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Distance Distribution and Reliability of Small-World Networks

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Chinese Physics Letters 2001年第3期18卷 452-454页

作者： SUN Kai ouyang qi Department of Physics and Mesoscopic Physics Laboratory Peking UniversityBeijing 100871

We have studied the distribution of distances in small-world network by computer *** found that in a small world network,the longest distance between two vertices is just slightly longer than the average distance,indicating that the efficiency of the network is absolute rather than in *** also investigated the robustness of a small-world network by randomly cutting some long paths in the *** results show that the network is reliable against random cutting.

关键词： absolute slightly Reliability

DNA storage: research landscape and future prospects

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National Science Review 2020年第6期7卷 1092-1107页

作者： Yiming Dong Fajia Sun Zhi Ping qi ouyang Long qian Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences Peking University Academician Workstation of BGI Synthetic Genomics BGI-Shenzhen The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics School of Physics Peking University

The global demand for data storage is currently outpacing the world’s storage capabilities. DNA, the carrier of natural genetic information, offers a stable, resource-and energy-efficient and sustainable data storage solution. In this review, we summarize the fundamental theory, research history, and technical challenges of DNA storage. From a quantitative perspective, we evaluate the prospect of DNA, and organic polymers in general, as a novel class of data storage medium.

关键词： DNA storage information compilation sequencing

Expanded flux variability analysis on metabolic network of Escherichia coli

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Chinese Science Bulletin 2009年第15期54卷 2610-2619页

作者： CHEN Tong XIE ZhengWei ouyang qi Center for Theoretical Biology and School of Physics Peking University Beijing 100871 China Department of Physics Hong Kong Baptist University Kowloon Tong Hong Kong China

Flux balance analysis, based on the mass conservation law in a cellular organism, has been extensively employed to study the interplay between structures and functions of cellular metabolic networks. Consequently, the phenotypes of the metabolism can be well elucidated. In this paper, we introduce the Expanded Flux Variability Analysis (EFVA) to characterize the intrinsic nature of metabolic reactions, such as flexibility, modularity and essentiality, by exploring the trend of the range, the maximum and the minimum flux of reactions. We took the metabolic network of Escherichia coli as an example and analyzed the variability of reaction fluxes under different growth rate constraints. The average variabil-ity of all reactions decreases dramatically when the growth rate increases. Consider the noise effect on the metabolic system, we thus argue that the microorganism may practically grow under a suboptimal state. Besides, under the EFVA framework, the reactions are easily to be grouped into catabolic and anabolic groups. And the anabolic groups can be further assigned to specific biomass constitute. We also discovered the growth rate dependent essentiality of reactions.

关键词：代谢网络变异性分析大肠杆菌通量代谢反应质量守恒定律细胞代谢增长速度

One-step functionalization of graphene via Diels-Alder reaction for improvement of dispersibility

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Frontiers of Materials Science 2020年第2期14卷 198-210页

作者： Jinxing ZHANG Kexing HU qi ouyang qilin GUI Xiaonong CHEN Beiing Laboratory of Biomedical Materials Beiing University of Chemical TechnologyBeiing 100029China

Good dispersibility of graphene in a medium or matrix is a critical issue in practical *** this work,graphene was functionalized using N-(4-hydroxyl phenyl)maleimide(4-HPM)via the Diels—Alder(DA)reaction by a one-step catalyst-free *** optimal reaction condition was found to be 90℃for 12 h using dimethytformamide(DMF)as the ***,Raman spectroscopy,XPS and EDS proved that 4-HPM moieties were successfully grafted onto the surface of *** and TGA confirmed that the grafting amount of 4-HPM was 3.75%-3.97%based on the mass of *** graphene showed excellent dispersion stability when dispersed in common solvents such as ethanol,DMF,water,tetrahydrofuran and ***,functionalized graphene also exhibited pH sensitivity in aqueous due to the phenolic hydroxyls from the 4-HPM *** a result of good dispersion stability and pH sensitivity,compared with graphene,functionalized graphene had better adsorption capacity for methylene blue(MB)from aqueous solution.

关键词： graphene functionalization dispersibility Diels-Alder reaction

Cryo-EM Data Statistics and Theoretical Analysis of KaiC Hexamer

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Chinese Physics Letters 2022年第7期39卷 24-29页

作者： Xu Han Zhaolong Wu Tian Yang qi ouyang Department of Physics Peking UniversityBeijing 100871China Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences AAICPeking UniversityBeijing 100871China

Cryo-electron microscopy(cryo-EM) provides a powerful tool to resolve the structure of biological macromolecules in natural state. One advantage of cryo-EM technology is that different conformation states of a protein complex structure can be simultaneously built, and the distribution of different states can be measured. This provides a tool to push cryo-EM technology beyond just to resolve protein structures, but to obtain the thermodynamic properties of protein machines. Here, we used a deep manifold learning framework to get the conformational landscape of Kai C proteins, and further obtained the thermodynamic properties of this central oscillator component in the circadian clock by means of statistical physics.

关键词： Cryo-EM Data Statistics and Theoretical Analysis of KaiC Hexamer

DNA duplex membrane effect for the electrochemical detection of single-base DNA mutations

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Frontiers in Biology 2006年第2期1卷 203-207页

作者： Luo Chunxiong Mao Yongdong ouyang qi Laboratory for Biophysics and Biotechnology Department of PhysicsBeijing 100871China Center for Theoretical Biology Peking UniversityBeijing 100871China

Here we report a new method to detect DNA point *** method is based on the formation and deformation of double-stranded DNA(dsDNA)membranes on a gold *** can encage reporter molecules between the gold surface and the double-stranded DNA or keep them away from the gold *** these systems,Fe(CN)63−was used as the *** the temperature increases,a sharp electrochemical signal change in the melting curve of wild-type dsDNA *** a special temperature,the method gives 100:1 selectivity for the perfect complement and single base mutation ***,the system provides a simple and sensitive method to detect DNA point mutations without labeling targets.

关键词： membrane effect nano-compartment single mutation electrochemistry

The determinant factors for map resolutions obtained using CryoEM single particle imaging method

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Chinese Physics B 2018年第12期27卷 563-571页

作者： Yihua Wang Daqi Yu qi ouyang Haiguang Liu Key Laboratory for Artificial Microstructure and Mesoscopic Physics Institute of Condensed Matter Physics School of Physics Center for Quantitative Biology School of Physics The Peking–Tsinghua Center for Life Sciences at School of Physics Peking University Complex Systems Division Beijing Computational Science Research Centre

The CryoEM single particle structure determination method has recently received broad attention in the field of structural biology. The structures can be resolved to near-atomic resolutions after model reconstructions from a large number of CryoEM images measuring molecules in different orientations. However, the determining factors for reconstructed map resolution need to be further explored. Here, we provide a theoretical framework in conjunction with numerical simulations to gauge the influence of several key factors to CryoEM map resolutions. If the projection image quality allows orientation assignment, then the number of measured projection images and the quality of each measurement(quantified using average signal-to-noise ratio) can be combined to a single factor, which is dominant to the resolution of reconstructed maps. Furthermore, the intrinsic thermal motion of molecules has significant effects on the resolution. These effects can be quantitatively summarized with an analytical formula that provides a theoretical guideline on structure resolutions for given experimental measurements.

关键词： Cryo-EM resolution noise conformation heterogeneity

Improving cooperativity of transcription activators by oligomerization domains in mammalian cells

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Synthetic and Systems Biotechnology 2023年第1期8卷 114-120页

作者： Xinmao Chen Ziming Liu Chunbo Lou Ying Guan qi ouyang Yanhui Xiang School of Physics Peking UniversityBeijing100871China Department of Chemical Engineering Tsinghua UniversityBeijing100871China Center for Cell and Gene Circuit Design CAS Key Laboratory of Quantitative Engineering BiologyGuangdong Provincial Key Laboratory of Synthetic GenomicsShenzhen Key Laboratory of Synthetic GenomicsShenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhen518055China

Cooperative activation is critical for the applications of synthetic biology in mammalian *** this study,we have developed cooperative transcription factor by fusing oligomerization domain in mammalian ***,we demonstrated that two oligomerized domains(CI434 and CI)successfully improved transcription factor cooperativity in bacterial cells but failed to increase cooperativity in mammalian cells,possibly because the additional mammalian activation domain disrupted their oligomerization ***,we chose a different type of oligomerized domain(CarHC),whose ability to oligomerize is not dependent on its C-terminal domains,to fuse with a transcription factor(RpaR)and activation domain(VTR3),forming a potential cooperative transcription activator RpaR-CarH-VTR3 for mammalian regulatory *** with RpaR-VTR3,the cooperativity of RpaR-CarH-VTR3 was significantly improved with higher Hill coefficient and a narrower input range in the inducible switch system in mammalian ***,a mathematical model based on statistical mechanics model was developed and the simulation results supported the hypothesis that the tetramer of the CarH domain in mammalian cells was the reason for the cooperative capacity of RpaR-CarH-VTR3.

关键词： activation narrow cooperative

The relationship between SPARC expression in primary tumor and metastatic lymph node of resected pancreatic cancer patients and patients' survival

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Hepatobiliary & Pancreatic Diseases International 2017年第1期16卷 104-109页

作者： Xin-Zhe Yu Zhong-Yi Guo Yang Di Feng Yang qi ouyang De-Liang Fu Chen Jin Department of Pancreatic Surgery Huashan HospitalFudan UniversityShanghai 200040China Department of Pathology Huashan HospitalFudan UniversityShanghai 200040China Institute of Pancreatic Disease Fudan UniversityShanghai 200040China

BACKGROUND： Previous researches in pancreatic cancer demonstrated a negative correlation between secreted protein acidic and rich in cysteine （SPARC） expression in primary tumor and survival, but not for SPARC expression in lymph node. In the present study, we aimed to evaluate the SPARC expression in various types of tissues and its impact on patients＇ prognosis. METHODS： The expression of SPARC was examined by immunohistochemistry in resected pancreatic cancer specimens. Kaplan-Meier analyses and Cox proportional hazards regres- sion were applied to assess the mortality risk. RESULTS： A total of 222 tissue samples from 73 patients were collected to evaluate the SPARC expression, which included 73 paired primary tumor and adjacent normal tissues, 38 paired metastatic and normal lymph nodes. The proportion of posi tive SPARC expression in metastatic lymph node was high （32/38）, whereas in normal lymph node it was negative （0/38）. Positive SPARC expression in primary tumor cells was associ- ated with a significantly decreased overall survival （P=0.007） and disease-free survival （P=0.003）, whereas in other types of tissues it did not show a predictive role for prognosis. Univariate and multivariate analyses both confirmed this significance. CONCLUSION： SPARC can serve a dual function role as both predictor for prognosis and potentially biomarker for lymph node metastasis in resected pancreatic cancer patients.

关键词： pancreatic cancer SPARC expression immunohistochemistry prognostic marker lymph node metastasis