Closed-loop control of complex networks : A trade-off between time and energy

W. L. is supported by the National Science Foundation of China (NSFC) (Grants No. 11322111 and No. 61773125). Y.-Z. S. is supported by the NSFC (Grant No. 61403393). Y.-C. L. acknowledges support from the Vannevar Bush Faculty Fellowship program sponsored by the Basic Research Office of the Assistant Secretary of Defense for Research and Engineering and funded by the Office of Naval Research through Grant No. N00014-16-1-2828. Y.-Z. S. and S.-Y. L. contributed equally to this work.Peer reviewedPublisher PD

Source Mechanism and Rupture Directivity of the 18 May 2009 M_W 4.6 Inglewood, California, Earthquake

On 18 May 2009, an M_w 4.6 earthquake occurred beneath Inglewood, California, and was widely felt. Though source mechanism and its location suggest that the Newport–Inglewood fault (NIF) may be involved in generating the earthquake, rupture directivity must be modeled to establish the connection between the fault and the earthquake. We first invert for the event’s source mechanism and depth with the cut-and-paste method in the long-period band (>5 s). Because of the low velocity shallow sediments in the Los Angeles (LA) basin, we use two velocity models in the inversion for stations inside and outside the LA basin. However, little difference is observed in the resolved source mechanism (M_w 4.6, strike 246°/145°, dip 50°/77°, rake 17°/138°) and depth (7 to ~9 km), compared to an inversion using the standard southern Calfornia model. With the resolved source parameters, we calibrate the amplitude anomaly of the short-period (0.5–2 Hz) P waves with amplitude adjustment factors (AAF). These AAFs are used as corrections when retrieving source mechanisms of the smaller aftershocks using short-period P waves alone. Most of the aftershocks show similar source mechanisms as that of the mainshock, providing ideal empirical Green’s functions (EGFs) for studying its rupture process. We use a forward modeling approach to retrieve rupture directivity of the mainshock, consistent with movement on the NIF with rupture toward the southeast. Although we focus on P waves for analyzing rupture directivity, the resolved unilateral pattern is also confirmed with the azimuthal variation of the duration of SH waves observed in the basin. The high rupture velocity near the shear velocity and relatively low stress drop are consistent with the hypothesis of rupture on a mature fault

Surface polaritons in two-dimensional left-handed photonic crystals

Using an extended plane-wave-based transfer-matrix method, the photonic band structures and the corresponding transmission spectrum of a two-dimensional left-handed photonic crystal are calculated. Comparisons between the periodic structure with a single left-handed cylindric rod are made, and many interesting similarities are found. It is shown that, due to the localized surface polaritons presented by an isolated left-handed rod, there exist many exciting physical phenomena in high-dimensional left-handed photonic crystals. As direct results of coupling of the localized surface polaritons of neighboring left-handed rod, a lot of almost dispersionless bands, anti-crossing behavior, and a zero $\bar{n}$ gap are exhibited in the left-handed periodic structure. Moreover, in a certain frequency region, except distorted by a lot of anti-crossing behavior, there exists a continual dispersion relation, which can be explained by the long-wavelength approximation. It is also pointed out that high-dimensional left-handed photonic crystals can be used to design narrow-band filter.Comment: sign errors in equation

Design of a zinc finger protein binding a sequence upstream of the A20 gene

<p>Abstract</p> <p>Background</p> <p>Artificial transcription factors (ATFs) are composed of DNA-binding and functional domains. These domains can be fused together to create proteins that can bind a chosen DNA sequence. To construct a valid ATF, it is necessary to design suitable DNA-binding and functional domains. The Cys₂-His₂zinc finger motif is the ideal structural scaffold on which to construct a sequence-specific protein. A20 is a cytoplasmic zinc finger protein that inhibits nuclear factor kappa-B activity and tumor necrosis factor (TNF)-mediated programmed cell death. A20 has been shown to prevent TNF-induced cytotoxicity in a variety of cell types including fibroblasts, B lymphocytes, WEHI 164 cells, NIH 3T3 cells and endothelial cells.</p> <p>Results</p> <p>In order to design a zinc finger protein (ZFP) structural domain that binds specific target sequences in the A20 gene promoter region, the structure and sequence composition of this promoter were analyzed by bioinformatics methods. The target sequences in the A20 promoter were submitted to the on-line ZF Tools server of the Barbas Laboratory, Scripps Research Institute (TSRI), to obtain a specific 18 bp target sequence and also the amino acid sequence of a ZFP that would bind to it. Sequence characterization and structural modeling of the predicted ZFP were performed by bioinformatics methods. The optimized DNA sequence of this artificial ZFP was recombined into the eukaryotic expression vector pIRES2-EGFP to construct pIRES2-EGFP/ZFP-flag recombinants, and the expression and biological activity of the ZFP were analyzed by RT-PCR, western blotting and EMSA, respectively. The ZFP was designed successfully and exhibited biological activity.</p> <p>Conclusion</p> <p>It is feasible to design specific zinc finger proteins by bioinformatics methods.</p

Upregulation of Endogenous HMOX1 Expression by a Computer-Designed Artificial Transcription Factor

Heme oxygenase-1 (HO-1) is well known as a cytoprotective factor. Research has revealed that it is a promising therapeutic target for cardiovascular diseases. In the current study, an HMOX1 (HO-1 gene) enhancer-specific artificial zinc-finger protein (AZP) was designed using bioinformatical methods. Then, an artificial transcription factor (ATF) was constructed based on the AZP. In the ATF, the p65 functional domain was used as the effector domain (ED), and a nuclear localization sequence (NLS) was also included. We next analyzed the affinity of the ATF to the HMOX1 enhancer and the effect of the ATF on endogenous HMOX1 expression. The results suggest that the ATF could effectively upregulate endogenous HMOX1 expression in ECV304 cells. With further research, the ATF could be developed as a potential drug for cardiovascular diseases