Our computational model of the circadian clock comprised the feedback loop between LATE ELONGATED HYPOCOTYL (LHY), CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and TIMING OF CAB EXPRESSION 1 (TOC1), and a predicted, interlocking feedback loop involving TOC1 and a hypothetical component Y. Experiments based on model predictions suggested GIGANTEA (GI) as a candidate for Y. We now extend the model to include a recently demonstrated feedback loop between the TOC1 homologues PSEUDO-RESPONSE REGULATOR 7 (PRR7), PRR9 and LHY and CCA1. This three-loop network explains the rhythmic phenotype of toc1 mutant alleles. Model predictions fit closely to new data on the gi;lhy;cca1 mutant, which confirm that GI is a major contributor to Y function. Analysis of the three-loop network suggests that the plant clock consists of morning and evening oscillators, coupled intracellularly, which may be analogous to coupled, morning and evening clock cells in Drosophila and the mouse.

We extend the current model of the plant circadian clock, in order to accommodate new and published data. Throughout our model development we use a global parameter search to ensure that any limitations we find are due to the network architecture and not to our selection of the parameter values, which have not been determined experimentally. Our final model includes two, interlocked loops of gene regulation and is reminiscent of the circuit structures previously identified by experiments on insect and fungal clocks. It is the first Arabidopsis clock model to show such good correspondence to experimental data.Our interlocked feedback loop model predicts the regulation of two unknown components. Experiments motivated by these predictions identify the GIGANTEA gene as a strong candidate for one component, with an unexpected pattern of light regulation.*

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We study the electronic properties of DNA by way of a tight-binding model applied to four particular DNA sequences. The charge transfer properties are presented in terms of localization lengths (crudely speaking, the length over which electrons travel). Various types of disorder, including random potentials, are employed to account for different real environments. We have performed calculations on poly(dG)-poly(dC), telomeric-DNA, random-ATGC DNA, and lambda-DNA. We find that random and lambda-DNA have localization lengths allowing for electron motion among a few dozen basepairs only. A novel enhancement of localization lengths is observed at particular energies for an increasing binary backbone disorder. We comment on the possible biological relevance of sequence-dependent charge transfer in DNA.

We present a model for the kinetics of spontaneous membrane domain (raft) assembly that includes the effect of membrane recycling ubiquitous in living cells. We show that domains can have a broad power-law distribution with an average radius that scales with the 1/4 power of the domain lifetime when the line tension at the domain edges is large. For biologically reasonable recycling and diffusion rates, the average domain radius is in the tens of nm range, consistent with observations. This represents one possible link between signaling (involving rafts) and traffic (recycling) in cells. Finally, we present evidence that suggests that the average raft size may be the same for all scale-free recycling schemes.

The static and dynamic properties of ring polymers in concentrated solutions remains one of the last deep unsolved questions in polymer physics. At the same time, the nature of the glass transition in polymeric systems is also not well understood. In this work, we study a novel glass transition in systems made of circular polymers by exploiting the topological constraints that are conjectured to populate concentrated solutions of rings. We show that such rings strongly interpenetrate through one another, generating an extensive network of topological interactions that dramatically affects their dynamics. We show that a kinetically arrested state can be induced by randomly pinning a small fraction of the rings. This occurs well above the classical glass transition temperature at which microscopic mobility is lost. Our work both demonstrates the existence of long-lived inter-ring penetrations and realizes a novel, topologically induced, glass transition.glass transition | ring polymers | topology | topological glass | molecular dynamics T he physics of ring polymers remains one of the last big mysteries in polymer physics (1). Concentrated systems of ring polymers have been observed, in both simulations and experiments, to display unique features that are not easily reconciled with the standard reptation theory of linear polymers (2-6). The main reason for this is that ring polymers do not possess free terminal segments, or ends, essential for end-directed curvilinear diffusion. In contrast, ring polymers possess a closed contour, which leads to markedly different relaxation and diffusion mechanisms. Recently, there has been much improvement in the production of purified systems of rings (6-8), with the consequent result that more and more experimental puzzling evidence requires a deeper understanding of their motion in concentrated solutions and melts from a theoretical point of view.Recently, it has been conjectured that ring polymers assume crumpled, segregated conformations in concentrated solution or the melt (5). On the other hand, numerical and experimental findings (5, 6) suggest that rings exhibit strong intercoil correlations, which have proved difficult to address in simplified theoretical models (9-12). Because of this, there have been many recent attempts to rigorously characterize these interchains' interactions (13-16), although a precise definition and unambiguous identification of these "threadings" in concentrated solutions of rings remains elusive. The primary reason for this is that the rings are assumed to remain strictly topologically unlinked from one another throughout if synthesized in this state.In the case of concentrated solutions of rings embedded in a gel, a method to identify these interpenetrating threadings has recently been proposed (13). Here it was shown that the number of threadings scales extensively in the polymer length (or mass) and can therefore be numerous for long rings, creating a hierarchical sequence of constraints that can span the entire system. It has also been con...

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