Minimum RMS from X-ray structures for three different algorithms.

<p>CSJD and CCD results were obtained from Table 1 and Table 2 of ref <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000478#pcbi.1000478-Coutsias1" target="_blank">[41]</a> and ref <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000478#pcbi.1000478-Canutescu1" target="_blank">[40]</a>, respectively. As in CCD, 5,000 trials were performed for each test loop in our SOS calculations. However, the majority of minimum RMSD's were reached within the first 3,000 trials. All the results reported here came from a single run per loop, using the same random seed. Some of these values can be improved if a different seed is chosen.</p

Minimum RMSD of the 5,000 conformers generated for each loop from their respective X-ray structures.

<p>The three series represent three independent SOS runs, each starting from a different random number seed and resulting in a different set of 5,000 conformers. The results are presented in 3 different panels for clarity. (A) 4-residue loops; (B) 8-residue loops; (C) 12-residue loops.</p

Decomposition of a 4-residue loop into a set of rigid fragments.

<p>The green, blue and red balls represent the carbon, nitrogen, and oxygen atoms, respectively. The gray area corresponds to the fixed part of the protein where the loop is anchored. The protein loop backbone can be decomposed into a series of alternating amide (in blue rectangular boxes) and methylene groups (in red elliptical boxes). The two structures on the right hand side are the corresponding reference templates with their attached atoms.</p

Electrically Controlled Scattering in a Hybrid Dielectric-Plasmonic Nanoantenna

Electrically tunable devices in nanophotonics offer an exciting opportunity to combine electrical and optical functions, opening up their applications in active photonic devices. Silicon as a kind of high refractive index dielectric material has shown comparable performances with plasmonic nanostructures in tailoring and modulating the electromagnetic waves. However, there are few studies on electrically tunable silicon nanoantennas. Here, for the first time we realize the spectral tailoring of an individual silicon nanoparticle in the visible range through changing the applied voltage. We observe that the plasmon-dielectric hybrid resonant peaks experience blue shift and obvious intensity attenuation with increasing the bias voltages from 0 to 1.5 V. A physical model has been established to explain how the applied voltage influences the carrier concentration and how carrier concentration modifies the permittivity of silicon and then the final scattering spectra. Our findings pave a new approach to build excellent tunable nanoantennas or other nanophotonics devices where the optical responses can be purposely controlled by electrical signals

Representative snapshots of the conformation generation process for an 8-residue loop.

<p>Starting from a completely random conformation (step 0), the SOS algorithm drives the atoms in the vicinity of their ideal locations within only 5 steps. At the end of step 20, the conformation has only one steric clash, as highlighted by the red ellipse. This clash is gradually resolved within 10 additional steps. The simulation continues until it converges at step 144. By relaxing our rather stringent convergence criteria, significant speedup can be achieved without a significant impact on the quality of the resulting conformation.</p

Histogram of the root mean square deviations of bond lengths and angles.

<p>The histograms are generated from all conformations for a given loop size. (A) Bond lengths, and (B) bond angles.</p

Midrefractive Dielectric Modulator for Broadband Unidirectional Scattering and Effective Radiative Tailoring in the Visible Region

Nanoantennas have found many applications in ultrasmall sensors, single-molecule detection, and all-optical communication. Conventional nanoantennas are based on noble-metal plasmonic structures, but suffer from large ohmic loss and only possess dipolar plasmon modes. This has driven an intense search for all-dielectric materials beyond noble metals. Here, we propose midrefractive nanospheres as a novel all-dielectric material to realize broadband unidirectional radiation and effective radiative tailoring in the visible region. Midrefractive all-dielectric materials such as boron nanospheres possess broad and overlapping electric and magnetic dipole modes. The internal interaction between these two modes can route the radiation almost on the one side covering the whole visible range. Unlike the elaborate design in plasmonic nanostructures to obtain strong coupled broad and narrow modes, the bright mode in boron nanospheres is intrinsic, independent, and easily coupled with adjacent narrow modes. So the strong interaction in boron-based heterodimer is able to realize an independent and precise tailoring of the radiant and subradiant states by simply changing the particle sizes, respectively. Our findings imply midrefractivity materials like boron are excellent building blocks to support electromagnetic coupling operation in nanoscale devices, which will lead to a variety of emerging applications such as nanoantennas with directing exciton emission, ultrasensitive nanosensors, or even potential new construction of photonic metamaterials

Additional file 2: Table S2. of Comparative transcriptional profiling of orange fruit in response to the biocontrol yeast Kloeckera apiculata and its active compounds

List and MapMan analysis of differentially expressed genes in citrus in response to K. apiculata, the extract and phenylethanol, respectively. (XLS 264 kb

Efficient and Rapid Hydrogen Extraction from Ammonia–Water <i>via</i> Laser Under Ambient Conditions without Catalyst

As a good carrier of hydrogen, ammonia–water has been employed to extract hydrogen in many ways. Here, we demonstrate a simple, green, ultrafast, and highly efficient method for hydrogen extraction from ammonia–water by laser bubbling in liquids (LBL) at room temperature and ambient pressure without catalyst. A maximum apparent yield of 33.7 mmol/h and a real yield of 93.6 mol/h were realized in a small operating space, which were far higher than the yields of most hydrogen evolution reactions from ammonia–water under ambient conditions. We also established that laser-induced cavitation bubbles generated a transient high temperature, which enabled a very suitable environment for hydrogen extraction from ammonia–water. The laser used here can serve as a demonstration of potentially solar-pumped catalyst-free hydrogen extraction and other chemical synthesis. We anticipate that the LBL technique will open unprecedented opportunities to produce chemicals