Dataset Information

Partial Shocks on Cooperative Multiplex Networks with Varying Degrees of Noise.

ABSTRACT: In many cooperative networks, such as alliance and trade networks, abrupt and intense changes to the state of the system (which we call "shocks"), can substantially change the network. We examine how such shocks affect multiplex networks via an agent-based model, in which agents add, drop, or change ties to increase their utility. At a certain time-point, some agents are "shocked" by changing (increasing or decreasing) the cost associated with tie-formation or tie-maintenance. Our model makes several improvements to previous models, including (a) only a fraction of nodes are shocked to simulate small wars or scattered tariff increases or decreases and (b) agents can make both utility-maximizing decisions and randomly rewire ties to explore the utility landscape. Interestingly, we find that randomly rewiring ties increases the utility of agents, for reasons similar to simulated annealing in physics. Furthermore, we create a novel metric to determine how networks change after a shock and find that the size of a shock and noise significantly changes the network, but only when agents' incentives for tie-formation are sufficiently high. Together, these results suggest that adding more realism to cooperation network models can give nuanced understanding to network shocks.

SUBMITTER: Burghardt K

PROVIDER: S-EPMC6134050 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature

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Partial Shocks on Cooperative Multiplex Networks with Varying Degrees of Noise.

Burghardt Keith K Maoz Zeev Z

Scientific reports 20180911 1

In many cooperative networks, such as alliance and trade networks, abrupt and intense changes to the state of the system (which we call "shocks"), can substantially change the network. We examine how such shocks affect multiplex networks via an agent-based model, in which agents add, drop, or change ties to increase their utility. At a certain time-point, some agents are "shocked" by changing (increasing or decreasing) the cost associated with tie-formation or tie-maintenance. Our model makes se ...[more]

PMID: 30206261

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Project description:Replication protein A (RPA) is known to interact with guanine- (G-) rich sequences that adopt G-quadruplex (GQ) structures. Most studies reported in the literature were performed on GQ formed by homogeneous sequences, such as the human telomeric repeat, and RPA's ability to unfold GQ structures of differing stability is not known. We compared the thermal stability of three potential GQ-forming DNA sequences (PQSs) to their stability against RPA-mediated unfolding using single-molecule fluorescence resonance energy transfer (FRET) and bulk biophysical and biochemical experiments. One of these sequences is the human telomeric repeat and the other two, located in the promoter region of tyrosine hydroxylase gene, are highly heterogeneous sequences that better represent PQSs in the genome. The three GQ constructs have thermal stabilities that differ significantly. Our measurements showed that the most thermally stable structure (Tm = 86 °C) was also the most stable against RPA-mediated unfolding, although the least thermally stable structure (Tm = 69 °C) had at least an order-of-magnitude higher stability against RPA-mediated unfolding than the structure with intermediate thermal stability (Tm = 78 °C). The significance of this observation becomes more evident when considered within the context of the cellular environment where protein-DNA interactions can be an important determinant of GQ viability. Considering these results, we conclude that thermal stability is not necessarily an adequate criterion for predicting the physiological viability of GQ structures. Finally, we measured the time it takes for an RPA molecule to unfold a GQ from a fully folded to a fully unfolded conformation using a single-molecule stopped-flow method. All three GQ structures were unfolded within ?t ? 0.30 ± 0.10 s, a surprising result considering that the unfolding time does not correlate with thermal stability or stability against RPA-mediated unfolding. These results suggest that the limiting step in G-quadruplex unfolding by RPA is simply the accessibility of the structure to the RPA protein.

Dataset Information

Partial Shocks on Cooperative Multiplex Networks with Varying Degrees of Noise.

Publications

Partial Shocks on Cooperative Multiplex Networks with Varying Degrees of Noise.

Similar Datasets

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