7,651 research outputs found

    Molecular Clock on a Neutral Network

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    The number of fixed mutations accumulated in an evolving population often displays a variance that is significantly larger than the mean (the overdispersed molecular clock). By examining a generic evolutionary process on a neutral network of high-fitness genotypes, we establish a formalism for computing all cumulants of the full probability distribution of accumulated mutations in terms of graph properties of the neutral network, and use the formalism to prove overdispersion of the molecular clock. We further show that significant overdispersion arises naturally in evolution when the neutral network is highly sparse, exhibits large global fluctuations in neutrality, and small local fluctuations in neutrality. The results are also relevant for elucidating the topological structure of a neutral network from empirical measurements of the substitution process.Comment: 10 page

    Number of adaptive steps to a local fitness peak

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    We consider a population of genotype sequences evolving on a rugged fitness landscape with many local fitness peaks. The population walks uphill until it encounters a local fitness maximum. We find that the statistical properties of the walk length depend on whether the underlying fitness distribution has a finite mean. If the mean is finite, all the walk length cumulants grow with the sequence length but approach a constant otherwise. Experimental implications of our analytical results are also discussed

    Stronger computational modelling of signalling pathways using both continuous and discrete-state methods

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    Starting from a biochemical signalling pathway model expresses in a process algebra enriched with quantitative information, we automatically derive both continuous-space and discrete-space representations suitable for numerical evaluation. We compare results obtained using approximate stochastic simulation thereby exposing a flaw in the use of the differentiation procedure producing misleading results

    Stochastic modeling of cargo transport by teams of molecular motors

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    Many different types of cellular cargos are transported bidirectionally along microtubules by teams of molecular motors. The motion of this cargo-motors system has been experimentally characterized in vivo as processive with rather persistent directionality. Different theoretical approaches have been suggested in order to explore the origin of this kind of motion. An effective theoretical approach, introduced by M\"uller et al., describes the cargo dynamics as a tug-of-war between different kinds of motors. An alternative approach has been suggested recently by Kunwar et al., who considered the coupling between motor and cargo in more detail. Based on this framework we introduce a model considering single motor positions which we propagate in continuous time. Furthermore, we analyze the possible influence of the discrete time update schemes used in previous publications on the system's dynamic.Comment: Cenference proceedings - Traffic and Granular Flow 1

    Addition to the Flora of Canada? A Specimen from the Arctic Archipelago, Northwest Territories Links Two Allopatric Species of Alkali Grass, Puccinellia

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    A single herbarium specimen from Banks Island in the Canadian National Herbarium, Ottawa, is closest to Puccinellia wrightii (Puccinellia sect. Pseudocolpodium). This would represent a species new to Canada and an extension of over 1100 km from the previously known range in NW Alaska and NE Russia. The morphological characteristics of this specimen are compared with all taxa in P. section Pseudocolpodium and the North American P. arctica aggregate. Principal components analysis supports placement of this specimen in P. section Pseudocolpodium near P. wrightii, where it contributes to a morphological continuum between this species and P. vahliana. The new combination Puccinellia wrightii var. flava is made and a map of the current known distribution of the species in P. section Pseudocolpodium is presented

    Negotiated control between the manual and visual systems for visually guided hand reaching movements

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    Abstract Background Control of reaching movements for manual work, vehicle operation, or interactions with manual interfaces requires concurrent gaze control for visual guidance of the hand. We hypothesize that reaching movements are based on negotiated strategies to resolve possible conflicting demands placed on body segments shared by the visual (gaze) and manual (hand) control systems. Further, we hypothesize that a multiplicity of possible spatial configurations (redundancy) in a movement system enables a resolution of conflicting demands that does not require sacrificing the goals of the two systems. Methods The simultaneous control of manual reach and gaze during seated reaching movements was simulated by solving an inverse kinematics model wherein joint trajectories were estimated from a set of recorded hand and head movements. A secondary objective function, termed negotiation function, was introduced to describe a means for the manual reach and gaze directing systems to balance independent goals against (possibly competing) demands for shared resources, namely the torso movement. For both systems, the trade-off may be resolved without sacrificing goal achievement by taking advantage of redundant degrees of freedom. Estimated joint trajectories were then compared to joint movement recordings from ten participants. Joint angles were predicted with and without the negotiation function in place, and model accuracy was determined using the root-mean-square errors (RMSEs) and differences between estimated and recorded joint angles. Results The prediction accuracy was generally improved when negotiation was included: the negotiated control reduced RMSE by 16% and 30% on average when compared to the systems with only manual or visual control, respectively. Furthermore, the RMSE in the negotiated control system tended to improve with torso movement amplitude. Conclusions The proposed model describes how multiple systems cooperate to perform goal-directed human movements when those movements draw upon shared resources. Allocation of shared resources can be undertaken by a negotiation process that is aware of redundancies and the existence of multiple solutions within the individual systems.http://deepblue.lib.umich.edu/bitstream/2027.42/134579/1/12984_2012_Article_626.pd

    Relaying: An Intercropping Approach to the Co-culture of Crawfish and Rice (Bulletin #862)

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    This study was designed to examine the biological and economic efficacy of relaying crawfish into a growing rice crop in an intercropping manner.https://digitalcommons.lsu.edu/agcenter_bulletins/1041/thumbnail.jp

    Inelastic final-state interaction

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    The final-state interaction in multichannel decay processes is sytematically studied with application to B decay in mind. Since the final-state inteaction is intrinsically interwoven with the decay interaction in this case, no simple phase theorem like "Watson's theorem" holds for experimentally observed final states. We first examine in detail the two-channel problem as a toy-model to clarify the issues and to remedy common mistakes made in earlier literature. Realistic multichannel problems are too challenging for quantitative analysis. To cope with mathematical complexity, we introduce a method of approximation that is applicable to the case where one prominant inelastic channel dominates over all others. We illustrate this approximation method in the amplitude of the decay B to pi K fed by the intermediate states of a charmed meson pair. Even with our approximation we need more accurate information of strong interactions than we have now. Nonethless we are able to obtain some insight in the issue and draw useful conclusions on general fearyres on the strong phases.Comment: The published version. One figure correcte
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