Virtual intermediates in photosynthetic electron transfer.

We explore the possibility of virtual transfer in the primary charge separation of photosynthetic bacteria within the context of several types of experimental data. We show that the peak that might be expected in the virtual rate as electric fields vary the intermediate state energy is severely broadened by coupling to high-frequency modes. The Stark absorption kinetics data are thus consistent with virtual transfer in the primary charge separation. High-frequency coupling also makes the temperature dependence weak over a wide range of parameters. We demonstrate that Stark fluorescence anisotropy data, usually taken as evidence of virtual transfer, can in fact be consistent with two-step transfer. We suggest a two-pulse excitation experiment to quantify the contributions from two-step and virtual transfer. We show that virtual absorption into a charge transfer state can make a substantial contribution to the Stark absorption spectrum in a way that is not related to any derivative of the absorption spectrum.     

Density-dependent dispersal in integrodifference equations

Many species exhibit dispersal processes with positive density- dependence. We model this behavior using an integrodifference equation where the individual dispersal probability is a monotone increasing function of local density. We investigate how this dispersal probability affects the spreading speed of a single population and its ability to persist in fragmented habitats. We demonstrate that density-dependent dispersal probability can act as a mechanism for coexistence of otherwise non-coexisting competitors. We show that in time-varying habitats, an intermediate dispersal probability will evolve. Analytically, we find that the spreading speed for the integrodifference equation with density-dependent dispersal probability is not linearly determined. Furthermore, the next-generation operator is not compact and, in general, neither order-preserving nor monotonicity-preserving. We give two explicit examples of non-monotone, discontinuous traveling-wave profiles.      

Spatial updating in human parietal cortex

Single neurons in monkey parietal cortex update visual information in conjunction with eye movements. This remapping of stimulus representations is thought to contribute to spatial constancy. We hypothesized that a similar process occurs in human parietal cortex and that we could visualize it with functional MRI. We scanned subjects during a task that involved remapping of visual signals across hemifields. We observed an initial response in the hemisphere contralateral to the visual stimulus, followed by a remapped response in the hemisphere ipsilateral to the stimulus. We ruled out the possibility that this remapped response resulted from either eye movements or visual stimuli alone. Our results demonstrate that updating of visual information occurs in human parietal cortex.     

Self-organized flocking in mobile robot swarms

In this paper, we study self-organized flocking in a swarm of mobile robots. We present Kobot, a mobile robot platform developed specifically for swarm robotic studies. We describe its infrared-based short range sensing system, capable of measuring the distance from obstacles and detecting kin robots, and a novel sensing system called the virtual heading system (VHS) which uses a digital compass and a wireless communication module for sensing the relative headings of neighboring robots. We propose a behavior based on heading alignment and proximal control that is capable of generating self-organized flocking in a swarm of Kobots. By self-organized flocking we mean that a swarm of mobile robots, initially connected via proximal sensing, is able to wander in an environment by moving as a coherent group in open space and to avoid obstacles as if it were a “super-organism”. We propose a number of metrics to evaluate the quality of flocking. We use a default set of behavioral parameter values that can generate acceptable flocking in robots, and analyze the sensitivity of the flocking behavior against changes in each of the parameters using the metrics that were proposed. We show that the proposed behavior can generate flocking in a small group of physical robots in a closed arena as well as in a swarm of 1000 simulated robots in open space. We vary the three main characteristics of the VHS, namely: (1) the amount and nature of noise in the measurement of heading, (2) the number of VHS neighbors, and (3) the range of wireless communication. Our experiments show that the range of communication is the main factor that determines the maximum number of robots that can flock together and that the behavior is highly robust against the other two VHS characteristics. We conclude by discussing this result in the light of related theoretical studies in statistical physics.     

Dielectric relaxation in proteins: the computational perspective

In photoexcitation and electron transfer, a new dipole or charge is introduced, and the structure is adjusted. This adjustment represents dielectric relaxation, which is the focus of this review. We concentrate on a few selected topics. We discuss linear response theory, as a unifying framework and a tool to describe non-equilibrium states. We review recent, molecular dynamics simulation studies that illustrate the calculation of dynamic and thermodynamic properties, such as Stokes shifts or reorganization free energies. We then turn to the macroscopic, continuum electrostatic view. We recall the physical definition of a dielectric constant and revisit the decomposition of the free energy into a reorganization and a static term. We review some illustrative continuum studies and discuss some difficulties that can arise with the continuum approach. In conclusion, we consider recent developments that will increase the accuracy and broaden the scope of all these methods.     

Stochastic effects in intercellular calcium spiking in hepatocytes

We carry out a Monte Carlo simulation of stochastic effects for two models of intercellular calcium wave propagation in rat hepatocytes. Both models involve gap junction diffusion by a second messenger. We find that, in general, the stochastic effects improve agreement with experiment, for a reasonable choice of model parameters. Both stochastic models exhibit baseline fluctuations and variations in the peak heights of Ca(2+). In addition, we find for one model that there is a distribution of latency times, rather than a single latency time, with a distribution width which is comparable to the experimental observation of spike widths. We also find for the other model with low gap junction diffusion that it is possible for cell multiplets to oscillate independently initially, but to subsequently become synchronized.     

Participation of proteasomes in Xenopus embryogenesis

We examined the effects of various protease substrates on Xenopus laevis embryogenesis. Thirty-three peptidyl-MCA substrates were added to the culture medium in which Xenopus embryos were developing. Five of the 33 substrates were found to inhibit embryogenesis at the early gastrula stage or much earlier ones. These results suggest that proteases that hydrolyze these substrates are involved in embryonic development. We found that the developmental stage of embryos is crucial for these substrates to inhibit their development. We purified a protease that hydrolyzes Pyr-Arg-Thr-Lys-Arg-MCA, a substrate that inhibits embryogenesis, from Xenopus embryos. This protease turned out to be a component of proteasomes. We found that 4 of the 5 substrates that inhibit embryogenesis are among the proteasome substrates. Thus, we concluded that proteasomes play a crucial role in the development of Xenopus embryos. Possibly, various catalytic subunits in proteasomes function independently, in stage-specific manners.     

Mathematical modelling of anisotropy in fibrous connective tissue

We present two modelling frameworks for studying dynamic anistropy in connective tissue, motivated by the problem of fibre alignment in wound healing. The first model is a system of partial differential equations operating on a macroscopic scale. We show that a model consisting of a single extracellular matrix material aligned by fibroblasts via flux and stress exhibits behaviour that is incompatible with experimental observations. We extend the model to two matrix types and show that the results of this extended model are robust and consistent with experiment. The second model represents cells as discrete objects in a continuum of ECM. We show that this model predicts patterns of alignment on macroscopic length scales that are lost in a continuum model of the cell population.     

Convergence Time towards Periodic Orbits in Discrete Dynamical Systems

We investigate the convergence towards periodic orbits in discrete dynamical systems. We examine the probability that a randomly chosen point converges to a particular neighborhood of a periodic orbit in a fixed number of iterations, and we use linearized equations to examine the evolution near that neighborhood. The underlying idea is that points of stable periodic orbit are associated with intervals. We state and prove a theorem that details what regions of phase space are mapped into these intervals (once they are known) and how many iterations are required to get there. We also construct algorithms that allow our theoretical results to be implemented successfully in practice.     

Indian hedgehog signaling in extraembryonic endoderm and ectoderm differentiation in ES embryoid bodies

We previously demonstrated that a member of the Hedgehog gene family, Indian hedgehog (Ihh), is expressed in the visceral endoderm of EC and ES cell embryoid bodies and mouse embryos. Overexpression studies suggested that Ihh was involved in visceral endoderm differentiation. We now provide evidence for a Hh response in the embryoid body core and in the mesothelial layer of the visceral yolk sac. We also demonstrate that treatment of ES embryoid bodies with the Hh antagonists cAMP and forskolin results in downregulation of the Hh response and altered embryoid body differentiation. The outer endoderm layer undergoes a transition to parietal endoderm while formation of an embryonic ectoderm layer surrounding a cavity is inhibited. These treatments also result in a decrease in the expression of markers for the mesoderm derivatives, blood and endothelial cells. We present a model to explain how Ihh and BMP signaling may regulate extraembryonic endoderm and embryonic ectoderm differentiation.     

Teams in animal societies

We review the existence of teams in animal societies. Teamshave previously been dismissed in all but a tiny minority ofinsect societies. "Team" is a term not generally used in studiesof vertebrates. We propose a new rigorous definition of a teamthat may be applied to both vertebrate and invertebrate societies.We reconsider what it means to work as a team or group andsuggest that there are many more teams in insect societies than previously thought. A team task requires different subtasksto be performed concurrently for successful completion. Thereis a division of labor within a team. Contrary to previousreviews of teams in social insects, we do not constrain teamsto consist of members of different castes and argue that teammembers may be interchangeable. Consequently, we suggest thata team is simply the set of individuals that performs a teamtask. We contrast teams with groups and suggest that a grouptask requires the simultaneous performance and cooperationof two or more individuals for successful completion. In agroup, there is no division of labor—each individual performs the same task. We also contrast vertebrate and invertebrateteams and find that vertebrate teams tend to be associatedwith hunting and are based on individual recognition. Invertebrateteams occur in societies characterized by a great deal of redundancy,and we predict that teams in insect societies are more likelyto be found in large polymorphic ("complex") societies thanin small monomorphic ("simple") societies.     

The effect of deleterious alleles on adaptation in asexual populations

We calculate the fixation probability of a beneficial allele that arises as the result of a unique mutation in an asexual population that is subject to recurrent deleterious mutation at rate U. Our analysis is an extension of previous works, which make a biologically restrictive assumption that selection against deleterious alleles is stronger than that on the beneficial allele of interest. We show that when selection against deleterious alleles is weak, beneficial alleles that confer a selective advantage that is small relative to U have greatly reduced probabilities of fixation. We discuss the consequences of this effect for the distribution of effects of alleles fixed during adaptation. We show that a selective sweep will increase the fixation probabilities of other beneficial mutations arising during some short interval afterward. We use the calculated fixation probabilities to estimate the expected rate of fitness improvement in an asexual population when beneficial alleles arise continually at some low rate proportional to U. We estimate the rate of mutation that is optimal in the sense that it maximizes this rate of fitness improvement. Again, this analysis relaxes the assumption made previously that selection against deleterious alleles is stronger than on beneficial alleles.     

The Role of Rewards in Motivating Participation in Simple Warfare

In the absence of explicit punitive sanctions, why do individuals voluntarily participate in intergroup warfare when doing so incurs a mortality risk? Here we consider the motivation of individuals for participating in warfare. We hypothesize that in addition to other considerations, individuals are incentivized by the possibility of rewards. We test a prediction of this “cultural rewards war-risk hypothesis” with ethnographic literature on warfare in small-scale societies. We find that a greater number of benefits from warfare is associated with a higher rate of death from conflict. This provides preliminary support for the relationship between rewards and participation in warfare.     

Pattern identification in biogeography

Identifying common patterns among area cladograms that arise in historical biogeography is an important tool for biogeographical inference. We develop the first rigorous formalization of these pattern-identification problems. We develop metrics to compare area cladograms. We define the maximum agreement area cladogram (MAAC) and we develop efficient algorithms for finding the MAAC of two area cladograms, while showing that it is NP-hard to find the MAAC of several binary area cladograms. We also describe a linear-time algorithm to identify if two area cladograms are identical     

Objective fidelity evaluation in multisensory virtual environments: auditory cue fidelity in flight simulation

We argue that objective fidelity evaluation of virtual environments, such as flight simulation, should be human-performance-centred and task-specific rather than measure the match between simulation and physical reality. We show how principled experimental paradigms and behavioural models to quantify human performance in simulated environments that have emerged from research in multisensory perception provide a framework for the objective evaluation of the contribution of individual cues to human performance measures of fidelity. We present three examples in a flight simulation environment as a case study: Experiment 1: Detection and categorisation of auditory and kinematic motion cues; Experiment 2: Performance evaluation in a target-tracking task; Experiment 3: Transferrable learning of auditory motion cues. We show how the contribution of individual cues to human performance can be robustly evaluated for each task and that the contribution is highly task dependent. The same auditory cues that can be discriminated and are optimally integrated in experiment 1, do not contribute to target-tracking performance in an in-flight refuelling simulation without training, experiment 2. In experiment 3, however, we demonstrate that the auditory cue leads to significant, transferrable, performance improvements with training. We conclude that objective fidelity evaluation requires a task-specific analysis of the contribution of individual cues.     

The Ross-Macdonald model in a patchy environment

We generalize to n patches the Ross-Macdonald model which describes the dynamics of malaria. We incorporate in our model the fact that some patches can be vector free. We assume that the hosts can migrate between patches, but not the vectors. The susceptible and infectious individuals have the same dispersal rate. We compute the basic reproduction ratio R(0). We prove that if R(0)1, then the disease-free equilibrium is globally asymptotically stable. When R(0)>1, we prove that there exists a unique endemic equilibrium, which is globally asymptotically stable on the biological domain minus the disease-free equilibrium.     

The influence of hydrodynamic interactions on protein dynamics in confined and crowded spaces-assessment in simple models

We consider several systems that are confined within a softly repulsive sphere. The first one is a model protein, crambin, which is described by a structure-based coarse grained model. We demonstrate that the folding process is accelerated by the hydrodynamic interactions (HI) in a way that depends on the radius of the sphere. The tighter the encompassing sphere, the smaller the effect, independent of the nature of the starting conformations. The second system is a protein surrounded by protein-like softly repulsive spheres that make the confined space crowded. In this case, the HI shorten the folding times in a way which depends on the degree of crowdedness only weakly. The third system is a collection of spheres that are meant to represent molecules. We show that confinement increases association times. We also observe that the HI either facilitate or obstruct association of two spheres depending on the crowding conditions. The dependence of the association time on crowdedness in the confining sphere is qualitatively distinct from that derived by Wieczorek and Zielenkiewicz for a cube with the periodic boundary conditions.     

Self-organization and productivity in semi-arid ecosystems: implications of seasonality in rainfall

Spatial self-organization including striking vegetation patterns observed in arid ecosystems has been studied in models with uniform rainfall. In this paper, we present a fully seasonal rainfall model that produces vegetation patterns found in nature by including the natural adaptation of plants to scarcity of water and the consequent seasonal variation in their growth and metabolic rate. We present results for the mean-field and spatially extended versions of the model. We find that the patterns depend on the duration of the wet season even with fixed total annual precipitation (PPT) showing how seasonality affects spatial self-organization. We observe that the productivity can vary for fixed PPT as a function of the duration thereby providing another source of observed variations. We compute the maximum vegetation cover as function of PPT and find that the behavior is consistent with observations. We comment on the implications for regime shifts due to increased interannual fluctuations caused by climatic changes. Our specific model calculations provide more general conclusions for ecosystems with competition for scarce resources due to seasonal variations in the resource, especially for self-organization and productivity.     

Microtubule dynamics in mitosis in Aspergillus nidulans

Mitosis in Aspergillus nidulans is very rapid, requiring less than 5 min at 37 °C in germlings (Bergen and Morris, 1983). In this time the cytoplasmic microtubules (MTs) must disassemble, the mitotic spindle assemble, function and disassemble, and cytoplasmic MTs reassemble. It follows that cytoplasmic MTs must be extremely dynamic in this period and we were interested, in particular, in examining the processes of MT disassembly in prophase and reassembly in anaphase and telophase. We observed a diploid strain that expressed GFP-α-tubulin. We used a spinning disk confocal microscope that allowed rapid image capture, which proved necessary because microtubule dynamics were extremely rapid. We found, for the first time, that microtubule severing occurs in prophase in a filamentous fungus and that catastrophe rather than nucleation limits astral microtubule growth.