Peidong Yang

Bio: Peidong Yang is an academic researcher from University of California, Berkeley. The author has contributed to research in topics: Nanowire & Perovskite (structure). The author has an hindex of 183, co-authored 562 publications receiving 144351 citations. Previous affiliations of Peidong Yang include Max Planck Society & University of California, Santa Barbara.

Precise, Fast and Comprehensive Analysis of Intact Glycopeptides and Monosaccharide-Modifications with pGlyco3

Abstract: We presented a glycan-first glycopeptide search engine, pGlyco3, to comprehensively analyze intact N- and O-glycopeptides, including glycopeptides with monosaccharide-modifications. We developed an algorithm, termed pGlycoSite, to localize the glycosylation sites and estimate the localization probabilities. We designed a number of experiments to validate the accuracy of pGlyco3 as well as other frequently used or recently developed software tools. These experiments showed that pGlyco3 outperformed the other tools on both N- and O-glycopeptide identification accuracy especially at the glycan level, without loss of the sensitivity. pGlyco3 also achieved a superior performance in terms of search speed. As pGlyco3 was shown to be accurate and flexible for glycopeptide search with monosaccharide-modifications, we then discovered a monosaccharide-modification of Hex (or an uncommon monosaccharide) "Hex+17.027 Da" on both O-mannose and N-glycopeptides in yeast samples, and confirmed this monosaccharide based on released N-glycans and isotopic labelling data. pGlyco3 is freely available on https://github.com/pFindStudio/pGlyco3/releases.

Photosynthetic biohybrid coculture for tandem and tunable CO2 and N2 fixation

Abstract: Significance Combining (photo)electrochemical platforms with CO2 -fixing bacteria as “living” biocatalysts has realized the highly selective reduction of CO2 to C2+ products, such as acetate. This approach also enables the downstream conversion of the initial CO2 product to a higher-value one. We report an advance on this concept by coculturing primary CO2-fixing bacteria producing acetate with secondary N2-fixing bacteria that employ the acetate to reduce N2 to NH3 and to generate a bioplastic. The symbiotic coculture can be controlled electrochemically and modularly tuned to generate a desired product stream. We foresee that this platform could be expanded to produce several additional products, including bioplastics, biofuels, and sugars, from only CO2, N2, H2O, and electricity.

Enhancing Biohybrid CO2 to Multicarbon Reduction via Adapted Whole-Cell Catalysts.

Abstract: Catalytic CO2 conversion to renewable fuel is of utmost importance to establish a carbon-neutral society. Bioelectrochemical CO2 reduction, in which a solid cathode interfaces with CO2-reducing bacteria, represents a promising approach for renewable and sustainable fuel production. The rational design of biocatalysts in the biohybrid system is imperative to effectively reduce CO2 into valuable chemicals. Here, we introduce methanol adapted Sporomusa ovata (S. ovata) to enhance the slow metabolic activity of wild-type microorganisms to our semiconductive silicon nanowires (Si NWs) array for efficient CO2 reduction. The adapted whole-cell catalysts enable an enhancement of CO2 fixation with a superior faradaic efficiency on the poised Si NWs cathode. The synergy of the high-surface-area cathode and the adapted strain achieves a CO2-reducing current density of 0.88 ± 0.11 mA/cm2, which is 2.4-fold higher than the wild-type strain. This new generation of biohybrids using adapted S. ovata also decreases the charge transfer resistance at the cathodic interface and facilitates the faster charge transfer from the solid electrode to bacteria.

Gallium nitride nanowires with a metal initiated metal‐organic chemical vapor deposition (MOCVD) approach [phys. stat. sol. (b) 241, 2775 (2004)]

Abstract: The authors add a missing reference to the article published in phys. stat. sol. (b) 241, 2775 (2004), referring to one of their own earlier papers in Nano Lett. 3, 1063 (2003). (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)

Fast parallel algorithms for short-range molecular dynamics

Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

Electronics and optoelectronics of two-dimensional transition metal dichalcogenides.

Abstract: Single-layer metal dichalcogenides are two-dimensional semiconductors that present strong potential for electronic and sensing applications complementary to that of graphene.

A comprehensive review of zno materials and devices

Abstract: The semiconductor ZnO has gained substantial interest in the research community in part because of its large exciton binding energy (60meV) which could lead to lasing action based on exciton recombination even above room temperature. Even though research focusing on ZnO goes back many decades, the renewed interest is fueled by availability of high-quality substrates and reports of p-type conduction and ferromagnetic behavior when doped with transitions metals, both of which remain controversial. It is this renewed interest in ZnO which forms the basis of this review. As mentioned already, ZnO is not new to the semiconductor field, with studies of its lattice parameter dating back to 1935 by Bunn [Proc. Phys. Soc. London 47, 836 (1935)], studies of its vibrational properties with Raman scattering in 1966 by Damen et al. [Phys. Rev. 142, 570 (1966)], detailed optical studies in 1954 by Mollwo [Z. Angew. Phys. 6, 257 (1954)], and its growth by chemical-vapor transport in 1970 by Galli and Coker [Appl. Phys. ...