It is well known that plants have functional equilibrium between their above-ground parts (shoots) and below-ground parts (roots), but whether the above-ground parts of plants have functional equilibrium between their...It is well known that plants have functional equilibrium between their above-ground parts (shoots) and below-ground parts (roots), but whether the above-ground parts of plants have functional equilibrium between their photosynthetic structures (leaves) and non-photosynthetic structures (branches and stem) is unknown. The purpose of this study is to test the hypotheses that: (1) the above-ground parts of plants have functional equilibriums between their photosynthetic structures and non-photosynthetic structures; (2) the maintenance of the equilibriums is guaranteed by the alteration of biomass partitioning to photosynthetic and non-photosynthetic structures. To test these hypotheses, a pruning experiment with four pruning intensities (0%, 20%, 50%, and 70%) were carried out with three subtropical Chinese tree species ( Ficus microcarpa, Ficus virens, Cinnamomum camphora). Pruning treatments were conducted in two successive years. The results were in conformity with the hypothesis, i.e. above-ground parts of trees had functional equilibriums between photosynthetic and non-photosynthetic structures. Pruning decreased instantaneously the mass ratios of photosynthetic structures to non-photosynthetic structures (P/NP) of all three tree species, the reduction in P/NP was strengthened with pruning intensity. However, one year after pruning, the P/NP of all pruned trees increased and were not smaller than those of unpruned trees. In agreement with the expectation, the biomass partitioning of pruned trees was altered, more newly produced above-ground biomass was partitioned to leaf growth and less to branch and stem growth, thus enabled the damaged trees to restore their functional equilibrium between photosynthetic and non-photosynthetic structures. It is clear that the maintenance of functional equilibrium between photosynthetic and non-photosynthetic structures guaranteed by the alteration of biomass partitioning provides plants a good strategy to resist external disturbance and damage.展开更多
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
Let X=(Ω,■,■,X_(t),θ_(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...Let X=(Ω,■,■,X_(t),θ_(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
文摘It is well known that plants have functional equilibrium between their above-ground parts (shoots) and below-ground parts (roots), but whether the above-ground parts of plants have functional equilibrium between their photosynthetic structures (leaves) and non-photosynthetic structures (branches and stem) is unknown. The purpose of this study is to test the hypotheses that: (1) the above-ground parts of plants have functional equilibriums between their photosynthetic structures and non-photosynthetic structures; (2) the maintenance of the equilibriums is guaranteed by the alteration of biomass partitioning to photosynthetic and non-photosynthetic structures. To test these hypotheses, a pruning experiment with four pruning intensities (0%, 20%, 50%, and 70%) were carried out with three subtropical Chinese tree species ( Ficus microcarpa, Ficus virens, Cinnamomum camphora). Pruning treatments were conducted in two successive years. The results were in conformity with the hypothesis, i.e. above-ground parts of trees had functional equilibriums between photosynthetic and non-photosynthetic structures. Pruning decreased instantaneously the mass ratios of photosynthetic structures to non-photosynthetic structures (P/NP) of all three tree species, the reduction in P/NP was strengthened with pruning intensity. However, one year after pruning, the P/NP of all pruned trees increased and were not smaller than those of unpruned trees. In agreement with the expectation, the biomass partitioning of pruned trees was altered, more newly produced above-ground biomass was partitioned to leaf growth and less to branch and stem growth, thus enabled the damaged trees to restore their functional equilibrium between photosynthetic and non-photosynthetic structures. It is clear that the maintenance of functional equilibrium between photosynthetic and non-photosynthetic structures guaranteed by the alteration of biomass partitioning provides plants a good strategy to resist external disturbance and damage.
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Let X=(Ω,■,■,X_(t),θ_(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).
