Fitness-driven deactivation in network evolution

Individual nodes in evolving real-world networks typically experience growth and decay --- that is, the popularity and influence of individuals peaks and then fades. In this paper, we study this phenomenon via an intrinsic nodal fitness function and an intuitive aging mechanism. Each node of the network is endowed with a fitness which represents its activity. All the nodes have two discrete stages: active and inactive. The evolution of the network combines the addition of new active nodes randomly connected to existing active ones and the deactivation of old active nodes with possibility inversely proportional to their fitnesses. We obtain a structured exponential network when the fitness distribution of the individuals is homogeneous and a structured scale-free network with heterogeneous fitness distributions. Furthermore, we recover two universal scaling laws of the clustering coefficient for both cases, $C(k) \sim k^{-1}$ and $C \sim n^{-1}$, where $k$ and $n$ refer to the node degree and the number of active individuals, respectively. These results offer a new simple description of the growth and aging of networks where intrinsic features of individual nodes drive their popularity, and hence degree.Comment: IoP Styl

Identification of the para-nitrophenol catabolic pathway, and characterization of three enzymes involved in the hydroquinone pathway, in pseudomonas sp. 1-7

<p>Abstract</p> <p>Background</p> <p><it>para</it>-Nitrophenol (PNP), a priority environmental pollutant, is hazardous to humans and animals. However, the information relating to the PNP degradation pathways and their enzymes remain limited.</p> <p>Results</p> <p><it>Pseudomonas </it>sp.1-7 was isolated from methyl parathion (MP)-polluted activated sludge and was shown to degrade PNP. Two different intermediates, hydroquinone (HQ) and 4-nitrocatechol (4-NC) were detected in the catabolism of PNP. This indicated that <it>Pseudomonas </it>sp.1-7 degraded PNP by two different pathways, namely the HQ pathway, and the hydroxyquinol (BT) pathway (also referred to as the 4-NC pathway). A gene cluster (<it>pdcEDGFCBA</it>) was identified in a 10.6 kb DNA fragment of a fosmid library, which cluster encoded the following enzymes involved in PNP degradation: PNP 4-monooxygenase (PdcA), <it>p</it>-benzoquinone (BQ) reductase (PdcB), hydroxyquinol (BT) 1,2-dioxygenase (PdcC), maleylacetate (MA) reductase (PdcF), 4-hydroxymuconic semialdehyde (4-HS) dehydrogenase (PdcG), and hydroquinone (HQ) 1,2-dioxygenase (PdcDE). Four genes (<it>pdcDEFG</it>) were expressed in <it>E. coli </it>and the purified <it>pdcDE</it>, <it>pdcG </it>and <it>pdcF </it>gene products were shown to convert HQ to 4-HS, 4-HS to MA and MA to β-ketoadipate respectively by <it>in vitro </it>activity assays.</p> <p>Conclusions</p> <p>The cloning, sequencing, and characterization of these genes along with the functional PNP degradation studies identified 4-NC, HQ, 4-HS, and MA as intermediates in the degradation pathway of PNP by <it>Pseudomonas </it>sp.1-7. This is the first conclusive report for both 4-NC and HQ- mediated degradation of PNP by one microorganism.</p

Heterogenization of Photochemical Molecular Devices: Embedding a Metal–Organic Cage into a ZIF-8-Derived Matrix To Promote Proton and Electron Transfer

Application of a molecular catalyst in artificial photosynthesis is confronted with challenges such as rapid deactivation due to photodegradation or detrimental aggregation in harsh conditions. In this work, a metal-organic cage [Pd-6(RUL3)(8)](28+) (MOC-16), characteristic of a photochemical molecular device (PMD) concurrently integrating eight Ru2+ light-harvesting centers and six Pd2+ catalytic centers for efficient homogeneous H-2 production, is successfully heterogenized through incorporation into a metal-organic framework (MOF) of ZIF-8 and then transformed into a carbonate matrix of Zn-x(MeIm)(x)(CO3)(x) (CZIF), leading to hybridized MOC-16@CZIF. This MOC@MOF integrated photocatalyst inherits a highly efficient and directional electron transfer in the picosecond domain of MOC-16 and possesses one order increased microsecond magnitude of the triplet excited-state electron in comparison to that of the primitive MOC-16. The carbonate CZIF matrix endows MOC-16@CZIF with water wettability, serving as a proton relay to facilitate proton delivery by virtue of H2O as proton carriers. Electron transfer during the photocatalytic process is also enhanced by infiltration of a sacrificial agent of BIH into the CZIF matrix to promote conductivity, owing to its strong reducing ability to induce free charge carriers. These synergistic effects contribute to the extra high activity for H-2 generation, making the turnover frequency of this heterogeneous MOC-16@CZIF photocatalyst maintain a level of similar to 0.4 H-2.s(-1), increased by 50-fold over that of a homogeneous PMD. Meanwhile, it is robust enough to tolerate harsh reaction conditions, presenting an unprecedented heterogenization example of homogeneous PMD with a MOF-derived matrix to mimic catalytic features of a natural photosystem, which may shed light on the design of multifunctional PMD@MOF materials to expand the number of molecular catalysts for practical application in artificial photosynthesis