Ecosystem stays far from thermodynamic equilibrium. Through the interactions among biotic and abiotic components, and encompassing physical environments, ecosystem forms a dissipative struc- ture that allows it to dis...Ecosystem stays far from thermodynamic equilibrium. Through the interactions among biotic and abiotic components, and encompassing physical environments, ecosystem forms a dissipative struc- ture that allows it to dissipate energy continuously and thereby remains functional over time. Biotic regulation of energy and material fluxes in and out of the ecosystem allows it to maintain a homeostatic state which corresponds to a self-organized state emerged in a non-equilibrium thermodynamic system. While the associated self-organizational processes approach to homeostatic state, entropy （a measure of irre- versibility） degrades and dissipation of energy increases. We propose here that at a homeostatic state of ecosystem, biodiversity which includes both phenotypic and functional diversity, attains optimal values. As long as biodiversity remains within its optimal range, the corresponding homeostatic state is maintained. However, while embedded environmental conditions fluctuate along the gradient of accelerating changes, phenotypic diversity and functional diversity contribute inversely to the associated self-organizing proc- esses. Furthermore, an increase or decrease in biodiversity outside of its optimal range makes the eco- system vulnerable to transition into a different state.展开更多
Ensemble simulations, which use multiple short independent trajectories from dispersive initial conformations, rather than a single long trajectory as used in traditional simulations, are expected to sample complex sy...Ensemble simulations, which use multiple short independent trajectories from dispersive initial conformations, rather than a single long trajectory as used in traditional simulations, are expected to sample complex systems such as biomolecules much more efficiently. The re-weighted ensemble dynamics（RED） is designed to combine these short trajectories to reconstruct the global equilibrium distribution. In the RED, a number of conformational functions, named as basis functions,are applied to relate these trajectories to each other, then a detailed-balance-based linear equation is built, whose solution provides the weights of these trajectories in equilibrium distribution. Thus, the sufficient and efficient selection of basis functions is critical to the practical application of RED. Here, we review and present a few possible ways to generally construct basis functions for applying the RED in complex molecular systems. Especially, for systems with less priori knowledge, we could generally use the root mean squared deviation（RMSD） among conformations to split the whole conformational space into a set of cells, then use the RMSD-based-cell functions as basis functions. We demonstrate the application of the RED in typical systems, including a two-dimensional toy model, the lattice Potts model, and a short peptide system. The results indicate that the RED with the constructions of basis functions not only more efficiently sample the complex systems, but also provide a general way to understand the metastable structure of conformational space.展开更多
Taking AuCu-sublattice system as an example, we present two discoveries and a method. First, the alloy gene sequences are the central characteristic atom sequences in the basic coordination cluster sequences. Second, ...Taking AuCu-sublattice system as an example, we present two discoveries and a method. First, the alloy gene sequences are the central characteristic atom sequences in the basic coordination cluster sequences. Second, the transmission mode of the information about structures and properties of the alloy genes is described by the alloy gene Gibbs energy partition function. The most valuable method in the system sciences is “the whole obtained from a few parts”. We have established the alloy gene database and holographic alloy positioning system of the Au-Cu system, as well as alloy gene Gibbs energy partition function and equilibrium holographic network phase diagrams of the AuCu-type sublattice system. It means that a standard way for researchers to share predictive algorithms and computational methods may be produced during designing advanced alloys.展开更多
The equilibrium geometry and electronic structure of pyrite has been studied using self consistent density functional theory within the local density approximation (LDA). The optimum bulk geometry is in good agreement...The equilibrium geometry and electronic structure of pyrite has been studied using self consistent density functional theory within the local density approximation (LDA). The optimum bulk geometry is in good agreement with crystallographic data. The calculated band structure and density of states in the region around the Fermi energy show that valence band maximum (VBM) is at X (100), and the conduction band minimum (CBM) is at G (000). The indirect and direct band gaps are 0.6?eV and 0.74?eV, respectively. The calculated contour map of difference of charge density shows excess charge in nonbonding d electron states on the Fe sites. The density increases between sulfur nuclei and between iron and sulfur nuclei qualitatively reveal that S-S bond and Fe-S bond are covalent binding.展开更多
A predator-prey model with linear capture term Holling-II functional response was studied by using differential equation theory. The existence and the stabilities of non-negative equilibrium points of the model were d...A predator-prey model with linear capture term Holling-II functional response was studied by using differential equation theory. The existence and the stabilities of non-negative equilibrium points of the model were discussed. The results show that under certain limited conditions, these two groups can maintain a balanced position, which provides a theoretical reference for relevant departments to make decisions on ecological protection.展开更多
针对传统数值预报模式计算时间长和计算资源消耗大的问题,以及现有深度学习预报方法在温度预报结果上不精确,且预测结果模糊的问题,提出了一个新的温度预报模型。首先,设计了一个时空信息捕捉模块,将该模块捕获的长期依赖信息,作为扩散...针对传统数值预报模式计算时间长和计算资源消耗大的问题,以及现有深度学习预报方法在温度预报结果上不精确,且预测结果模糊的问题,提出了一个新的温度预报模型。首先,设计了一个时空信息捕捉模块,将该模块捕获的长期依赖信息,作为扩散模型的生成条件,赋予扩散模型预报的能力;其次,设计了一个新的平衡损失函数,同时保护了扩散模型的生成能力和时空信息捕捉模块对时空信息的捕捉能力;最后,基于美国国家环境预报中心的再分析数据进行预报,与现有的深度学习方法相比,所提模型预报结果的质量在均方误差(mean square error,MSE)上降低了17.3%,在均方根误差(root mean square error,RMSE)上降低了9.14%,在峰值信噪比(peak signal to noise ratio,PSNR)上提升了5.1%。改进的扩散模型能有效地捕捉时空依赖的关系,有效地进行时空序列预测,效果优于其他对比方法。展开更多
Let X=(Omega,F,F-t,X(t),theta(t),P-x) be a jump Markov process with q-pair q(x)-q(x, A). In this paper, the equilibrium principle is established and equilibrium functions, energy, capacity and related problems is inve...Let X=(Omega,F,F-t,X(t),theta(t),P-x) be a jump Markov process with q-pair q(x)-q(x, A). In this paper, the equilibrium principle is established and equilibrium functions, energy, capacity and related problems is investigated in terms of the q-pair q(x)-q(x, A).展开更多
基金supported by the U.S. National Science Foundation's Biocomplexity Program (DEB-0421530)Long-Term Ecological Research Program (Sevilleta LTER,DEB-0620482)
文摘Ecosystem stays far from thermodynamic equilibrium. Through the interactions among biotic and abiotic components, and encompassing physical environments, ecosystem forms a dissipative struc- ture that allows it to dissipate energy continuously and thereby remains functional over time. Biotic regulation of energy and material fluxes in and out of the ecosystem allows it to maintain a homeostatic state which corresponds to a self-organized state emerged in a non-equilibrium thermodynamic system. While the associated self-organizational processes approach to homeostatic state, entropy （a measure of irre- versibility） degrades and dissipation of energy increases. We propose here that at a homeostatic state of ecosystem, biodiversity which includes both phenotypic and functional diversity, attains optimal values. As long as biodiversity remains within its optimal range, the corresponding homeostatic state is maintained. However, while embedded environmental conditions fluctuate along the gradient of accelerating changes, phenotypic diversity and functional diversity contribute inversely to the associated self-organizing proc- esses. Furthermore, an increase or decrease in biodiversity outside of its optimal range makes the eco- system vulnerable to transition into a different state.
基金Project supported by the National Natural Science Foundation of China(Grant No.11175250)
文摘Ensemble simulations, which use multiple short independent trajectories from dispersive initial conformations, rather than a single long trajectory as used in traditional simulations, are expected to sample complex systems such as biomolecules much more efficiently. The re-weighted ensemble dynamics（RED） is designed to combine these short trajectories to reconstruct the global equilibrium distribution. In the RED, a number of conformational functions, named as basis functions,are applied to relate these trajectories to each other, then a detailed-balance-based linear equation is built, whose solution provides the weights of these trajectories in equilibrium distribution. Thus, the sufficient and efficient selection of basis functions is critical to the practical application of RED. Here, we review and present a few possible ways to generally construct basis functions for applying the RED in complex molecular systems. Especially, for systems with less priori knowledge, we could generally use the root mean squared deviation（RMSD） among conformations to split the whole conformational space into a set of cells, then use the RMSD-based-cell functions as basis functions. We demonstrate the application of the RED in typical systems, including a two-dimensional toy model, the lattice Potts model, and a short peptide system. The results indicate that the RED with the constructions of basis functions not only more efficiently sample the complex systems, but also provide a general way to understand the metastable structure of conformational space.
文摘Taking AuCu-sublattice system as an example, we present two discoveries and a method. First, the alloy gene sequences are the central characteristic atom sequences in the basic coordination cluster sequences. Second, the transmission mode of the information about structures and properties of the alloy genes is described by the alloy gene Gibbs energy partition function. The most valuable method in the system sciences is “the whole obtained from a few parts”. We have established the alloy gene database and holographic alloy positioning system of the Au-Cu system, as well as alloy gene Gibbs energy partition function and equilibrium holographic network phase diagrams of the AuCu-type sublattice system. It means that a standard way for researchers to share predictive algorithms and computational methods may be produced during designing advanced alloys.
文摘The equilibrium geometry and electronic structure of pyrite has been studied using self consistent density functional theory within the local density approximation (LDA). The optimum bulk geometry is in good agreement with crystallographic data. The calculated band structure and density of states in the region around the Fermi energy show that valence band maximum (VBM) is at X (100), and the conduction band minimum (CBM) is at G (000). The indirect and direct band gaps are 0.6?eV and 0.74?eV, respectively. The calculated contour map of difference of charge density shows excess charge in nonbonding d electron states on the Fe sites. The density increases between sulfur nuclei and between iron and sulfur nuclei qualitatively reveal that S-S bond and Fe-S bond are covalent binding.
文摘A predator-prey model with linear capture term Holling-II functional response was studied by using differential equation theory. The existence and the stabilities of non-negative equilibrium points of the model were discussed. The results show that under certain limited conditions, these two groups can maintain a balanced position, which provides a theoretical reference for relevant departments to make decisions on ecological protection.
文摘针对传统数值预报模式计算时间长和计算资源消耗大的问题,以及现有深度学习预报方法在温度预报结果上不精确,且预测结果模糊的问题,提出了一个新的温度预报模型。首先,设计了一个时空信息捕捉模块,将该模块捕获的长期依赖信息,作为扩散模型的生成条件,赋予扩散模型预报的能力;其次,设计了一个新的平衡损失函数,同时保护了扩散模型的生成能力和时空信息捕捉模块对时空信息的捕捉能力;最后,基于美国国家环境预报中心的再分析数据进行预报,与现有的深度学习方法相比,所提模型预报结果的质量在均方误差(mean square error,MSE)上降低了17.3%,在均方根误差(root mean square error,RMSE)上降低了9.14%,在峰值信噪比(peak signal to noise ratio,PSNR)上提升了5.1%。改进的扩散模型能有效地捕捉时空依赖的关系,有效地进行时空序列预测,效果优于其他对比方法。
文摘Let X=(Omega,F,F-t,X(t),theta(t),P-x) be a jump Markov process with q-pair q(x)-q(x, A). In this paper, the equilibrium principle is established and equilibrium functions, energy, capacity and related problems is investigated in terms of the q-pair q(x)-q(x, A).
