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Li, Yongfeng

Publications and source records attributed to Li, Yongfeng.

10 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Mathematical Model of ATM Activation and Chromatin Relaxation by Ionizing Radiation

We propose a comprehensive mathematical model to study the dynamics of ionizing radiation induced Ataxia-telangiectasia mutated (ATM) activation that consists of ATM activation through dual mechanisms: the initiative activation pathway triggered by the DNA damage-induced local chromatin relaxation and the primary activation pathway consisting of a self-activation loop by interplay with chromatin relaxation. The model is expressed as a series of biochemical reactions, governed by a system of differential equations and analyzed by dynamical systems techniques. Radiation induced double strand breaks (DSBs) cause rapid local chromatin relaxation, which is independent of ATM but initiates ATM activation at damage sites. Key to the model description is how chromatin relaxation follows when active ATM phosphorylates KAP-1, which subsequently spreads throughout the chromatin and induces global chromatin relaxation. Additionally, the model describes how oxidative stress activation of ATM triggers a self-activation loop in which PP2A and ATF2 are released so that ATM can undergo autophosphorylation and acetylation for full activation in relaxed chromatin. In contrast, oxidative stress alone can partially activate ATM because phosphorylated ATM remains as a dimer. The model leads to predictions on ATM mediated responses to DSBs, oxidative stress, or both that can be tested by experiments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Synthesis and characterization of noble metal borides: RuB{sub x}(x > 1)

Highlights: • Hexagonal RuB{sub 1.1} were synthesized using ruthenium and boron powders as raw materials during ball milling process. • Orthorhombic RuB{sub 2} were synthesized under high pressure (5 GPa) and high temperature (1000 °C) conditions. • Hexagonal Ru{sub 2}B{sub 3} have been synthesized under 5 GPa and 1200 °C. - Abstract: Noble metal borides RuB{sub 1.1}, RuB{sub 2} and Ru{sub 2}B{sub 3} have been synthesized by mechanical alloying and high pressure sintering methods using ruthenium (Ru) and boron (B) powders as raw materials. The crystal structures of borides were characterized by X-ray diffraction (XRD) and scanning electron microscopy (SEM). The results shown that only RuB{sub 1.1} with hexagonal crystal structure was synthesized during the ball milling process, the orthorhombic RuB{sub 2} was synthesized under high pressure (5 GPa) and high temperature (1000 °C) conditions, while the hexagonal Ru{sub 2}B{sub 3} can be synthesized under 5 GPa and 1200 °C. The mechanism of synthesis for the ruthenium borides (RuB{sub x}) are discussed in details.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Wideband radar cross section reduction using two-dimensional phase gradient metasurfaces

Phase gradient metasurface (PGMs) are artificial surfaces that can provide pre-defined in-plane wave-vectors to manipulate the directions of refracted/reflected waves. In this Letter, we propose to achieve wideband radar cross section (RCS) reduction using two-dimensional (2D) PGMs. A 2D PGM was designed using a square combination of 49 split-ring sub-unit cells. The PGM can provide additional wave-vectors along the two in-plane directions simultaneously, leading to either surface wave conversion, deflected reflection, or diffuse reflection. Both the simulation and experiment results verified the wide-band, polarization-independent, high-efficiency RCS reduction induced by the 2D PGM.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2014

Modeling Damage Complexity-Dependent Non-Homologous End-Joining Repair Pathway

Non-homologous end joining (NHEJ) is the dominant DNA double strand break (DSB) repair pathway and involves several repair proteins such as Ku, DNA-PKcs, and XRCC4. It has been experimentally shown that the choice of NHEJ proteins is determined by the complexity of DSB. In this paper, we built a mathematical model, based on published data, to study how NHEJ depends on the damage complexity. Under an appropriate set of parameters obtained by minimization technique, we can simulate the kinetics of foci track formation in fluorescently tagged mammalian cells, Ku80-EGFP and DNA-PKcs-YFP for simple and complex DSB repair, respectively, in good agreement with the published experimental data, supporting the notion that simple DSB undergo fast repair in a Ku-dependent, DNA-PKcs-independent manner, while complex DSB repair requires additional DNA-PKcs for end processing, resulting in its slow repair, additionally resulting in slower release rate of Ku and the joining rate of complex DNA ends. Based on the numerous experimental descriptions, we investigated several models to describe the kinetics for complex DSB repair. An important prediction of our model is that the rejoining of complex DSBs is through a process of synapsis formation, similar to a second order reaction between ends, rather than first order break filling/joining. The synapsis formation (SF) model allows for diffusion of ends before the synapsis formation, which is precluded in the first order model by the rapid coupling of ends. Therefore, the SF model also predicts the higher number of chromosomal aberrations observed with high linear energy transfer (LET) radiation due to the higher proportion of complex DSBs compared to low LET radiation, and an increased probability of misrejoin following diffusion before the synapsis is formed, while the first order model does not provide a mechanism for the increased effectiveness in chromosomal aberrations observed.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2013

Modeling Non-homologous End Joining

Non-homologous end joining (NHEJ) is the dominant DNA double strand break (DSB) repair pathway and involves several NHEJ proteins such as Ku, DNA-PKcs, XRCC4, Ligase IV and so on. Once DSBs are generated, Ku is first recruited to the DNA end, followed by other NHEJ proteins for DNA end processing and ligation. Because of the direct ligation of break ends without the need for a homologous template, NHEJ turns out to be an error-prone but efficient repair pathway. Some mechanisms have been proposed of how the efficiency of NHEJ repair is affected. The type of DNA damage is an important factor of NHEJ repair. For instance, the length of DNA fragment may determine the recruitment efficiency of NHEJ protein such as Ku [1], or the complexity of the DNA breaks [2] is accounted for the choice of NHEJ proteins and subpathway of NHEJ repair. On the other hand, the chromatin structure also plays a role of the accessibility of NHEJ protein to the DNA damage site. In this talk, some mathematical models of NHEJ, that consist of series of biochemical reactions complying with the laws of chemical reaction (e.g. mass action, etc.), will be introduced. By mathematical and numerical analysis and parameter estimation, the models are able to capture the qualitative biological features and show good agreement with experimental data. As conclusions, from the viewpoint of modeling, how the NHEJ proteins are recruited will be first discussed for connection between the classical sequential model [4] and recently proposed two-phase model [5]. Then how the NHEJ repair pathway is affected, by the length of DNA fragment [6], the complexity of DNA damage [7] and the chromatin structure [8], will be addressed

Li, Yongfeng↗
NASA NTRS2013

NASA Human Research Program Space Radiation Program Element

The goal of the NASA Human Research Program's Space Radiation Program Element is to ensure that crews can safely live and work in the space radiation environment. Current work is focused on developing the knowledge base and tools required for accurate assessment of health risks resulting from space radiation exposure including cancer and circulatory and central nervous system diseases, as well as acute risks from solar particle events. Division of Space Life Sciences (DSLS) Space Radiation Team scientists work at multiple levels to advance this goal, with major projects in biological risk research; epidemiology; and physical, biophysical, and biological modeling.

Chappell, Lori↗
DOE OSTI2013

Conversion mechanism of conductivity of phosphorus-doped ZnO films induced by post-annealing

The effects of post-annealing on conductivity of phosphorus-doped ZnO (PZO) films grown at 500 Degree-Sign C by radio frequency magnetron sputtering are investigated in a temperature ranging from 600 Degree-Sign C to 900 Degree-Sign C. The as-grown PZO exhibits n-type conductivity with an electron concentration of 1.19 Multiplication-Sign 10{sup 20} cm{sup -3}, and keeps n-type conductivity as annealed at 600 Degree-Sign C-700 Degree-Sign C but electron concentration decreases with increasing temperature. However, it converts to p-type conductivity as annealed at 800 Degree-Sign C. Further increasing temperature, it still shows p-type conductivity but the hole concentration decreases. It is found that the P occupies mainly Zn site (P{sub Zn}) in the as-grown PZO, which accounts for good n-type conductivity of the as-grown PZO. The amount of the P{sub Zn} decreases with increasing temperature, while the amount of Zn vacancy (V{sub Zn}) increases from 600 Degree-Sign C to 800 Degree-Sign C but decreases greatly at 900 Degree-Sign C, resulting in that the amount of P{sub Zn}-2V{sub Zn} complex increases with increasing temperature up to 800 Degree-Sign C but decreases above 800 Degree-Sign C. It is suggested that the P{sub Zn}-2V{sub Zn} complex acceptor is responsible for p-type conductivity, and that the conversion of conductivity is due to the change of the amount of the P{sub Zn} and P{sub Zn}-2V{sub Zn} with annealing temperature.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2012

The Structural Basis for Tight Control of PP2A Methylation and Function by LCMT-1

Proper formation of protein phosphatase 2A (PP2A) holoenzymes is essential for the fitness of all eukaryotic cells. Carboxyl methylation of the PP2A catalytic subunit plays a critical role in regulating holoenzyme assembly; methylation is catalyzed by PP2A-specific methyltransferase LCMT-1, an enzyme required for cell survival. We determined crystal structures of human LCMT-1 in isolation and in complex with PP2A stabilized by a cofactor mimic. The structures show that the LCMT-1 active-site pocket recognizes the carboxyl terminus of PP2A, and, interestingly, the PP2A active site makes extensive contacts to LCMT-1. We demonstrated that activation of the PP2A active site stimulates methylation, suggesting a mechanism for efficient conversion of activated PP2A into substrate-specific holoenzymes, thus minimizing unregulated phosphatase activity or formation of inactive holoenzymes. A dominant-negative LCMT-1 mutant attenuates the cell cycle without causing cell death, likely by inhibiting uncontrolled phosphatase activity. Our studies suggested mechanisms of LCMT-1 in tight control of PP2A function, important for the cell cycle and cell survival.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2011

Modularized TGFbeta-Smad Signaling Pathway

The Transforming Growth Factor beta (TGFbeta) signaling pathway is a prominent regulatory signaling pathway controlling various important cellular processes. It can be induced by several factors, including ionizing radiation. It is regulated by Smads in a negative feedback loop through promoting increases in the regulatory Smads in the cell nucleus, and subsequent expression of inhibitory Smad, Smad7 to form a ubiquitin ligase with Smurf targeting active TGF receptors for degradation. In this work, we proposed a mathematical model to study the radiation-induced Smad-regulated TGF signaling pathway. By modularization, we are able to analyze each module (subsystem) and recover the nonlinear dynamics of the entire network system. Meanwhile the excitability, a common feature observed in the biological systems, along the TGF signaling pathway is discussed by mathematical analysis and numerical simulation.

Li, Yongfeng↗