Engineering topics

Bi, Lei

Publications and source records attributed to Bi, Lei.

6 records

DOE OSTI2021

CRL4A DTL degrades DNA-PKcs to modulate NHEJ repair and induce genomic instability and subsequent malignant transformation

Genomic instability induced by DNA damage and improper DNA damage repair is one of the main causes of malignant transformation and tumorigenesis. DNA double strand breaks (DSBs) are the most detrimental form of DNA damage, and nonhomologous end-joining (NHEJ) mechanisms play dominant and priority roles in initiating DSB repair. A well-studied oncogene, the ubiquitin ligase Cullin 4A (CUL4A), is reported to be recruited to DSB sites in genomic DNA, but whether it regulates NHEJ mechanisms of DSB repair is unclear. Here, we discovered that the CUL4A-DTL ligase complex targeted the DNA-PKcs protein in the NHEJ repair pathway for nuclear degradation. Overexpression of either CUL4A or DTL reduced NHEJ repair efficiency and subsequently increased the accumulation of DSBs. Moreover, we demonstrated that overexpression of either CUL4A or DTL in normal cells led to genomic instability and malignant proliferation. Consistent with the in vitro findings, in human precancerous lesions, CUL4A expression gradually increased with increasing malignant tendency and was negatively correlated with DNA-PKcs and positively correlated with γ-H2AX expression. Collectively, this study provided strong evidence that the CUL4A-DTL axis increases genomic instability and enhances the subsequent malignant transformation of normal cells by inhibiting NHEJ repair. These results also suggested that CUL4A may be a prognostic marker of precancerous lesions and a potential therapeutic target in cancer.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2014

Assessment of the Accuracy of the Conventional Ray-Tracing Technique: Implications in Remote Sensing and Radiative Transfer Involving Ice Clouds.

A fundamental problem in remote sensing and radiative transfer simulations involving ice clouds is the ability to compute accurate optical properties for individual ice particles. While relatively simple and intuitively appealing, the conventional geometric-optics method (CGOM) is used frequently for the solution of light scattering by ice crystals. Due to the approximations in the ray-tracing technique, the CGOM accuracy is not well quantified. The result is that the uncertainties are introduced that can impact many applications. Improvements in the Invariant Imbedding T-matrix method (II-TM) and the Improved Geometric-Optics Method (IGOM) provide a mechanism to assess the aforementioned uncertainties. The results computed by the II-TMþIGOM are considered as a benchmark because the IITM solves Maxwell's equations from first principles and is applicable to particle size parameters ranging into the domain at which the IGOM has reasonable accuracy. To assess the uncertainties with the CGOM in remote sensing and radiative transfer simulations, two independent optical property datasets of hexagonal columns are developed for sensitivity studies by using the CGOM and the II-TMþIGOM, respectively. Ice cloud bulk optical properties obtained from the two datasets are compared and subsequently applied to retrieve the optical thickness and effective diameter from Moderate Resolution Imaging Spectroradiometer (MODIS) measurements. Additionally, the bulk optical properties are tested in broadband radiative transfer (RT) simulations using the general circulation model (GCM) version of the Rapid Radiative Transfer Model (RRTMG) that is adopted in the National Center for Atmospheric Research (NCAR) Community Atmosphere Model (CAM, version 5.1). For MODIS retrievals, the mean bias of uncertainties of applying the CGOM in shortwave bands (0.86 and 2.13 micrometers) can be up to 5% in the optical thickness and as high as 20% in the effective diameter, depending on cloud optical thickness and effective diameter. In the MODIS infrared window bands centered at 8.5, 11, and 12 micrometers biases in the optical thickness and effective diameter are up to 12% and 10%, respectively. The CGOM-based simulation errors in ice cloud radiative forcing calculations are on the order of 10Wm(exp 2).

remote sensing↗

NASA NTRS2013

A Numerical Combination of Extended Boundary Condition Method and Invariant Imbedding Method Applied to Light Scattering by Large Spheroids and Cylinders

The extended boundary condition method (EBCM) and invariant imbedding method (IIM) are two fundamentally different T-matrix methods for the solution of light scattering by nonspherical particles. The standard EBCM is very efficient but encounters a loss of precision when the particle size is large, the maximum size being sensitive to the particle aspect ratio. The IIM can be applied to particles in a relatively large size parameter range but requires extensive computational time due to the number of spherical layers in the particle volume discretization. A numerical combination of the EBCM and the IIM (hereafter, the EBCM+IIM) is proposed to overcome the aforementioned disadvantages of each method. Even though the EBCM can fail to obtain the T-matrix of a considered particle, it is valuable for decreasing the computational domain (i.e., the number of spherical layers) of the IIM by providing the initial T-matrix associated with an iterative procedure in the IIM. The EBCM+IIM is demonstrated to be more efficient than the IIM in obtaining the optical properties of large size parameter particles beyond the convergence limit of the EBCM. The numerical performance of the EBCM+IIM is illustrated through representative calculations in spheroidal and cylindrical particle cases.

invariant imbeddings↗

NASA NTRS2013

Spectrally Consistent Scattering, Absorption, and Polarization Properties of Atmospheric Ice Crystals at Wavelengths from 0.2 to 100 um

A data library is developed containing the scattering, absorption, and polarization properties of ice particles in the spectral range from 0.2 to 100 microns. The properties are computed based on a combination of the Amsterdam discrete dipole approximation (ADDA), the T-matrix method, and the improved geometric optics method (IGOM). The electromagnetic edge effect is incorporated into the extinction and absorption efficiencies computed from the IGOM. A full set of single-scattering properties is provided by considering three-dimensional random orientations for 11 ice crystal habits: droxtals, prolate spheroids, oblate spheroids, solid and hollow columns, compact aggregates composed of eight solid columns, hexagonal plates, small spatial aggregates composed of 5 plates, large spatial aggregates composed of 10 plates, and solid and hollow bullet rosettes. The maximum dimension of each habit ranges from 2 to 10,000 microns in 189 discrete sizes. For each ice crystal habit, three surface roughness conditions (i.e., smooth, moderately roughened, and severely roughened) are considered to account for the surface texture of large particles in the IGOM applicable domain. The data library contains the extinction efficiency, single-scattering albedo, asymmetry parameter, six independent nonzero elements of the phase matrix (P11, P12, P22, P33, P43, and P44), particle projected area, and particle volume to provide the basic single-scattering properties for remote sensing applications and radiative transfer simulations involving ice clouds. Furthermore, a comparison of satellite observations and theoretical simulations for the polarization characteristics of ice clouds demonstrates that ice cloud optical models assuming severely roughened ice crystals significantly outperform their counterparts assuming smooth ice crystals.

Optical properties↗

NASA NTRS2012

Efficient Implementation of the Invariant Imbedding T-Matrix Method and the Separation of Variables Method Applied to Large Nonspherical Inhomogeneous Particles

Three terms, ''Waterman's T-matrix method'', ''extended boundary condition method (EBCM)'', and ''null field method'', have been interchangeable in the literature to indicate a method based on surface integral equations to calculate the T-matrix. Unlike the previous method, the invariant imbedding method (IIM) calculates the T-matrix by the use of a volume integral equation. In addition, the standard separation of variables method (SOV) can be applied to compute the T-matrix of a sphere centered at the origin of the coordinate system and having a maximal radius such that the sphere remains inscribed within a nonspherical particle. This study explores the feasibility of a numerical combination of the IIM and the SOV, hereafter referred to as the IIMþSOV method, for computing the single-scattering properties of nonspherical dielectric particles, which are, in general, inhomogeneous. The IIMþSOV method is shown to be capable of solving light-scattering problems for large nonspherical particles where the standard EBCM fails to converge. The IIMþSOV method is flexible and applicable to inhomogeneous particles and aggregated nonspherical particles (overlapped circumscribed spheres) representing a challenge to the standard superposition T-matrix method. The IIMþSOV computational program, developed in this study, is validated against EBCM simulated spheroid and cylinder cases with excellent numerical agreement (up to four decimal places). In addition, solutions for cylinders with large aspect ratios, inhomogeneous particles, and two-particle systems are compared with results from discrete dipole approximation (DDA) computations, and comparisons with the improved geometric-optics method (IGOM) are found to be quite encouraging.

Invariant imbedding method↗

NASA NTRS2010

Modeling Optical Properties of Mineral Aerosol Particles by Using Nonsymmetric Hexahedra

We explore the use of nonsymmetric geometries to simulate the single-scattering properties of airborne dust particles with complicated morphologies. Specifically, the shapes of irregular dust particles are assumed to be nonsymmetric hexahedra defined by using the Monte Carlo method. A combination of the discrete dipole approximation method and an improved geometric optics method is employed to compute the single-scattering properties of dust particles for size parameters ranging from 0.5 to 3000. The primary optical effect of eliminating the geometric symmetry of regular hexahedra is to smooth the scattering features in the phase function and to decrease the backscatter. The optical properties of the nonsymmetric hexahedra are used to mimic the laboratory measurements. It is demonstrated that a relatively close agreement can be achieved by using only one shape of nonsymmetric hexahedra. The agreement between the theoretical results and their measurement counterparts can be further improved by using a mixture of nonsymmetric hexahedra. It is also shown that the hexahedron model is much more appropriate than the "equivalent sphere" model for simulating the optical properties of dust particles, particularly, in the case of the elements of the phase matrix that associated with the polarization state of scattered light.

Bi, Lei↗