The initial shape of the secondary arc considerably influences its subsequent shape.To establish the model for the arcing time of the secondary arc and modify the single-phase reclosing sequence,theoretical and experi...The initial shape of the secondary arc considerably influences its subsequent shape.To establish the model for the arcing time of the secondary arc and modify the single-phase reclosing sequence,theoretical and experimental analysis of the evolution process of the short-circuit arc to the secondary arc is critical.In this study,an improved charge simulation method was used to develop the internal-space electric-field model of the short-circuit arc.The intensity of the electric field was used as an independent variable to describe the initial shape of the secondary arc.A secondary arc evolution model was developed based on this model.Moreover,the accuracy of the model was evaluated by comparison with physical experimental results.When the secondary arc current increased,the arcing time and dispersion increased.There is an overall trend of increasing arc length with increasing arcing time.Nevertheless,there is a reduction in arc length during arc ignition due to short circuits between the arc columns.Furthermore,the arcing time decreased in the range of 0°-90°as the angle between the wind direction and the x-axis increased.This work investigated the method by which short-circuit arcs evolve into secondary arcs.The results can be used to develop the secondary arc evolution model and to provide both a technical and theoretical basis for secondary arc suppression.展开更多
The main stream of research into the diffusion of innovations neglected stochastic considerations for a long time.In rreality such stochastic phenomena have considerable influence on innovation diffusion.In thi paper ...The main stream of research into the diffusion of innovations neglected stochastic considerations for a long time.In rreality such stochastic phenomena have considerable influence on innovation diffusion.In thi paper it is tried to give a systeatic account of such stochastic influences.From a methodological perspective we point at some difficulties展开更多
Deciphering biogeographic patterns of microorganisms is important for evaluating the maintenance of microbial diversity with respect to the ecosystem functions they drives.However,ecological processes shaping distribu...Deciphering biogeographic patterns of microorganisms is important for evaluating the maintenance of microbial diversity with respect to the ecosystem functions they drives.However,ecological processes shaping distribution patterns of microorganisms across large spatial‐scale watersheds remain largely unknown.Using Illumina sequencing and multiple statistical methods,we characterized distribution patterns and maintenance diversity of microorganisms(i.e.,archaea,bacteria,and fungi)in soils and sediments along the Yangtze River.Distinct microbial distribution patterns were found between soils and sediments,and microbial community similarity significantly decreased with increasing geographical distance.Physicochemical properties showed a larger effect on microbial community composition than geospatial and climatic factors.Archaea and fungi displayed stronger species replacements and weaker environmental constraints in soils than that in sediments,but opposite for bacteria.Archaea,bacteria,and fungi in soils showed broader environmental breadths and stronger phylogenetic signals compared to those in sediments,suggesting stronger environmental adaptation.Stochasticity dominated community assemblies of archaea and fungi in soils and sediments,whereas determinism dominated bacterial community assembly.Our results have therefore highlighted distinct microbial distribution patterns and diversity maintenance mechanisms between soils and sediments,and emphasized important roles of species replacement,environmental adaptability,and ecological assembly processes on microbial landscape.Our findings are helpful in predicting loss of microbial diversity in the Yangtze River Basin,and might assist the establishment of environmental policies for protecting fragile watersheds.展开更多
With the aid of stochastic delayed-feedback differential equations, we derive an analytic expression for the power spectra of reacting molecules included in a generic biological network motif that is incorporated with...With the aid of stochastic delayed-feedback differential equations, we derive an analytic expression for the power spectra of reacting molecules included in a generic biological network motif that is incorporated with a feedback mechanism and time delays in gene regulation. We systematically analyse the effects of time delays, the feedback mechanism, and biological stochasticity on the power spectra. It has been clarified that the time delays together with the feedback mechanism can induce stochastic oscillations at the molecular level and invalidate the noise addition rule for a modular description of the noise propagator. Delay-induced stochastic resonance can be expected, which is related to the stability loss of the reaction systems and Hopf bifurcation occurring for solutions of the corresponding deterministic reaction equations. Through the analysis of the power spectrum, a new approach is proposed to estimate the oscillation period.展开更多
Theory allows studying why Evolution might select core genetic commitment circuit topologies over alternatives. The nonlinear dynamics of the underlying gene regulation together with the unescapable subtle interplay o...Theory allows studying why Evolution might select core genetic commitment circuit topologies over alternatives. The nonlinear dynamics of the underlying gene regulation together with the unescapable subtle interplay of intrinsic biochemical noise impact the range of possible evolutionary choices. The question of why certain genetic regulation circuits might present robustness to phenotype-delivery breaking over others, is therefore of high interest. Here, the behavior of systematically more complex commitment circuits is studied, in the presence of intrinsic noise, with a focus on two aspects relevant to biology： parameter asymmetry and time-scale separation. We show that phenotype delivery is broken in simple two- and three-gene circuits. In the two-gene circuit, we show how stochastic potential wells of different depths break commitment. In the three-gene circuit, we show that the onset of oscillations breaks the commitment phenotype in a systematic way. Finally, we also show that higher dimensional circuits （four-gene and five-gene circuits） may be intrinsically more robust.展开更多
The ordinary differential magnetic field line equations are solved numerically; the tokamak magnetic structure is studied on Hefei Tokamak-7 Upgrade （HT-TU） when the equilibrium field with a monotonic q-profile is p...The ordinary differential magnetic field line equations are solved numerically; the tokamak magnetic structure is studied on Hefei Tokamak-7 Upgrade （HT-TU） when the equilibrium field with a monotonic q-profile is perturbed by a helical magnetic field. We find that a single mode （m, n） helical perturbation can cause the formation of islands on rational surfaces with q=m/n and q=（m±1,±2,±3,...）/n due to the toroidicity and plasma shape （i.e. elongation and triangularity）, while there are many undestroyed magnetic surfaces called Kolmogorov-Arnold-Moser （KAM） barriers on irrational surfaces. The islands on the same rational surface do not have the same size. When the ratio between the perturbing magnetic field Br（r） and the toroidal magnetic field amplitude Bφ0 is large enough, the magnetic island chains on different rational surfaces will overlap and chaotic orbits appear in the overlapping area, and the magnetic field becomes stochastic. It is remarkable that the stochastic layer appears first in the plasma edge region.展开更多
Living cells are open systems that exist far away from a state of thermodynamical equilibrium. They utilize the high-grade chemical energy provided by food to produce ATP and re- lease ADP and Pi together with heat di...Living cells are open systems that exist far away from a state of thermodynamical equilibrium. They utilize the high-grade chemical energy provided by food to produce ATP and re- lease ADP and Pi together with heat dissipation. Living cells exist in a non-equilibrium steady state （NESS）, they replicate themselves and respond to various environmental changes via signal transduction pathways. Because the majority of cells exist at room temperature, the stochasticity of chemical reac- tions in the cells is unavoidable. Recent research into fluores- cent proteins and microscopy techniques have enabled us to observe the dynamic process of mRNA and proteins in single living bacterial cells [1], and these have resulted in new in- sights into regulation mechanisms in molecular biology, i.e., in cellular signal transduction pathways.展开更多
Background： One of the underlying assumptions of synthetic biology is that biological processes can be engineered in a controllable way. Results： Here we discuss this assumption as it relates to synthetic gene regul...Background： One of the underlying assumptions of synthetic biology is that biological processes can be engineered in a controllable way. Results： Here we discuss this assumption as it relates to synthetic gene regulatory networks （GRNs）. We first cover the theoretical basis of GRN control, then address three major areas in which control has been leveraged： engineering and analysis of network stability, temporal dynamics, and spatial aspects. Conclusion： These areas lay a strong foundation for further expansion of control in synthetic GRNs and pave the way for future work synthesizing these disparate concepts.展开更多
Stochastic dynamics pervades gene regulation. Despite being random, the dynamics displays a kind of innate structure. In fact, two stochastic forces combine driving efforts： one force originates from the gradient of ...Stochastic dynamics pervades gene regulation. Despite being random, the dynamics displays a kind of innate structure. In fact, two stochastic forces combine driving efforts： one force originates from the gradient of the underlying stochastic potential, and the other originates from the mathematical curl of the probability flux. The curl force gives rise to rotation. The gradient force gives rise to drift. Together they give rise to helical behavior. Here, it is shown that around and about the vicinity of attractive fixed points, the gradient force naturally wanes but the curl force is found to remain high. This leads to a locally noticeably different type of stochastic track near and about attractive fixed points, compared to tracks in regions where drift dominates. The consistency of this observation with the experimental fact that, in biology, fate commitment appears to not be a-priory locked-in, but rather necessitating active maintenance, is discussed. Hence attractive fixed-points are not only fuzzy, but may effectively be, locally, ＂more free＂.展开更多
One of the most complex questions in quantitative biology is how to manage noise sources and the subsequent consequences for cell functions. Noise in genetic networks is inevitable, as chemical reactions are probabili...One of the most complex questions in quantitative biology is how to manage noise sources and the subsequent consequences for cell functions. Noise in genetic networks is inevitable, as chemical reactions are probabilistic and often, genes, mRNAs and proteins are present in variable numbers per cell. Previous research has focused on counting these numbers using experimental methods such as complex fluorescent techniques or theoretical methods by characterizing the probability distribution of mRNAs and proteins numbers in cells. In this work, we propose a modeling based approach;we build a mathematical model that is used to predict the number of mRNAs and proteins over time, and develop a computational method to extract the noise-related information in such a biological system. Our approach contributes to answering the question of how the number of mRNA and proteins change in living cells over time and how these changes induce noise. Moreover, we calculate the entropy of the system;this turns out to be important information for prediction which could allow us to understand how noise information is generated and expanded.展开更多
基金supported by National Natural Science Foundation of China(Nos.92066108 and 51277061)。
文摘The initial shape of the secondary arc considerably influences its subsequent shape.To establish the model for the arcing time of the secondary arc and modify the single-phase reclosing sequence,theoretical and experimental analysis of the evolution process of the short-circuit arc to the secondary arc is critical.In this study,an improved charge simulation method was used to develop the internal-space electric-field model of the short-circuit arc.The intensity of the electric field was used as an independent variable to describe the initial shape of the secondary arc.A secondary arc evolution model was developed based on this model.Moreover,the accuracy of the model was evaluated by comparison with physical experimental results.When the secondary arc current increased,the arcing time and dispersion increased.There is an overall trend of increasing arc length with increasing arcing time.Nevertheless,there is a reduction in arc length during arc ignition due to short circuits between the arc columns.Furthermore,the arcing time decreased in the range of 0°-90°as the angle between the wind direction and the x-axis increased.This work investigated the method by which short-circuit arcs evolve into secondary arcs.The results can be used to develop the secondary arc evolution model and to provide both a technical and theoretical basis for secondary arc suppression.
文摘The main stream of research into the diffusion of innovations neglected stochastic considerations for a long time.In rreality such stochastic phenomena have considerable influence on innovation diffusion.In thi paper it is tried to give a systeatic account of such stochastic influences.From a methodological perspective we point at some difficulties
基金supported by the National Natural Science Foundation of China(42107147)Youth Innovation Promotion Association of the Chinese Academy of Sciences(2017388)+1 种基金National Science and Technology Fundamental Resources Investigation Program of China(2019FY100603)the Open Foundation of the State Key Laboratory of Urban and Regional Ecology of China(SKLURE2021-2-5).
文摘Deciphering biogeographic patterns of microorganisms is important for evaluating the maintenance of microbial diversity with respect to the ecosystem functions they drives.However,ecological processes shaping distribution patterns of microorganisms across large spatial‐scale watersheds remain largely unknown.Using Illumina sequencing and multiple statistical methods,we characterized distribution patterns and maintenance diversity of microorganisms(i.e.,archaea,bacteria,and fungi)in soils and sediments along the Yangtze River.Distinct microbial distribution patterns were found between soils and sediments,and microbial community similarity significantly decreased with increasing geographical distance.Physicochemical properties showed a larger effect on microbial community composition than geospatial and climatic factors.Archaea and fungi displayed stronger species replacements and weaker environmental constraints in soils than that in sediments,but opposite for bacteria.Archaea,bacteria,and fungi in soils showed broader environmental breadths and stronger phylogenetic signals compared to those in sediments,suggesting stronger environmental adaptation.Stochasticity dominated community assemblies of archaea and fungi in soils and sediments,whereas determinism dominated bacterial community assembly.Our results have therefore highlighted distinct microbial distribution patterns and diversity maintenance mechanisms between soils and sediments,and emphasized important roles of species replacement,environmental adaptability,and ecological assembly processes on microbial landscape.Our findings are helpful in predicting loss of microbial diversity in the Yangtze River Basin,and might assist the establishment of environmental policies for protecting fragile watersheds.
基金Project supported by the National Natural Science Foundation of China (Grant No. 10975019)the Foundation of the Ministry of Personnel of China for Returned Scholars (Grant No. MOP2006138)the Fundamental Research Funds for the Central Universities
文摘With the aid of stochastic delayed-feedback differential equations, we derive an analytic expression for the power spectra of reacting molecules included in a generic biological network motif that is incorporated with a feedback mechanism and time delays in gene regulation. We systematically analyse the effects of time delays, the feedback mechanism, and biological stochasticity on the power spectra. It has been clarified that the time delays together with the feedback mechanism can induce stochastic oscillations at the molecular level and invalidate the noise addition rule for a modular description of the noise propagator. Delay-induced stochastic resonance can be expected, which is related to the stability loss of the reaction systems and Hopf bifurcation occurring for solutions of the corresponding deterministic reaction equations. Through the analysis of the power spectrum, a new approach is proposed to estimate the oscillation period.
文摘Theory allows studying why Evolution might select core genetic commitment circuit topologies over alternatives. The nonlinear dynamics of the underlying gene regulation together with the unescapable subtle interplay of intrinsic biochemical noise impact the range of possible evolutionary choices. The question of why certain genetic regulation circuits might present robustness to phenotype-delivery breaking over others, is therefore of high interest. Here, the behavior of systematically more complex commitment circuits is studied, in the presence of intrinsic noise, with a focus on two aspects relevant to biology： parameter asymmetry and time-scale separation. We show that phenotype delivery is broken in simple two- and three-gene circuits. In the two-gene circuit, we show how stochastic potential wells of different depths break commitment. In the three-gene circuit, we show that the onset of oscillations breaks the commitment phenotype in a systematic way. Finally, we also show that higher dimensional circuits （four-gene and five-gene circuits） may be intrinsically more robust.
基金Project supported by the National Natural Science Foundation of China （Grant Nos 10405030 and 10135020）.
文摘The ordinary differential magnetic field line equations are solved numerically; the tokamak magnetic structure is studied on Hefei Tokamak-7 Upgrade （HT-TU） when the equilibrium field with a monotonic q-profile is perturbed by a helical magnetic field. We find that a single mode （m, n） helical perturbation can cause the formation of islands on rational surfaces with q=m/n and q=（m±1,±2,±3,...）/n due to the toroidicity and plasma shape （i.e. elongation and triangularity）, while there are many undestroyed magnetic surfaces called Kolmogorov-Arnold-Moser （KAM） barriers on irrational surfaces. The islands on the same rational surface do not have the same size. When the ratio between the perturbing magnetic field Br（r） and the toroidal magnetic field amplitude Bφ0 is large enough, the magnetic island chains on different rational surfaces will overlap and chaotic orbits appear in the overlapping area, and the magnetic field becomes stochastic. It is remarkable that the stochastic layer appears first in the plasma edge region.
基金supported by the National Natural Science Foundation of China(Grant Nos.11174011,and 91130005)the National Key Basic Research Project of China(Grant No.2015CB910300)
文摘Living cells are open systems that exist far away from a state of thermodynamical equilibrium. They utilize the high-grade chemical energy provided by food to produce ATP and re- lease ADP and Pi together with heat dissipation. Living cells exist in a non-equilibrium steady state （NESS）, they replicate themselves and respond to various environmental changes via signal transduction pathways. Because the majority of cells exist at room temperature, the stochasticity of chemical reac- tions in the cells is unavoidable. Recent research into fluores- cent proteins and microscopy techniques have enabled us to observe the dynamic process of mRNA and proteins in single living bacterial cells [1], and these have resulted in new in- sights into regulation mechanisms in molecular biology, i.e., in cellular signal transduction pathways.
文摘Background： One of the underlying assumptions of synthetic biology is that biological processes can be engineered in a controllable way. Results： Here we discuss this assumption as it relates to synthetic gene regulatory networks （GRNs）. We first cover the theoretical basis of GRN control, then address three major areas in which control has been leveraged： engineering and analysis of network stability, temporal dynamics, and spatial aspects. Conclusion： These areas lay a strong foundation for further expansion of control in synthetic GRNs and pave the way for future work synthesizing these disparate concepts.
文摘Stochastic dynamics pervades gene regulation. Despite being random, the dynamics displays a kind of innate structure. In fact, two stochastic forces combine driving efforts： one force originates from the gradient of the underlying stochastic potential, and the other originates from the mathematical curl of the probability flux. The curl force gives rise to rotation. The gradient force gives rise to drift. Together they give rise to helical behavior. Here, it is shown that around and about the vicinity of attractive fixed points, the gradient force naturally wanes but the curl force is found to remain high. This leads to a locally noticeably different type of stochastic track near and about attractive fixed points, compared to tracks in regions where drift dominates. The consistency of this observation with the experimental fact that, in biology, fate commitment appears to not be a-priory locked-in, but rather necessitating active maintenance, is discussed. Hence attractive fixed-points are not only fuzzy, but may effectively be, locally, ＂more free＂.
文摘One of the most complex questions in quantitative biology is how to manage noise sources and the subsequent consequences for cell functions. Noise in genetic networks is inevitable, as chemical reactions are probabilistic and often, genes, mRNAs and proteins are present in variable numbers per cell. Previous research has focused on counting these numbers using experimental methods such as complex fluorescent techniques or theoretical methods by characterizing the probability distribution of mRNAs and proteins numbers in cells. In this work, we propose a modeling based approach;we build a mathematical model that is used to predict the number of mRNAs and proteins over time, and develop a computational method to extract the noise-related information in such a biological system. Our approach contributes to answering the question of how the number of mRNA and proteins change in living cells over time and how these changes induce noise. Moreover, we calculate the entropy of the system;this turns out to be important information for prediction which could allow us to understand how noise information is generated and expanded.
