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Global view of bionetwork dynamics:adaptive landscape

Journal of Genetics and Genomics 2009年第2期36卷 63-73页

作者： ping ao Department of Mechanical Engineering and Department of Physics University of Washington Seattle WA 98195 USA Shanghai Center for Systems Biomedicine Key Laboratory of Systems Biomedicine of Ministry of Education Shanghai Jiao Tong University Shanghai 200240 China

Based on recent work, I will give a nontechnical brief review of a powerful quantitative concept in biology, adaptive landscape, ini- tially proposed by S. Wright over 70 years ago, reintroduced by one of the founders of molecular biology and by others in different bio- logical contexts, but apparently forgotten by modem biologists for many years. Nevertheless, this concept finds an increasingly important role in the development of systems biology and bionetwork dynamics modeling, from phage lambda genetic switch to endogenous net- work for cancer genesis and progression. It is an ideal quantification to describe the robustness and stability of bionetworks. Here, I will first introduce five landmark proposals in biology on this concept, to demonstrate an important common thread in theoretical biology. Then I will discuss a few recent results, focusing on the studies showing theoretical consistency of adaptive landscape. From the perspec- tive of a working scientist and of what is needed logically for a dynamical theory when confronting empirical data, the adaptive landscape is useful both metaphorically and quantitatively, and has captured an essential aspect of biological dynamical processes. Though at the theoretical level the adaptive landscape must exist and it can be used across hierarchical boundaries in biology, many associated issues are indeed vague in their initial formulations and their quantitative realizations are not easy, and are good research topics for quantitative biologists. I will discuss three types of open problems associated with the adaptive landscape in a broader perspective.

关键词： adaptive landscape stochastic dynamics, bionetworks systems biology

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Is philosophy of any use for scientists？

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Science Bulletin 2018年第16期63卷 1017-1018页

作者： ping ao Shanghai Center for Quantitative Life Sciences and Department of Physics Shanghai University.Shanghai 200444 China

This is a question which would certainly divide physicists in particular and scientists in *** aware of that,here I would like to take the successful career path of an excellent physicist as a positive example,supplemented by my own humble and negligible experience.I do hope that a bit of such discussion would be useful in the current rash state of scientific research in China.

关键词：科学家哲学物理学家科学研究

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A review on photoelectrochemical cathodic protection semiconductor thin films for metals

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Green Energy & Environment 2017年第4期2卷 331-362页

作者： Yuyu Bu Jin-ping ao Institute of Technology and Science Tokushima University

Photoelectrochemical(PEC) cathodic protection is considered as an environment friendly method for metals anticorrosion. In this technology, a n-type semiconductor photoanode provides the photogenerated electrons for metal to achieve cathodic protection. Comparing with traditional PEC photoanode for water splitting, it requires the photoanode providing a suitable cathodic potential for the metal, instead of pursuit ultimate photon to electric conversion efficiency, thus it is a more possible PEC technology for engineering application. To date, great efforts have been devoted to developing novel n-type semiconductors and advanced modification method to improve the performance on PEC cathodic protection metals. Herein, recent progresses in this field are summarized. We highlight the fabrication process of PEC cathodic protection thin film, various nanostructure controlling, doping, compositing methods and their operation mechanism. Finally, the current challenges and future potential works on improving the PEC cathodic protection performance are discussed.

关键词： Photoelectrochemical cathodic protection TiO2photoanode SrTiO3 g-C3N4 Photo-electron storage

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SDE decomposition and A-type stochastic interpretation in nonequilibrium processes

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Frontiers of physics 2017年第6期12卷 1-9页

作者： Ruoshi Yuan Ying Tang ping ao Key Laboratory of Systems Biomedicine Ministry of Education Shanghai Center for Systems Biomedicine Shanghai Jiao Tong University Shanghai 200240 China Department of Physics and Astronomy Shanghai-Jiao Tong University Shanghai 200240 China

An innovative theoretical framework for stochastic dynamics based on the decomposition of a stochas- tic differential equation （SDE） into a dissipative component, a detailed-balance-breaking component, and a dual-role potential landscape has been developed, which has fruitful applications in physics, engineering, chemistry, and biology. It introduces the A-type stochastic interpretation of the SDE beyond the traditional Ito or Stratonovich interpretation or even the a-type interpretation for multi- dimensional systems. The potential landscape serves as a Hmniltonian-like function in nonequilibrimn processes without detailed balance, which extends this important concept from equilibrium statistical physics to the nonequilibrium region. A question on the uniqueness of the SDE decomposition was recently raised. Our review of both the mathematical and physical aspects shows that uniqueness is guaranteed. The demonstration leads to a better understanding of the robustness of the novel frame- work. In addition, we discuss related issues including the limitations of an approach to obtaining the potential function from a steady-state distribution.

关键词： nonequilibrium statistical physics nonequilibrium potential Lyapunov function,nonlinear stochastic dynamics systems biology

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Influence of laterite nickel ore on extracting iron from Bayer red mud by carbothermal smelting reduction

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Journal of Iron and Steel Research International 2021年第6期28卷 661-668页

作者： ao-ping He Jian-min Zeng Shi-hong Liu Guangxi Key Laboratory of Processing for Non-Ferrous Metal and Featured Materials Guangxi UniversityNanning 530004GuangxiChina

In view of the difficulty of extracting iron from Bayer red mud,a new idea of adding laterite nickel ore into red mud was proposed to prepare a high value-added *** this,the influences of laterite nickel ore on thermodynamic reaction,slagging and smelting reduction of extracting iron from red mud were *** results indicated that the product of extracting iron from red mud(R100)was changed with the addition of laterite nickel ore(R70L30).The slag of R100 was strongly basic,while the R70L30 was weakly acidic with composition closer to the ideal blast furnace *** metal recovery of R100 was 75.16%and that of R70L30 was 94.05%.At the same temperature,the slag viscosity of R70L30 was significantly lower than that of R100,which proved that laterite nickel ore can adjust the basicity,reduce melting point of slag and improve metal *** Fe,Ni and Cr in red mud and laterite nickel ore can be reduced sufficiently,a low Ni–Cr alloy cast iron can be directly prepared.

关键词： Bayer red mud Laterite nickel ore Iron extraction Slagging Carbothermal smelting reduction

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Construction of Lyapunov Function for Dissipative Gyroscopic System

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Chinese Physics Letters 2011年第5期28卷 1-3页

作者： XU Wei YUAN Bo ao ping Shanghai Center for Systems Biomedicine Key Laboratory of Systems Biomedicine of Ministry of EducationShanghai Jiao Tong UniversityShanghai 200240 Department of Computer Science and Engineering Shanghai Jiao Tong UniversityShanghai 200240 Department of Physics Shanghai Jiao Tong UniversityShanghai 200240

We introduce a force decomposition to construct a potential function in deterministic dynamics described by ordinary differential equations in the context of dissipative gyroscopic *** a potential function serves as the corresponding Lyapunov function for the dynamics,hence it gives both quantitative and qualitative descriptions for stability of *** an example we apply our force decomposition to a four-dimensional dissipative gyroscopic *** explicitly obtain the potential function for all parameter regimes in the linear limit,including those regimes where the Lyapunov function was previously believed not to exist.

关键词： motion function dissipative

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Regulation of the photogenerated carrier transfer process during photoelectrochemical water splitting:A review

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Green Energy & Environment 2021年第4期6卷 479-495页

作者： Yaping Zhang Yuyu Bu Lin Wang Jin-ping ao Key Laboratory of Wide Band-Gap Semiconductor Materials and Devices School of MicroelectronicsXidian UniversityXi'an710071China

Photoelectrochemical(PEC)water splitting is considered as an ideal technology to produce *** carrier migration is one of the most important roles in the whole process of PEC water *** includes bulk transfer inside of the photoelectrode and the exchange at the solid-liquid *** energy barriers during the migration process lead to the dramatic recombination of photogenerated hot carrier and the reducing of their redox ***,an applied bias voltage should be provided to overcome these energy barriers,which brings the additional loss of *** researches indicate that some methods for the regulation of photogenerated hot carrier,such as p-n junction,unique transfer nanochannel,tandem nanostructure and Z-Scheme transfer structure et al.,show great potential to achieve high-efficient PEC water overall splitting without any applied bias *** to now,many reviews have summarized and analyzed the methods to enhance the PEC or photocatalysis water splitting from the perspectives of materials,nanostructures and surface modification ***,few of them focus on the topic of photogenerated carrier transfer regulation,which is an important and urgent developing *** this reason,this review focuses on the regulation of photogenerated carriers generated by the photoelectrodes and summarizes different advanced methods for photogenerated carrier regulation developed in recent *** comments and outlooks are also provided at the end of this review.

关键词： PEC water Splitting Photogenerated carrier migration Charge transfer regulation Energy band engineering Solid-liquid interface modification

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Dynamical Decomposition of Markov Processes without Detailed Balance

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Chinese Physics Letters 2013年第7期30卷 1-4页

作者： ao ping CHEN Tian-Qi SHI Jiang-Hong Key Laboratory of Systems Biomedicine of Ministry of Education Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghai 200240 Department of Computer Science and Engineering Shanghai Jiao Tong UniversityShanghai 200240 Department of Physics Shanghai Jiao Tong UniversityShanghai 200240

We introduce a dynamical decomposition view in dealing with Markov processes without detailed *** work generalizes a previous decomposition framework on continuous-state Markov processes and explicitly gives its correspondence in discrete-state *** investigate the dynamical roles of decomposed parts by studying the evolution of relative-entropy-like *** find a special definition of relative entropy to unify the dynamical roles played by the detailed balance part and the breaking detailed balance *** evolution of the relative entropy naturally bounds the convergence of the process.

关键词： functions. process. entropy

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Fabrication of CuO_x thin-film photocathodes by magnetron reactive sputtering for photoelectrochemical water reduction

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Green Energy & Environment 2018年第3期3卷 239-246页

作者： Tian Xie Tao Zheng Ruiling Wang Yuyu Bu Jin-ping ao Institute of Technology and Science Tokushima University National Institute of Technology Anan College Key Laboratory of Wide Band-Gap Semiconductor Materials and Devices School of MicroelectronicsXidian University

The CuO_x thin film photocathodes were deposited on F-doped Sn O_2 (FTO)transparent conducting glasses by alternating current(AC)magnetron reactive sputtering under different Ar:O_2 *** advantage of this deposited method is that it can deposit a CuO_x thin film uniformly and rapidly with large *** the photoelectrochemical(PEC)properties of these CuO_x photocathodes,it can be found that the CuO_x photocathode with Ar/O_2 30:7 provide a photocurrent density ofà3.2 m A cm^(à2)under a bias potentialà0.5 V(***/Ag Cl),which was found to be twice higher than that of Ar/O_2 with 30:5.A detailed characterization on the structure,morphology and electrochemical properties of these CuO_x thin film photocathodes was carried out,and it is found that the improved PEC performance of CuO_x semiconductor photocathode with Ar/O_230:7 attributed to the less defects in it,indicating that this Ar/O_230:7 is an optimized condition for excellent CuO_x semiconductor photocathode fabrication.

关键词： CuOx thin film Magnetron sputtering Photocathode Defect controlling

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Decoding early myelopoiesis from dynamics of core endogenous network

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Science China(Life Sciences) 2017年第6期60卷 627-646页

作者： Hang Su Gaowei Wang Ruoshi Yuan Junqiang Wang Ying Tang ping ao Xiaomei Zhu Key Laboratory of Systems Biomedicine(Ministry of Education) Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghai 200240China School of Biomedical Engineering Shanghai Jiao Tong UniversityShanghai 200240China Department of Physics and Astronomy Shanghai Jiao Tong UniversityShanghai 200240China State Key Laboratory for Oncogenes and Related Genes Shanghai Cancer InstituteShanghai Jiao Tong University School of MedicineShanghai 200240China Shanghai Center for Quantitative Life Sciences and Physics Department Shanghai UniversityShanghai 200444China

A decade ago mainstream molecular biologists regarded it impossible or biologically ill-motivated to understand the dynamics of complex biological phenomena, such as cancer genesis and progression, from a network perspective. Indeed, there are numerical difficulties even for those who were determined to explore along this direction. Undeterred, seven years ago a group of Chinese scientists started a program aiming to obtain quantitative connections between tumors and network dynamics. Many interesting results have been obtained. In this paper we wish to test such idea from a different angle: the connection between a normal biological process and the network dynamics. We have taken early myelopoiesis as our biological model. A standard roadmap for the cell-fate diversification during hematopoiesis has already been well established experimentally, yet little was known for its underpinning dynamical mechanisms. Compounding this difficulty there were additional experimental challenges, such as the seemingly conflicting hematopoietic roadmaps and the cell-fate inter-conversion events. With early myeloid cell-fate determination in mind, we constructed a core molecular endogenous network from well-documented gene regulation and signal transduction knowledge. Turning the network into a set of dynamical equations, we found computationally several structurally robust states. Those states nicely correspond to known cell phenotypes. We also found the states connecting those stable *** reveal the developmental routes—how one stable state would most likely turn into another stable state. Such interconnected network among stable states enabled a natural organization of cell-fates into a multi-stable state landscape. Accordingly, both the myeloid cell phenotypes and the standard roadmap were explained mechanistically in a straightforward manner. Furthermore,recent challenging observations were also explained naturally. Moreover, the landscape visually enables a prediction o

关键词： developmental scheme early myeloid cell-fate determination endogenous network stable state transition state landscape

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