Modelling of the electron transfer reactions in Photosystem I by electron tunnelling theory: The phylloquinones bound to the PsaA and the PsaB reaction centre subunits of PS I are almost isoenergetic to the iron–sulfur cluster FX

AbstractPhotosystem I is a large macromolecular complex located in the thylakoid membranes of chloroplasts and in cyanobacteria that catalyses the light driven reduction of ferredoxin and oxidation of plastocyanin. Due to the very negative redox potential of the primary electron transfer cofactors accepting electrons, direct estimation by redox titration of the energetics of the system is hampered. However, the rates of electron transfer reactions are related to the thermodynamic properties of the system. Hence, several spectroscopic and biochemical techniques have been employed, in combination with the classical Marcus theory for electron transfer tunnelling, in order to access these parameters. Nevertheless, the values which have been presented are very variable. In particular, for the case of the tightly bound phylloquinone molecule A1, the values of the redox potentials reported in the literature vary over a range of about 350 mV. Previous models of Photosystem I have assumed a unidirectional electron transfer model. In the present study, experimental evidence obtained by means of time resolved absorption, photovoltage, and electron paramagnetic resonance measurements are reviewed and analysed in terms of a bi-directional kinetic model for electron transfer reactions. This model takes into consideration the thermodynamic equilibrium between the iron–sulfur centre FX and the phylloquinone bound to either the PsaA (A1A) or the PsaB (A1B) subunit of the reaction centre and the equilibrium between the iron–sulfur centres FA and FB. The experimentally determined decay lifetimes in the range of sub-picosecond to the microsecond time domains can be satisfactorily simulated, taking into consideration the edge-to-edge distances between redox cofactors and driving forces reported in the literature. The only exception to this general behaviour is the case of phylloquinone (A1) reoxidation. In order to describe the reported rates of the biphasic decay, of about 20 and 200 ns, associated with this electron transfer step, the redox potentials of the quinones are estimated to be almost isoenergetic with that of the iron sulfur centre FX. A driving force in the range of 5 to 15 meV is estimated for these reactions, being slightly exergonic in the case of the A1B quinone and slightly endergonic, in the case of the A1A quinone. The simulation presented in this analysis not only describes the kinetic data obtained for the wild type samples at room temperature and is consistent with estimates of activation energy by the analysis of temperature dependence, but can also explain the effect of the mutations around the PsaB quinone binding pocket. A model of the overall energetics of the system is derived, which suggests that the only substantially irreversible electron transfer reactions are the reoxidation of A0 on both electron transfer branches and the reduction of FA by FX

Elastic constants of 3-, 4- and 6-connected chiral and anti-chiral honeycombs subject to uniaxial in-plane loading

Finite Element models are developed for the in-plane linear elastic constants of a family of honeycombs comprising arrays of cylinders connected by ligaments. Honeycombs having cylinders with 3, 4 and 6 ligaments attached to them are considered, with two possible configurations explored for each of the 3- (trichiral and anti-trichiral) and 4- (tetrachiral and anti-tetrachiral) connected systems. Honeycombs for each configuration have been manufactured using rapid prototyping and subsequently characterised for mechanical properties through in-plane uniaxial loading to verify the models. An interesting consequence of the family of 'chiral' honeycombs presented here is the ability to produce negative Poisson's ratio (auxetic) response. The deformation mechanisms responsible for auxetic functionality in such honeycombs are discussed

Whisker-object contact speed affects radial distance estimation

Whiskered mammals such as rats are experts in tactile perception. By actively palpating surfaces with their whiskers, rats and mice are capable of acute texture discrimination and shape perception. We present a novel system for investigating whisker-object contacts repeatably and reliably. Using an XY positioning robot and a biomimetic artificial whisker we can generate signals for different whisker-object contacts under a wide range of conditions. Our system is also capable of dynamically altering the velocity and direction of the contact based on sensory signals. This provides a means for investigating sensory motor interaction in the tactile domain. Here we implement active contact control, and investigate the effect that speed has on radial distance estimation when using different features for classification. In the case of a moving object contacting a whisker, magnitude of deflection can be ambiguous in distinguishing a nearby object moving slowly from a more distant object moving rapidly. This ambiguity can be resolved by finding robust features for contact speed, which then informs classification of radial distance. Our results are verified on a dataset from SCRATCHbot, a whiskered mobile robot. Building whiskered robots and modelling these tactile perception capabilities would allow exploration and navigation in environments where other sensory modalities are impaired, for example in dark, dusty or loud environments such as disaster areas. © 2010 IEEE

Whiskered texture classification with uncertain contact pose geometry

Tactile sensing can be an important source of information for robots, and texture discrimination in particular is useful in object recognition and terrain identification. Whisker based tactile sensing has recently been shown to be a promising approach for mobile robots, using simple sensors and many classification approaches. However these approaches have often been tested in limited environments, and have not been compared against one another in a controlled way. A wide range of whisker-object contact poses are possible on a mobile robot, and the effect such contact variability has on sensing has not been properly investigated. We present a novel, carefully controlled study of simple surface texture classifiers on a large set of varied pose conditions that mimic those encountered by mobile robots. Namely, single brief whisker contacts with textured surfaces at a range of surface orientations and contact speeds. Results show that different classifiers are appropriate for different settings, with spectral template and feature based approaches performing best in surface texture, and contact speed estimation, respectively. The results may be used to inform selection of classifiers in tasks such as tactile SLAM

Naive Bayes texture classification applied to whisker data from a moving robot

Many rodents use their whiskers to distinguish objects by surface texture. To examine possible mechanisms for this discrimination, data from an artificial whisker attached to a moving robot was used to test texture classification algorithms. This data was examined previously using a template-based classifier of the whisker vibration power spectrum [1]. Motivated by a proposal about the neural computations underlying sensory decision making [2], we classified the raw whisker signal using the related ‘naive Bayes’ method. The integration time window is important, with roughly 100ms of data required for good decisions and 500ms for the best decisions. For stereotyped motion, the classifier achieved hit rates of about 80% using a single (horizontal or vertical) stream of vibration data and 90% using both streams. Similar hit rates were achieved on natural data, apart from a single case in which the performance was only about 55%. Therefore this application of naive Bayes represents a biologically motivated algorithm that can perform well in a real-world robot task

CrunchBot : a mobile whiskered robot platform

CrunchBot is a robot platform for developing models of tactile perception and navigation. We present the architecture of CrunchBot, and show why tactile navigation is difficult. We give novel real-time performance results from components of a tactile navigation system and a description of how they may be integrated at a systems level. Components include floor surface classification, radial distance estimation and navigation. We show how tactile-only navigation differs fundamentally from navigation tasks using vision or laser sensors, in that the assumptions about the data preclude standard algorithms (such as extended Kalman Filters) and require brute-force methods

Algorithm for numerical integration of the rigid-body equations of motion

A new algorithm for numerical integration of the rigid-body equations of motion is proposed. The algorithm uses the leapfrog scheme and the quantities involved are angular velocities and orientational variables which can be expressed in terms of either principal axes or quaternions. Due to specific features of the algorithm, orthonormality and unit norms of the orientational variables are integrals of motion, despite an approximate character of the produced trajectories. It is shown that the method presented appears to be the most efficient among all known algorithms of such a kind.Comment: 4 pages, 1 figur

Rebounce and Black hole formation in a Gravitational Collapse Model with Vanishing Radial Pressure

We examine spherical gravitational collapse of a matter model with vanishing radial pressure and non-zero tangential pressure. It is seen analytically that the collapsing cloud either forms a black hole or disperses depending on values of the initial parameters which are initial density, tangential pressure and velocity profile of the cloud. A threshold of black hole formation is observed near which a scaling relation is obtained for the mass of black hole, assuming initial profiles to be smooth. The similarities in the behaviour of this model at the onset of black hole formation with that of numerical critical behaviour in other collapse models are indicated.Comment: 15 pages, To be published in Gen.Rel.Gra

Cluster size distributions in particle systems with asymmetric dynamics

We present exact and asymptotic results for clusters in the one-dimensional totally asymmetric exclusion process (TASEP) with two different dynamics. The expected length of the largest cluster is shown to diverge logarithmically with increasing system size for ordinary TASEP dynamics and as a logarithm divided by a double logarithm for generalized dynamics, where the hopping probability of a particle depends on the size of the cluster it belongs to. The connection with the asymptotic theory of extreme order statistics is discussed in detail. We also consider a related model of interface growth, where the deposited particles are allowed to relax to the local gravitational minimum.Comment: 12 pages, 3 figures, RevTe

Criticality and Bifurcation in the Gravitational Collapse of a Self-Coupled Scalar Field

We examine the gravitational collapse of a non-linear sigma model in spherical symmetry. There exists a family of continuously self-similar solutions parameterized by the coupling constant of the theory. These solutions are calculated together with the critical exponents for black hole formation of these collapse models. We also find that the sequence of solutions exhibits a Hopf-type bifurcation as the continuously self-similar solutions become unstable to perturbations away from self-similarity.Comment: 18 pages; one figure, uuencoded postscript; figure is also available at http://www.physics.ucsb.edu/people/eric_hirschman