Browsing by Author "Yang, Yang"
Results Per Page
Sort Options
Item Open Access Gallium plasmonics: deep subwavelength spectroscopic imaging of single and interacting gallium nanoparticles.(ACS Nano, 2015-02-24) Knight, Mark W; Coenen, Toon; Yang, Yang; Brenny, Benjamin JM; Losurdo, Maria; Brown, April S; Everitt, Henry O; Polman, AlbertGallium has recently been demonstrated as a phase-change plasmonic material offering UV tunability, facile synthesis, and a remarkable stability due to its thin, self-terminating native oxide. However, the dense irregular nanoparticle (NP) ensembles fabricated by molecular-beam epitaxy make optical measurements of individual particles challenging. Here we employ hyperspectral cathodoluminescence (CL) microscopy to characterize the response of single Ga NPs of various sizes within an irregular ensemble by spatially and spectrally resolving both in-plane and out-of-plane plasmonic modes. These modes, which include hybridized dipolar and higher-order terms due to phase retardation and substrate interactions, are correlated with finite difference time domain (FDTD) electrodynamics calculations that consider the Ga NP contact angle, substrate, and native Ga/Si surface oxidation. This study experimentally confirms previous theoretical predictions of plasmonic size-tunability in single Ga NPs and demonstrates that the plasmonic modes of interacting Ga nanoparticles can hybridize to produce strong hot spots in the ultraviolet. The controlled, robust UV plasmonic resonances of gallium nanoparticles are applicable to energy- and phase-specific applications such as optical memory, environmental remediation, and simultaneous fluorescence and surface-enhanced Raman spectroscopies.Item Open Access Gallium-based Ultraviolet Nanoplasmonics(2013) Yang, YangNanometer-scale metallic structures have been widely and intensively studied over the last decade because of their remarkable plasmonic properties that can enhance local electromagnetic (EM) fields. However, most plasmonic applications are restricted to the visible and near infrared photon energies due to the limitations of the surface plasmon resonance energies of the most commonly used plasmonic metals: Au and Ag. Plasmonic applications in ultraviolet (UV) are of great interest because Raman scattering sections are larger and do not overlap fluorescence spectra. UV plasmonics also benefit from high spatial resolution and low penetration depth. However, an appropriate UV plasmonic material must be identified.
We proposed and demonstrated that gallium is a highly-promising and compelling material for UV nanoplasmonics through synthesis of size-controlled nanoparticle arrays, EM modeling of local field enhancement, ellipsometric and spatial characterization of the arrays, and analytical measurement of UV- enhanced Raman and fluorescence spectra. Self-assembled arrays of hemispherical gallium nanoparticles deposited by molecular beam epitaxy on a sapphire support are characterized with spatial and ellipsometric measurements. Spin-casting a thin film of crystal violet upon these nanoparticles permitted the demonstration of surface-enhanced Raman spectra, fluorescence, and molecular photodegradation following excitation by a HeCd laser operating at 325 nm (UV). Measured local Raman enhancement factors exceeding 107 demonstrated the potential of gallium nanoparticle arrays for plasmonically-enhanced ultraviolet detection and remediation.
Item Open Access Ground and Electronic Excited States from Pairing Matrix Fluctuation and Particle-Particle Random Phase Approximation(2016) Yang, YangThe accurate description of ground and electronic excited states is an important and challenging topic in quantum chemistry. The pairing matrix fluctuation, as a counterpart of the density fluctuation, is applied to this topic. From the pairing matrix fluctuation, the exact electron correlation energy as well as two electron addition/removal energies can be extracted. Therefore, both ground state and excited states energies can be obtained and they are in principle exact with a complete knowledge of the pairing matrix fluctuation. In practice, considering the exact pairing matrix fluctuation is unknown, we adopt its simple approximation --- the particle-particle random phase approximation (pp-RPA) --- for ground and excited states calculations. The algorithms for accelerating the pp-RPA calculation, including spin separation, spin adaptation, as well as an iterative Davidson method, are developed. For ground states correlation descriptions, the results obtained from pp-RPA are usually comparable to and can be more accurate than those from traditional particle-hole random phase approximation (ph-RPA). For excited states, the pp-RPA is able to describe double, Rydberg, and charge transfer excitations, which are challenging for conventional time-dependent density functional theory (TDDFT). Although the pp-RPA intrinsically cannot describe those excitations excited from the orbitals below the highest occupied molecular orbital (HOMO), its performances on those single excitations that can be captured are comparable to TDDFT. The pp-RPA for excitation calculation is further applied to challenging diradical problems and is used to unveil the nature of the ground and electronic excited states of higher acenes. The pp-RPA and the corresponding Tamm-Dancoff approximation (pp-TDA) are also applied to conical intersections, an important concept in nonadiabatic dynamics. Their good description of the double-cone feature of conical intersections is in sharp contrast to the failure of TDDFT. All in all, the pairing matrix fluctuation opens up new channel of thinking for quantum chemistry, and the pp-RPA is a promising method in describing ground and electronic excited states.
Item Open Access PCNA-binding activity separates RNF168 functions in DNA replication and DNA double-stranded break signaling.(Nucleic acids research, 2024-10) Yang, Yang; Jayaprakash, Deepika; Jhujh, Satpal S; Reynolds, John J; Chen, Steve; Gao, Yanzhe; Anand, Jay Ramanlal; Mutter-Rottmayer, Elizabeth; Ariel, Pablo; An, Jing; Cheng, Xing; Pearce, Kenneth H; Blanchet, Sophie-Anne; Nandakumar, Nandana; Zhou, Pei; Fradet-Turcotte, Amélie; Stewart, Grant S; Vaziri, CyrusRNF168 orchestrates a ubiquitin-dependent DNA damage response to regulate the recruitment of repair factors, such as 53BP1 to DNA double-strand breaks (DSBs). In addition to its canonical functions in DSB signaling, RNF168 may facilitate DNA replication fork progression. However, the precise role of RNF168 in DNA replication remains unclear. Here, we demonstrate that RNF168 is recruited to DNA replication factories in a manner that is independent of the canonical DSB response pathway regulated by Ataxia-Telangiectasia Mutated (ATM) and RNF8. We identify a degenerate Proliferating Cell Nuclear Antigen (PCNA)-interacting peptide (DPIP) motif in the C-terminus of RNF168, which together with its Motif Interacting with Ubiquitin (MIU) domain mediates binding to mono-ubiquitylated PCNA at replication factories. An RNF168 mutant harboring inactivating substitutions in its DPIP box and MIU1 domain (termed RNF168 ΔDPIP/ΔMIU1) is not recruited to sites of DNA synthesis and fails to support ongoing DNA replication. Notably, the PCNA interaction-deficient RNF168 ΔDPIP/ΔMIU1 mutant fully rescues the ability of RNF168-/- cells to form 53BP1 foci in response to DNA DSBs. Therefore, RNF168 functions in DNA replication and DSB signaling are fully separable. Our results define a new mechanism by which RNF168 promotes DNA replication independently of its canonical functions in DSB signaling.Item Open Access Rad18 confers hematopoietic progenitor cell DNA damage tolerance independently of the Fanconi Anemia pathway in vivo.(Nucleic Acids Res, 2016-05-19) Yang, Yang; Poe, Jonathan C; Yang, Lisong; Fedoriw, Andrew; Desai, Siddhi; Magnuson, Terry; Li, Zhiguo; Fedoriw, Yuri; Araki, Kimi; Gao, Yanzhe; Tateishi, Satoshi; Sarantopoulos, Stefanie; Vaziri, CyrusIn cultured cancer cells the E3 ubiquitin ligase Rad18 activates Trans-Lesion Synthesis (TLS) and the Fanconi Anemia (FA) pathway. However, physiological roles of Rad18 in DNA damage tolerance and carcinogenesis are unknown and were investigated here. Primary hematopoietic stem and progenitor cells (HSPC) co-expressed RAD18 and FANCD2 proteins, potentially consistent with a role for Rad18 in FA pathway function during hematopoiesis. However, hematopoietic defects typically associated with fanc-deficiency (decreased HSPC numbers, reduced engraftment potential of HSPC, and Mitomycin C (MMC) -sensitive hematopoiesis), were absent in Rad18(-/-) mice. Moreover, primary Rad18(-/-) mouse embryonic fibroblasts (MEF) retained robust Fancd2 mono-ubiquitination following MMC treatment. Therefore, Rad18 is dispensable for FA pathway activation in untransformed cells and the Rad18 and FA pathways are separable in hematopoietic cells. In contrast with responses to crosslinking agents, Rad18(-/-) HSPC were sensitive to in vivo treatment with the myelosuppressive agent 7,12 Dimethylbenz[a]anthracene (DMBA). Rad18-deficient fibroblasts aberrantly accumulated DNA damage markers after DMBA treatment. Moreover, in vivo DMBA treatment led to increased incidence of B cell malignancy in Rad18(-/-) mice. These results identify novel hematopoietic functions for Rad18 and provide the first demonstration that Rad18 confers DNA damage tolerance and tumor-suppression in a physiological setting.