Stable motifs delay species loss in simulated food webs

Some three-species motifs (unique patterns of interactions between three species) are both more stable when modeled in isolation and over-represented in empirical food webs. This suggests that these motifs may reduce extinction risk for species participating in them, ultimately stabilizing the food web as a whole. We test whether a species' time to extinction following a perturbation is related to its participation in stable and unstable motifs and assess how motif roles co-vary with a species' degree or trophic level. We found that species' motif roles are related to their times to extinction following a disturbance. Specifically, participating in many omnivory motifs (whether in absolute terms, as a proportion of the species' role, or relative to other species in the network) was associated with more rapid extinction, even though omnivory has previously been identified as a stable motif. Participating in the other three stable motifs (three-species chain, apparent competition, and direct competition) was associated with longer times to extinction. While motif roles were associated with extinction risk, they also varied strongly with degree and trophic level. This means that these simpler measures of a species' role may be sufficient to roughly predict which species are most vulnerable to disturbance, but the additional information encapsulated in a motif role can further refine predictions of vulnerability. Moreover, where researchers are a priori interested in motif roles, our results confirm that these roles can be interpreted with respect to extinction risk.

Reaction Mechanism for Methane-to-Methanol in Cu-SSZ-13: First-Principles Study of the Z2[Cu2O] and Z2[Cu2OH] Motifs

As transportation continues to increase world-wide, there is a need for more efficient utilization of fossil fuel. One possibility is direct conversion of the solution gas bi-product CH4 into an energy-rich, easily usable liquid fuel such as CH3OH. However, new catalytic materials to facilitate the methane-to-methanol reaction are needed. Using density functional calculations, the partial oxidation of methane is investigated over the small-pore copper-exchanged zeolite SSZ-13. The reaction pathway is identified and the energy landscape elucidated over the proposed motifs Z2[Cu2O] and Z2[Cu2OH]. It is shown that the Z2[Cu2O] motif has an exergonic reaction path, provided water is added as a solvent for the desorption step. However, a micro-kinetic model shows that neither Z2[Cu2O] nor Z2[Cu2OH] has any notable activity under the reaction conditions. These findings highlight the importance of the detailed structure of the active site and that the most stable motif is not necessarily the most active.

A feedback loop of conditionally stable circuits drives the cell cycle from checkpoint to checkpoint

We perform logic-based network analysis on a model of the mammalian cell cycle. This model is composed of a Restriction Switch driving cell cycle commitment and a Phase Switch driving mitotic entry and exit. By generalizing the concept of stable motif, i.e., a self-sustaining positive feedback loop that maintains an associated state, we introduce the concept of a conditionally stable motif, the stability of which is contingent on external conditions. We show that the stable motifs of the Phase Switch are contingent on the state of three nodes through which it receives input from the rest of the network. Biologically, these conditions correspond to cell cycle checkpoints. Holding these nodes locked (akin to a checkpoint-free cell) transforms the Phase Switch into an autonomous oscillator that robustly toggles through the cell cycle phases G1, G2 and mitosis. The conditionally stable motifs of the Phase Switch Oscillator are organized into an ordered sequence, such that they serially stabilize each other but also cause their own destabilization. Along the way they channel the dynamics of the module onto a narrow path in state space, lending robustness to the oscillation. Self-destabilizing conditionally stable motifs suggest a general negative feedback mechanism leading to sustained oscillations.

A feedback loop of conditionally stable circuits drives the cell cycle from checkpoint to checkpoint

We perform logic-based network analysis on a model of the mammalian cell cycle. This model is composed of a Restriction Switch driving cell cycle commitment and a Phase Switch driving mitotic entry and exit. By generalizing the concept of stable motif, i.e., a self-sustaining positive feedback loop that maintains an associated state, we introduce the concept of conditionally stable motif, the stability of which is contingent on external conditions. We show that the stable motifs of the Phase Switch are contingent on the state of three nodes through which it receives input from the rest of the network. Biologically, these conditions correspond to cell cycle checkpoints. Holding these nodes locked (akin to a checkpoint-free cell) transforms the Phase Switch into an autonomous oscillator that robustly toggles through the cell cycle phases G1, G2 and mitosis. The conditionally stable motifs of the Phase Switch Oscillator are organized into an ordered sequence, such that they serially stabilize each other but also cause their own destabilization. Along the way they channel the dynamics of the module onto a narrow path in state space, lending robustness to the oscillation. Self-destabilizing conditionally stable motifs suggest a general negative feedback mechanism leading to sustained oscillations.