A simplified hollow-core microstructured fiber was fabricated and investigated. The diameter of the core is about 31 μm, and the thickness of the bridges t is about 280 nm. Three broad band transmission windows with relative low loss were measured in IR domain with the large bandwidth of ~600 nm. A Gaussian-shaped beam profile with visible pattern guided by the large core was observed in far field. The curvature behavior was also studied. This large core broad band transmission fiber offers a good medium for applications in high energy delivery, novel gas-cell based laser and sensing devices.
Using 300-fs 1039-nm Yb-doped fiber laser, we experimentally demonstrate blue light generation in a high-\Delta and high nonlinear photonic crystal fiber (PCF). The zero dispersion wavelength of PCF is 793 nm, detuning 245.8 nm from the pump wavelength. PCF allows a frequency conversion exceeding the octave of pump wavelength. The visible component of the measured output spectrum occurs in the fundamental mode and spans from 391.3 to 492.3 nm. The peak wavelength of 441.8 nm has a frequency detuning of 390 THz from the pump wavelength of 1039 nm.
<p>2019-nCoV has caused more than 560 deaths as of 6 February 2020 worldwide, mostly in China. Although there are no effective drugs approved, many clinical trials are incoming or ongoing in China which utilize traditional chinese medicine or modern medicine. Moreover, many groups are working on the cytopathic effect assay to fight against 2019-nCoV, which will result in compounds with good activity yet unknown targets. Identifying potential drug targets will be of great importance to understand the underlying mechanism of how the drug works. Here, we <a></a><a>compiled</a> the 3D structures of 17 2019-nCoV proteins and 3 related human proteins, which resulted in 208 binding pockets. Each submitted compound will be docked to these binding pockets by the docking software smina and the docking results will be presented in ascending order of compound-target interaction energy (kcal/mol). We hope the computational tool will shed some light on the potential drug target for the identified antivirals. D3Targets-2019-nCoV is available free of charge at https://www.d3pharma.com/D3Targets-2019-nCoV/D3Docking/index.php.</p>
Abstract Background: Knowledge of protein motions is significant to understand its functions. The currently available databases for protein motions, in general, are focused on overall domain motions, which pay little attention to local residue motions. Albeit with relatively small scale, the local residue motions may play crucial roles in protein functions and its binding with ligand, in particular for those residues within binding pockets. Results: A comprehensive protein motion database (D3PM) was constructed in this study to facilitate the analysis of protein motions. The D3PM has the motion information ranging from the overall structural changes of macromolecule to the local flip motion of the residues in ligand binding site. Currently, the D3PM has 5,339 entries of overall motions and 2,319 entries of pocket residues’ motions. The motion patterns in the database are classified into 4 types of overall structural change and 5 types of pocket residues’ shift. Impressively, it was found that less than 15% of the protein pairs have obvious overall conformational adaptations induced by ligand binding, while more than 50% of the protein pairs have significant structural changes in the ligand binding sites, indicating that ligand-induced conformational changes are drastic whereas they are mostly confined around the ligand. By the analysis of pocket residues’ preference, we classified amino acids into “pocketphilic” and “pocketphobic” residues, which is helpful to pocket prediction and ligand design. Conclusion: D3PM is a comprehenssive database about protein motions ranging from residue to domain, which should be useful for exploring diverse protein motions and for understanding protein functions. The database is freely available on www.d3pharma.com/D3PM/index.php.
2019-nCoV has caused more than 560 deaths as of 6 February 2020 worldwide, mostly in China. Although there are no effective drugs approved, many clinical trials are incoming or ongoing in China which utilize traditional chinese medicine or modern medicine. Moreover, many groups are working on the cytopathic effect assay to fight against 2019-nCoV, which will result in compounds with good activity yet unknown targets. Identifying potential drug targets will be of great importance to understand the underlying mechanism of how the drug works. Here, we compiled the 3D structures of 17 2019-nCoV proteins and 3 related human proteins, which resulted in 208 binding pockets. Each submitted compound will be docked to these binding pockets by the docking software smina and the docking results will be presented in ascending order of compound-target interaction energy (kcal/mol). We hope the computational tool will shed some light on the potential drug target for the identified antivirals. D3Targets-2019-nCoV is available free of charge at https://www.d3pharma.com/D3Targets-2019-nCoV/D3Docking/index.php.
We report a GeO2 doped triangular-core photonic crystal fiber which is allow the generation of a hollow beam supercontinuum ranging from 540 to 1540 nm through a nonlinear-optical transformation by femtosecond pulses at 1038 nm.
The spike protein of SARS-CoV-2 (SARS-CoV-2-S) helps the virus attach to and infect human cells. With various computational methods applied in this work, the accessibility of its RBD to ACE2, its key residues for stronger binding to ACE2 than the SARS-CoV spike (SARS-CoV-S), the origin of the stronger binding, and its potential sites for drug and antibody design were explored. It was found that the SARS-CoV-2-S could bind ACE2 with an RBD-angle ranging from 52.2º to 84.8º, which demonstrated that the RBD does not need to fully open to bind ACE2. Free energy calculation by an MM/GBSA approach not only revealed much stronger binding of SARS-CoV-2-S to ACE2 (Δ G =-21.7~-29.9 kcal/mol) than SARS-CoV-S (Δ G =-10.2~-16.4 kcal/mol) at different RBD-angles but also demonstrated that the binding becomes increasingly stronger as the RBD-angle increases. In comparison with the experimental results, the free energy decomposition disclosed more key residues interacting strongly with ACE2 than with the SARS-CoV-S, among which the Q493 might be the decisive residue variation (-5.84 kcal/mol) to the strong binding. With the mutation of all 18 different residues of SARS-CoV-S on the spike-ACE2 interface to the corresponding residues of SARS-CoV-2-S, it was found that the mutated SARS-CoV-S has almost the same binding affinity as SARS-CoV-2-S to ACE2, demonstrating that the remaining mutations outside the spike-ACE2 interface have little effect on its binding affinity to ACE2. Simulation of the conformational change pathway from “down” to “up” states disclosed 5 potential ligand-binding pockets correlated to the conformational change. Taking together the key residues, accessible RBD-angle and pocket correlation, potential sites for drug and antibody design were proposed, which should be helpful for interpreting the high infectiousness of SARS-CoV-2 and for developing a cure.
The SARS-CoV-2 has caused more than 2,000 deaths as of 20 February 2020 worldwide but there is no approved effective drug. The SARS-CoV-2 spike (S) glycoprotein is a key drug target due to its indispensable function for viral infection and fusion with ACE2 as a receptor. To facilitate the drug discovery and development with S protein as drug target, various computational techniques were used in this study to evaluate the binding mechanisms between S protein and its acceptor ACE2. Impressively, SARS-CoV-2 S protein has higher affinity binding to ACE2 at two different “up” angles of RBD than SARS-CoV S protein to ACE2 at the same angles. The energy decomposition analysis showed that more interactions formed between SARS-CoV-2 S protein and ACE2, which may partially account for its higher infectiousness than SARS-CoV. In addition, we found that 52.2° is a starting accessible “up” angle of the BRD of SARS-CoV-2 S protein to bind ACE2, demonstrating that BRD is not necessary to be fully opened in order to bind ACE2. We hope that this work will be helpful for the design of effective SARS-CoV-2 S protein inhibitors to address the ongoing public health crisis.
A photonic crystal fiber (PCF) with nanosize airholes in the core is designed for the blue extension of supercontinuum generation. Simulated results show an improvement of >60 nm comparing common PCF.
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