Computational prediction, characterization, and methodology development for two-dimensional nanostructures: phosphorene and phosphide binary compounds.

In this thesis, a comprehensive computational simulation was carried out for predicting, characterizing, and applications of two-dimensional (2D) materials. The newly discovered GaP and InP layers were selected as an example to demonstrate how to explore new 2D materials using computational simulations. The performance of phosphorene as the anode material of Lithium-ion battery was discussed as the example of the application of 2D material. Furthermore, the semi-empirical Hamiltonian for phosphorous and lithium elements have been developed for our future work on the application of phosphorus and lithium-based systems. The novel 2D materials of GaP and InP binary compounds were found to possess unique anisotropic structural, electronic, and mechanical properties. Their crystalline structures show orthorhombic lattices symmetry and high buckling of 2.14 Å-2.46 Å. They have strong directional dependence of Young’s moduli and effective nonlinear elastic moduli. They have wide fundamental bandgaps which were also found to be tunable under the strain. In particular, a direct-indirect bandgap transition was found under certain strains, reflecting their promising applications for the strain-induced bandgap engineering in nanoelectronics and photovoltaics. To completely understand the performance of phosphorene as the anode material of Li-ion battery, the lithium adsorption energy landscape, diffusion mobility, intercalation, and capacity of phosphorene were studied. The calculations show the anisotropic diffusivity and the ultrafast diffusion mobility of lithium along the zigzag direction. Phosphorene could accommodate up to the ratio of one Li per P atom (i.e., Li16P16). In particular, there was no lithium clustering even at the high Li concentration. The structure of phosphorene, when it was fractured at high concentration, is reversible during the lithium intercalation. The theoretical value of the lithium capacity for a monolayer phosphorene is predicted to be above 433 mAh/g. The SCED-LCAO Hamiltonians for phosphorus and lithium were developed in this thesis. The optimized parameters were obtained by fitting the structural and electronic properties of small clusters and bulk phases, which were calculated by the ab-initial methods. The robustness tests of phosphorus parameters were executed by relaxing the back phosphorus, phosphorene, and blue phosphorene with SCED-LCAO-MD code. The energy order and band gap of black phosphorus, phosphorene and blue phosphorene are all consistent with the DFT calculations and experimental measurements. The robustness tests of Li parameters were executed for the BCC bulk of Li and its stability was proved

Collaborative Perception in Autonomous Driving: Methods, Datasets and Challenges

Collaborative perception is essential to address occlusion and sensor failure issues in autonomous driving. In recent years, theoretical and experimental investigations of novel works for collaborative perception have increased tremendously. So far, however, few reviews have focused on systematical collaboration modules and large-scale collaborative perception datasets. This work reviews recent achievements in this field to bridge this gap and motivate future research. We start with a brief overview of collaboration schemes. After that, we systematically summarize the collaborative perception methods for ideal scenarios and real-world issues. The former focuses on collaboration modules and efficiency, and the latter is devoted to addressing the problems in actual application. Furthermore, we present large-scale public datasets and summarize quantitative results on these benchmarks. Finally, we highlight gaps and overlook challenges between current academic research and real-world applications. The project page is https://github.com/CatOneTwo/Collaborative-Perception-in-Autonomous-DrivingComment: 18 pages, 6 figures. Accepted by IEEE Intelligent Transportation Systems Magazine. URL: https://github.com/CatOneTwo/Collaborative-Perception-in-Autonomous-Drivin

Tracing evolutionary footprints to identify novel gene functional linkages.

Systematic determination of gene function is an essential step in fully understanding the precise contribution of each gene for the proper execution of molecular functions in the cell. Gene functional linkage is defined as to describe the relationship of a group of genes with similar functions. With thousands of genomes sequenced, there arises a great opportunity to utilize gene evolutionary information to identify gene functional linkages. To this end, we established a computational method (called TRACE) to trace gene footprints through a gene functional network constructed from 341 prokaryotic genomes. TRACE performance was validated and successfully tested to predict enzyme functions as well as components of pathway. A so far undescribed chromosome partitioning-like protein ro03654 of an oleaginous bacteria Rhodococcus sp. RHA1 (RHA1) was predicted and verified experimentally with its deletion mutant showing growth inhibition compared to RHA1 wild type. In addition, four proteins were predicted to act as prokaryotic SNARE-like proteins, and two of them were shown to be localized at the plasma membrane. Thus, we believe that TRACE is an effective new method to infer prokaryotic gene functional linkages by tracing evolutionary events

Long-read sequencing-based transcriptomic landscape in longissimus dorsi and transcriptome-wide association studies for growth traits of meat rabbits

Rabbits are an attractive meat livestock species that can efficiently convert human-indigestible plant biomass, and have been commonly used in biological and medical researches. Yet, transcriptomic landscape in muscle tissue and association between gene expression level and growth traits have not been specially studied in meat rabbits. In this study Oxford Nanopore Technologies (ONT) long-read sequencing technology was used for comprehensively exploring transcriptomic landscape in Longissimus dorsi for 115 rabbits at 84 days of age, and transcriptome-wide association studies (TWAS) were performed for growth traits, including body weight at 84 days of age and average daily gain during three growth periods. The statistical analysis of TWAS was performed using a mixed linear model, in which polygenic effect was fitted as a random effect according to gene expression level-based relationships. A total of 18,842 genes and 42,010 transcripts were detected, among which 35% of genes and 47% of transcripts were novel in comparison with the reference genome annotation. Furthermore, 45% of genes were widely expressed among more than 90% of individuals. The proportions (±SE) of phenotype variance explained by genome-wide gene expression level ranged from 0.501 ± 0.216 to 0.956 ± 0.209, and the similar results were obtained when explained by transcript expression level. In contrast, neither gene nor transcript was detected by TWAS to be statistically significantly associated with these growth traits. In conclusion, these novel genes and transcripts that have been extensively profiled in a single muscle tissue using long-read sequencing technology will greatly improve our understanding on transcriptional diversity in rabbits. Our results with a relatively small sample size further revealed the important contribution of global gene expression to phenotypic variation on growth performance, but it seemed that no single gene has an outstanding effect; this knowledge is helpful to include intermediate omics data for implementing genetic evaluation of growth traits in meat rabbits

Possible Luttinger liquid behavior of edge transport in monolayer transition metal dichalcogenide crystals.

In atomically-thin two-dimensional (2D) semiconductors, the nonuniformity in current flow due to its edge states may alter and even dictate the charge transport properties of the entire device. However, the influence of the edge states on electrical transport in 2D materials has not been sufficiently explored to date. Here, we systematically quantify the edge state contribution to electrical transport in monolayer MoS2/WSe2 field-effect transistors, revealing that the charge transport at low temperature is dominated by the edge conduction with the nonlinear behavior. The metallic edge states are revealed by scanning probe microscopy, scanning Kelvin probe force microscopy and first-principle calculations. Further analyses demonstrate that the edge-state dominated nonlinear transport shows a universal power-law scaling relationship with both temperature and bias voltage, which can be well explained by the 1D Luttinger liquid theory. These findings demonstrate the Luttinger liquid behavior in 2D materials and offer important insights into designing 2D electronics

Syncytin-mediated open-ended membrane tubular connections facilitate the intercellular transfer of cargos including Cas9 protein

Much attention has been focused on the possibility that cytoplasmic proteins and RNA may be conveyed between cells in extracellular vesicles (EVs) and tunneling nanotube (TNT) structures. Here, we set up two quantitative delivery reporters to study cargo transfer between cells. We found that EVs are internalized by reporter cells but do not efficiently deliver functional Cas9 protein to the nucleus. In contrast, donor and acceptor cells co-cultured to permit cell contact resulted in a highly effective transfer. Among our tested donor and acceptor cell pairs, HEK293T and MDA-MB-231 recorded optimal intercellular transfer. Depolymerization of F-actin greatly decreased Cas9 transfer, whereas inhibitors of endocytosis or knockdown of genes implicated in this process had little effect on transfer. Imaging results suggest that intercellular transfer of cargos occurred through open-ended membrane tubular connections. In contrast, cultures consisting only of HEK293T cells form close-ended tubular connections ineffective in cargo transfer. Depletion of human endogenous fusogens, syncytins, especially syncytin-2 in MDA-MB-231 cells, significantly reduced Cas9 transfer. Full-length mouse syncytin, but not truncated mutants, rescued the effect of depletion of human syncytins on Cas9 transfer. Mouse syncytin overexpression in HEK293T cells partially facilitated Cas9 transfer among HEK293T cells. These findings suggest that syncytin may serve as the fusogen responsible for the formation of an open-ended connection between cells

Syncytin-mediated open-ended membrane tubular connections facilitate the intercellular transfer of cargos including Cas9 protein

Much attention has been focused on the possibility that cytoplasmic proteins and RNA may be conveyed between cells in extracellular vesicles (EVs) and tunneling nanotube (TNT) structures. Here, we set up two quantitative delivery reporters to study cargo transfer between cells. We found that EVs are internalized by reporter cells but do not efficiently deliver functional Cas9 protein to the nucleus. In contrast, donor and acceptor cells co-cultured to permit cell contact resulted in a highly effective transfer. Among our tested donor and acceptor cell pairs, HEK293T and MDA-MB-231 recorded optimal intercellular transfer. Depolymerization of F-actin greatly decreased Cas9 transfer, whereas inhibitors of endocytosis or knockdown of genes implicated in this process had little effect on transfer. Imaging results suggest that intercellular transfer of cargos occurred through open-ended membrane tubular connections. In contrast, cultures consisting only of HEK293T cells form close-ended tubular connections ineffective in cargo transfer. Depletion of human endogenous fusogens, syncytins, especially syncytin-2 in MDA-MB-231 cells, significantly reduced Cas9 transfer. Full-length mouse syncytin, but not truncated mutants, rescued the effect of depletion of human syncytins on Cas9 transfer. Mouse syncytin overexpression in HEK293T cells partially facilitated Cas9 transfer among HEK293T cells. These findings suggest that syncytin may serve as the fusogen responsible for the formation of an open-ended connection between cells

The lipid droplet: A conserved cellular organelle

ABSTRACT The lipid droplet (LD) is a unique multi-functional organelle that contains a neutral lipid core covered with a phospholipid monolayer membrane. The LDs have been found in almost all organisms from bacteria to humans with similar shape. Several conserved functions of LDs have been revealed by recent studies, including lipid metabolism and trafficking, as well as nucleic acid binding and protection. We summarized these findings and proposed a hypothesis that the LD is a conserved organelle