Engineering Papers⌕ Search

Engineering topics

Zhang, Zeyu

Publications and source records attributed to Zhang, Zeyu.

Pinoresinol rescues developmental phenotypes of Arabidopsis phenylpropanoid mutants overexpressing FERULATE 5-HYDROXYLASE

Most phenylpropanoid pathway flux is directed toward the production of monolignols, but this pathway also generates multiple bioactive metabolites. The monolignols coniferyl and sinapyl alcohol polymerize to form guaiacyl (G) and syringyl (S) units in lignin, components that are characteristic of plant secondary cell walls. Lignin negatively impacts the saccharification potential of lignocellulosic biomass. Although manipulation of its content and composition through genetic engineering has reduced biomass recalcitrance, in some cases, these genetic manipulations lead to impaired growth. Here, the reduced-growth phenotype is often attributed to poor water transport due to xylem collapse in low-lignin mutants, but alternative models suggest that it could be caused by the hyper- or hypoaccumulation of phenylpropanoid intermediates. In Arabidopsis thaliana, overexpression of FERULATE 5-HYDROXYLASE (F5H) shifts the normal G/S lignin ratio to nearly pure S lignin and does not result in substantial changes to plant growth. In contrast, when we overexpressed F5H in the low-lignin mutants cinnamyl dehydrogenase c and d (cadc cadd), cinnamoyl-CoA reductase 1, and reduced epidermal fluorescence 3, plant growth was severely compromised. In addition, cadc cadd plants overexpressing F5H exhibited defects in lateral root development. Exogenous coniferyl alcohol (CA) and its dimeric coupling product, pinoresinol, rescue these phenotypes. These data suggest that mutations in the phenylpropanoid pathway limit the biosynthesis of pinoresinol, and this effect is exacerbated by overexpression of F5H, which further draws down cellular pools of its precursor, CA. Overall, these genetic manipulations appear to restrict the synthesis of pinoresinol or a downstream metabolite that is necessary for plant growth.

59 BASIC BIOLOGICAL SCIENCES↗

Comparing Deep Learning Approaches for Understanding Genotype × Phenotype Interactions in Biomass Sorghum

We explore the use of deep convolutional neural networks (CNNs) trained on overhead imagery of biomass sorghum to ascertain the relationship between single nucleotide polymorphisms (SNPs), or groups of related SNPs, and the phenotypes they control. We consider both CNNs trained explicitly on the classification task of predicting whether an image shows a plant with a reference or alternate version of various SNPs as well as CNNs trained to create data-driven features based on learning features so that images from the same plot are more similar than images from different plots, and then using the features this network learns for genetic marker classification. We characterize how efficient both approaches are at predicting the presence or absence of a genetic markers, and visualize what parts of the images are most important for those predictions. We find that the data-driven approaches give somewhat higher prediction performance, but have visualizations that are harder to interpret; and we give suggestions of potential future machine learning research and discuss the possibilities of using this approach to uncover unknown genotype × phenotype relationships.

Zhang, Zeyu↗

Physics and applications of quantum dot lasers for silicon photonics

Abstract Photonic integrated circuits (PICs) have enabled numerous high performance, energy efficient, and compact technologies for optical communications, sensing, and metrology. One of the biggest challenges in scaling PICs comes from the parasitic reflections that feed light back into the laser source. These reflections increase noise and may cause laser destabilization. To avoid parasitic reflections, expensive and bulky optical isolators have been placed between the laser and the rest of the PIC leading to large increases in device footprint for on-chip integration schemes and significant increases in packaging complexity and cost for lasers co-packaged with passive PICs. This review article reports new findings on epitaxial quantum dot lasers on silicon and studies both theoretically and experimentally the connection between the material properties and the ultra-low reflection sensitivity that is achieved. Our results show that such quantum dot lasers on silicon exhibit much lower linewidth enhancement factors than any quantum well lasers. Together with the large damping factor, we show that the quantum dot gain medium is fundamentally dependent on dot uniformity, but through careful optimization, even epitaxial lasers on silicon can operate without an optical isolator, which is of paramount importance for the future high-speed silicon photonic systems.

36 MATERIALS SCIENCE↗

Multimode description of self-mode locking in a single-section quantum-dot laser

This paper describes a theory for mode locking and frequency comb generation by four-wave mixing in a semiconductor quantum-dot active medium. The derivation uses a multimode semiclassical laser theory that accounts for fast carrier collisions within an inhomogeneous distribution of quantum dots. Numerical simulations are presented to illustrate the role of active medium nonlinearities in mode competition, gain saturation, carrier-induced refractive index and creation of combination tones that lead to locking of beat frequencies among lasing modes in the presence of cavity material dispersion.

Chow, Weng W.↗

On quantum-dot lasing at gain peak with linewidth enhancement factor $α$ H = 0

This paper describes an investigation of the linewidth enhancement factor α H in a semiconductor quantum-dot laser. Results are presented for active region parameters and laser configurations important for minimizing α H . In particular, the feasibility of lasing at the gain peak with α H = 0 is explored. The study uses a many-body theory with dephasing effects from carrier scattering treated at the level of quantum-kinetic equations. InAs quantum-dot lasers with different p-modulation doping densities are fabricated and measured to verify the calculated criteria on laser cavity design and epitaxial growth conditions.

42 ENGINEERING↗