| 1. |
|
|
| 2. |
- Li, Junhao, 1989-, et al.
(författare)
-
Dissecting the Structural Plasticity and Dynamics of Cytochrome P450 2B4 by Molecular Dynamics Simulations
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The plasticity of cytochrome P450 enzymes (P450s) is known to contribute significantly to their catalytic capacity of metabolizing various substrates. Although numerous studies have been performed, factors governing the plasticity and dynamics of P450s are still not fully understood. In this study, taking CYP2B4 as an example, we dissect the protein plasticity and dynamics in different environments. CYP2B4 is featured by a high degree of plasticity that exhibits open, closed, and intermediate states. By analyzing the CYP2B4 crystal structures, we identified the structural features for the closed, open and intermediate states. Interestingly, formation of the dimer structure was found in the open and intermediate structures. The subsequent MD simulations of the open structure in water confirmed the importance of the dimer form in stabilizing the open conformations. MD simulations of the closed and open structures in the membrane environment and the free energies for opening the F-G cassette obtained from the umbrella sampling calculations indicate that the membrane environment is important for stabilizing the F-G cassette. The dynamical network analysis indicates that Asp105 on the B-C loop plays an important role in transiting the structure from the open to intermediate. Our results thus unveil the mechanism of dimer formation and open-to-intermediate transition for CYP2B4 in the water and membrane environments.
|
|
| 3. |
- Li, Junhao, 1989-, et al.
(författare)
-
Mechanism of the Homotropic Cooperativity of Midazolam Metabolism by Cytochrome P450 3A4: Insight from Computational Studies
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Midazolam (MDZ) is a commonly used drug and is metabolized by cytochrome P450 3A4 (CYP3A4). It has been reported that the ratio of the hydroxylation products, 1'-OH-MDZ/4-OH-MDZ, is dependent on the MDZ concentration, which reflects that there exists the homotropic cooperative behavior in the CYP3A4-mediated hydroxylation of MDZ. Here, we used quantum chemistry (QC), molecular docking, conventional molecular dynamics (cMD) simulation, and Gaussian accelerated molecular dynamics (GaMD) simulation approaches to investigate the mechanism of the interactions between CYP3A4 and MDZ. Our study suggests that the H41 site, i.e. the pro-R center, is the most reactive site for the hydrogen abstraction, followed by the C1' site. However, the product 4-OH-MDZ is likely to be racemic due to the chirality inversion in the rebound step. We found that the allosteric site was not involved in the ligand cooperativity and the observation that there exists one or two MDZs in the productive site is in line with the experimental observations.
|
|
| 4. |
|
|
| 5. |
|
|
| 6. |
|
|
| 7. |
- Li, Yun
(författare)
-
Coding of Three-dimensional Video Content : Diffusion-based Coding of Depth Images and Displacement Intra-Coding of Plenoptic Contents
- 2015
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In recent years, the three-dimensional (3D) movie industry has reaped massive commercial success in the theaters. With the advancement of display technologies, more experienced capturing and generation of 3D contents, TV broadcasting, movies, and games in 3D have entered home entertainment, and it is likely that 3D applications will play an important role in many aspects of people's life in a not distant future. 3D video contents contain at least two views from different perspectives for the left and the right eye of viewers. The amount of coded information is doubled if these views are encoded separately. Moreover, for multi-view displays (i.e. different perspectives of a scene in 3D are presented to the viewer at the same time through different angles), either video streams of all the required views must be transmitted to the receiver, or the displays must synthesize the missing views with a subset of the views. The latter approach has been widely proposed to reduce the amount of data being transmitted and make data adjustable to 3D-displays. The virtual views can be synthesized by the Depth Image Based Rendering (DIBR) approach from textures and associated depth images. However, it is still the case that the amount of information for the textures plus the depths presents a significant challenge for the network transmission capacity. Compression techniques are vital to facilitate the transmission. In addition to multi-view and multi-view plus depth for reproducing 3D, light field techniques have recently become a hot topic. The light field capturing aims at acquiring not only spatial but also angular information of a view, and an ideal light field rendering device should be such that the viewers would perceive it as looking through a window. Thus, the light field techniques are a step forward to provide us with a more authentic perception of 3D. Among many light field capturing approaches, focused plenoptic capturing is a solution that utilize microlens arrays. The plenoptic cameras are also portable and commercially available. Multi-view and refocusing can be obtained during post-production from these cameras. However, the captured plenoptic images are of a large size and contain significant amount of a redundant information. An efficient compression of the above mentioned contents will, therefore, increase the availability of content access and provide a better quality experience under the same network capacity constraints. In this thesis, the compression of depth images and of plenoptic contents captured by focused plenoptic cameras are addressed. The depth images can be assumed to be piece-wise smooth. Starting from the properties of depth images, a novel depth image model based on edges and sparse samples is presented, which may also be utilized for depth image post-processing. Based on this model, a depth image coding scheme that explicitly encodes the locations of depth edges is proposed, and the coding scheme has a scalable structure. Furthermore, a compression scheme for block-based 3D-HEVC is also devised, in which diffusion is used for intra prediction. In addition to the proposed schemes, the thesis illustrates several evaluation methodologies, especially the subjective test of the stimulus-comparison method. This is suitable for evaluating the quality of two impaired images, as the objective metrics are inaccurate with respect to synthesized views. For the compression of plenoptic contents, displacement intra prediction with more than one hypothesis is applied and implemented in the HEVC for an efficient prediction. In addition, a scalable coding approach utilizing a sparse set and disparities is introduced for the coding of focused plenoptic images. The MPEG test sequences were used for the evaluation of the proposed depth image compression, and public available plenoptic image and video contents were applied to the assessment of the proposed plenoptic compression. For depth image coding, the results showed that virtual views synthesized from post-processed depth images by using the proposed model are better than those synthesized from original depth images. More importantly, the proposed coding schemes using such a model produced better synthesized views than the state of the art schemes. For the plenoptic contents, the proposed scheme achieved an efficient prediction and reduced the bit rate significantly while providing coding and rendering scalability. As a result, the outcome of the thesis can lead to improving quality of the 3DTV experience and facilitate the development of 3D applications in general.
|
|
| 8. |
- Li, Yun
(författare)
-
Coding of three-dimensional video content : Depth image coding by diffusion
- 2013
-
Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Three-dimensional (3D) movies in theaters have become a massive commercial success during recent years, and it is likely that, with the advancement of display technologies and the production of 3D contents, TV broadcasting in 3D will play an important role in home entertainments in the not too distant future. 3D video contents contain at least two views from different perspectives for the left and the right eye of viewers. The amount of coded information is doubled if these views are encoded separately. Moreover, for multi-view displays (i.e. different perspectives of a scene in 3D are presented to the viewer at the same time through different angles), either video streams of all the required views must be transmitted to the receiver, or the displays must synthesize the missing views with a subset of the views. The latter approach has been widely proposed to reduce the amount of data being transmitted. The virtual views can be synthesized by the Depth Image Based Rendering (DIBR) approach from textures and associated depth images. However it is still the case that the amount of information for the textures plus the depths presents a significant challenge for the network transmission capacity. An efficient compression will, therefore, increase the availability of content access and provide a better video quality under the same network capacity constraints.In this thesis, the compression of depth images is addressed. These depth images can be assumed as being piece-wise smooth. Starting from the properties of depth images, a novel depth image model based on edges and sparse samples is presented, which may also be utilized for depth image post-processing. Based on this model, a depth image coding scheme that explicitly encodes the locations of depth edges is proposed, and the coding scheme has a scalable structure. Furthermore, a compression scheme for block-based 3D-HEVC is also devised, in which diffusion is used for intra prediction. In addition to the proposed schemes, the thesis illustrates several evaluation methodologies, especially, the subjective test of the stimulus-comparison method. It is suitable for evaluating the quality of two impaired images, as the objective metrics are inaccurate with respect to synthesized views.The MPEG test sequences were used for the evaluation. The results showed that virtual views synthesized from post-processed depth images by using the proposed model are better than those synthesized from original depth images. More importantly, the proposed coding schemes using such a model produced better synthesized views than the state of the art schemes. As a result, the outcome of the thesis can lead to a better quality of 3DTV experience.
|
|
| 9. |
- Li, Zhen, et al.
(författare)
-
Photocatalytic Hydrogen Production
- 2022
-
Ingår i: Photo‐ and Electro‐Catalytic Processes. - : John Wiley & Sons. ; , s. 415-483
-
Bokkapitel (övrigt vetenskapligt/konstnärligt)
|
|
| 10. |
- Lidén, Magnus, 1951-, et al.
(författare)
-
Papaveraceae-Fumarioideae
- 2008
-
Ingår i: Flora of China. Vol. 7, Menispermaceae through Capparaceae. - Beijing : Science Press. - 9781930723818 ; , s. 288-428
-
Bokkapitel (övrigt vetenskapligt/konstnärligt)
|
|
