations can be observed for a range of the shape factor $h$, being the prism-height/edge-length ratio. A hysteretic behavior is found, due to the occurence of another local minima in the free energy. Contrary to a common belief, soap films can be trapped in a particular configuration being different from a global surface minimization. This metastability can be evidenced from a geometrical model based on idealized structures. Depending on the configuration, the transition is either first or second order, providing clues on the structural relaxations taking place into three-dimensional foams, such as T1 rearrangements.

Many motile eukaryotic cells determine their direction by measuring external chemical gradients through the binding of ligands to membrane bound receptors. This process is limited by fluctuations arising from the binding process and from the diffusion of the ligand molecules. Here, we apply estimation-theoretic methods to determine the physical limits of gradient sensing for cells that are noncircular and for cells that have an internal bias. Specifically, we derive theoretical expressions for the accuracy of gradient sensing in elliptical cells. This accuracy for highly elliptical cells can significantly deviate from the gradient sensing limits derived for circular cells. Furthermore, we find that a cell cannot improve its sensing of the gradient steepness and direction simultaneously by elongating its cell body. Finally, we derive a lower bound on the accuracy of gradient sensing for cells that possess an internal bias and compare our analytical results with recent experimental findings.

Icicles form when cool water drips from an overhanging support under ambient conditions which are below freezing. Ice growth is controlled by the removal of latent heat, which is transferred into the surrounding air via a thin film of water flowing over the ice surface. We describe laboratory experiments in which icicles were grown under controlled conditions. We used image analysis to probe the evolution of the icicle shape under various conditions. A recent asymptotic theory suggests that, overall, icicles converge to self-similar shapes which are predicted to be attractors. On the other hand, stability theory predicts that the ice-water interface can become unstable to form ripple patterns on the icicle surface. Our experimental results show that the predicted self-similar profile is only found in certain cases, and that icicles can also exhibit unpredicted nonuniformities such as branching near the tip. We find that pure water icicles are more likely to be self-similar than those grown from tap water. Ripples, which are also deviations from the self-similar profile, were observed to climb upward during icicle growth.

Depinning of two-dimensional liquid ridges and three-dimensional drops on an inclined substrate is studied within the lubrication approximation. The structures are pinned to wetting heterogeneities arising from variations of the strength of the short-range contribution to the disjoining pressure. The case of a periodic array of hydrophobic stripes transverse to the slope is studied in detail using a combination of direct numerical simulation and branch-following techniques. Under appropriate conditions the ridges may either depin and slide downslope as the slope is increased, or first break up into drops via a transverse instability, prior to depinning. The different transition scenarios are examined together with the stability properties of the different possible states of the system.

A localized source of buoyancy flux in a nonreactive fluid medium creates a plume. The flux can be provided by either heat, a compositional difference between the fluid comprising the plume and its surroundings, or a combination of both. For autocatalytic plumes produced by the iodate-arsenous acid reaction, however, buoyancy is produced along the entire reacting interface between the plume and its surroundings. Buoyancy production at the moving interface drives fluid motion, which in turn generates flow that advects the reaction front. As a consequence of this interplay between fluid flow and chemical reaction, autocatalytic plumes exhibit a rich dynamics during their ascent through the reactant medium. One of the more interesting dynamical features is the production of an accelerating vortical plume head that in certain cases pinches-off and detaches from the upwelling conduit. After pinch-off, a new plume head forms in the conduit below, and this can lead to multiple generations of plume heads for a single plume initiation. We investigated the pinch-off process using both experimentation and simulation. Experiments were performed using various concentrations of glycerol, in which it was found that repeated pinch-off occurs exclusively in a specific concentration range. Autocatalytic plume simulations revealed that pinch-off is triggered by the appearance of accelerating flow in the plume conduit.

In living organisms, branching structures are often observed in open systems. During the process of structure formation/deformation, signal propagation can be observed. Branching paths often deform depending on the history of signal propagation. To gain a better understanding of the process of pattern formation that results in characteristic geometrical paths, we adopt a system in which the dynamics of path formation are correlated with signal propagation. This model involves both branch-generation dynamics and signal-propagation dynamics, and we introduced positive feedback between these two dynamic processes. We studied the geometrical properties of path deformation and the pattern of signal propagation using a discretized reaction-diffusion model. The proposed model can qualitatively reproduce different branching patterns and means of signal propagation. One remarkable result is that the mutual interaction of these two dynamic processes leads to autonomous wave generation, similar to a pacemaker or the generation of spiral waves. Because the autonomous wave generation in the signal is spontaneous, the shapes of the branching paths become distorted. We discuss the correlation between path deformation and signal propagation as a first step in understanding signal processing for such complex deformable paths.

Drying experiments have been carried out with model soils made of different pastes filling granular packings. A detailed information concerning the time evolution of the water saturation distribution inside the sample was obtained from magnetic resonance imaging measurements. This study makes it possible to understand the physical origin of the drying characteristics of these materials. The drying curves exhibit a constant-rate period (CRP) and a falling-rate period (FRP) but the relative durations of these periods depend on the paste structure. With a kaolin suspension the CRP lasts down to very low water densities and is associated with a homogeneous drying of the paste throughout the sample. With a bentonite suspension the CRP is shorter and the drying in the FRP results from a complex process involving fractures progressing downward through the pasty matrix. With a gel the CRP period is even shorter and the drying in the FRP results from the progression of a dry front through the packing as a result of the shrinkage of the gel matrix. This provides an overview of the main possible processes at work when drying a soil as a function of its components along with some practical means for slowing down drying from soils.

The butterfly Pierella luna (Nymphalidae) shows an intriguing rainbow iridescence effect: the forewings of the male, when illuminated along the axis from the body to the wing tip, decompose a white light beam as a diffraction grating would do. Violet light, however, emerges along a grazing angle, near the wing surface, while the other colors, from blue to red, exit respectively at angles progressively closer to the direction perpendicular to the wing plane. This sequence is the reverse of the usual decomposition of light by a grating with a periodicity parallel to the wing surface. It is shown that this effect is produced by a macroscopic deformation of the entire scale, which curls in such a way that it forms a “vertical” grating, perpendicular to the wing surface, and functions in transmission instead of reflection.

We obtain a Fokker-Planck equation describing experimental data on the collective motion of locusts. The noise is of internal origin and due to the discrete character and finite number of constituents of the swarm. The stationary probability distribution shows a rich phenomenology including nonmonotonic behavior of several order and disorder transition indicators in noise intensity. This complex behavior arises naturally as a result of the randomness in the system. Its counterintuitive character challenges standard interpretations of noise induced transitions and calls for an extension of this theory in order to capture the behavior of certain classes of biologically motivated models. Our results suggest that the collective switches of the group’s direction of motion might be due to a random ergodic effect and, as such, they are inherent to group formation.

Up to now, the effects of having heterogeneous networks of contacts have been studied mostly for diseases which are not persistent in time, i.e., for diseases where the infectious period can be considered very small compared to the lifetime of an individual. Moreover, all these previous results have been obtained for closed populations, where the number of individuals does not change during the whole duration of the epidemics. Here, we go one step further and analyze, both analytically and numerically, a radically different kind of diseases: those that are persistent and can last for an individual’s lifetime. To be more specific, we particularize to the case of tuberculosis’ (TB) infection dynamics, where the infection remains latent for a period of time before showing up and spreading to other individuals. We introduce an epidemiological model for TB-like persistent infections taking into account the heterogeneity inherent to the population structure. This sort of dynamics introduces new analytical and numerical challenges that we are able to sort out. Our results show that also for persistent diseases the epidemic threshold depends on the ratio of the first two moments of the degree distribution so that it goes to zero in a class of scale-free networks when the system approaches the thermodynamic limit.

The generation of arbitrarily shaped nonspherical laser-induced cavitation bubbles is demonstrated with a optical technique. The nonspherical bubbles are formed using laser intensity patterns shaped by a spatial light modulator using linear absorption inside a liquid gap with a thickness of $40\mu \text{m}$. In particular we demonstrate the dynamics of elliptic, toroidal, square, and V-shaped bubbles. The bubble dynamics is recorded with a high-speed camera at framing rates of up to $300000$ frames per second. The observed bubble evolution is compared to predictions from an axisymmetric boundary element simulation which provides good qualitative agreement. Interesting dynamic features that are observed in both the experiment and simulation include the inversion of the major and minor axis for elliptical bubbles, the rotation of the shape for square bubbles, and the formation of a unidirectional jet for V-shaped bubbles. Further we demonstrate that specific bubble shapes can either be formed directly through the intensity distribution of a single laser focus, or indirectly using secondary bubbles that either confine the central bubble or coalesce with the main bubble. The former approach provides the ability to generate in principle any complex bubble geometry.

If a fluctuating medium is confined, the ensuing perturbation of its fluctuation spectrum generates Casimir-like effective forces acting on its confining surfaces. Near a continuous phase transition of such a medium the corresponding order parameter fluctuations occur on all length scales and therefore close to the critical point this effect acquires a universal character, i.e., to a large extent it is independent of the microscopic details of the actual system. Accordingly it can be calculated theoretically by studying suitable representative model systems. We report on the direct measurement of critical Casimir forces by total internal reflection microscopy with femtonewton resolution. The corresponding potentials are determined for individual colloidal particles floating above a substrate under the action of the critical thermal noise in the solvent medium, constituted by a binary liquid mixture of water and 2,6-lutidine near its lower consolute point. Depending on the relative adsorption preferences of the colloid and substrate surfaces with respect to the two components of the binary liquid mixture, we observe that, upon approaching the critical point of the solvent, attractive or repulsive forces emerge and supersede those prevailing away from it. Based on the knowledge of the critical Casimir forces acting in film geometries within the Ising universality class and with equal or opposing boundary conditions, we provide the corresponding theoretical predictions for the sphere—planar wall geometry of the experiment. The experimental data for the effective potential can be interpreted consistently in terms of these predictions and a remarkable quantitative agreement is observed.

We investigate simple three-dimensionally crossed wires carrying electric currents which generate chaotic magnetic-field lines (CMFLs). As such wire systems, cross-ring and perturbed parallel-ring wires are studied, since topologically equivalent configurations to these systems can often be found in contemporary electric and integrated circuits. For realistic fundamental wire configurations, the conditions for wire dimensions (size) and current values to generate CMFLs are numerically explored under the presence of the weak but inevitable geomagnetic field. As a result, it is concluded that CMFLs can exist everywhere; i.e., they are ubiquitous in the modern technological world.

This is a comprehensive report on the phase transition between two turbulent states of electroconvection in nematic liquid crystals, which was recently found by the authors to be in the directed percolation (DP) universality class [K. A. Takeuchi et al., Phys. Rev. Lett. 99, 234503 (2007)]. We further investigate both static and dynamic critical behaviors of this phase transition, measuring a total of 12 critical exponents, 5 scaling functions, and 8 scaling relations, all in full agreement with those characterizing the DP class in $2+1$ dimensions. Developing an experimental technique to create a seed of topological-defect turbulence by pulse laser, we confirm in particular the rapidity symmetry, which is a basic but nontrivial consequence of the field-theoretic approach to DP. This provides a clear experimental realization of this outstanding truly out-of-equilibrium universality class, dominating most phase transitions into an absorbing state.

Recently, the abundance of digital data is enabling the implementation of graph-based ranking algorithms that provide system level analysis for ranking publications and authors. Here, we take advantage of the entire Physical Review publication archive (1893–2006) to construct authors’ networks where weighted edges, as measured from opportunely normalized citation counts, define a proxy for the mechanism of scientific credit transfer. On this network, we define a ranking method based on a diffusion algorithm that mimics the spreading of scientific credits on the network. We compare the results obtained with our algorithm with those obtained by local measures such as the citation count and provide a statistical analysis of the assignment of major career awards in the area of physics. A website where the algorithm is made available to perform customized rank analysis can be found at the address http://www.physauthorsrank.org.

The momentum transfer to a scatterer from fluorescence photons was detected using an optical system that permits one to simultaneously measure the radiation force exerted on and fluorescence emission from the scatterer. The core of this technique is a partially metal covered dielectric bead optically trapped in a liquid with dye molecules. Fluorescence emission from the volume that includes the bead is measured simultaneously with the Brownian motion of the bead. The perturbed motion of the bead is a result of photon momentum transfer from the fluorescence of the dye to the trapped scatterer. The bead position fluctuations indicate the presence of the fluorescence and its bleaching nature. The results demonstrate the capability of the photonic force microscopy technique to be a complement to spectroscopy in the study of optical processes.