Finite-difference(FD) methods are widely used in seismic forward modeling owing to their computational efficiency but are not readily applicable to irregular topographies. Thus, several FD methods based on the transfo...Finite-difference(FD) methods are widely used in seismic forward modeling owing to their computational efficiency but are not readily applicable to irregular topographies. Thus, several FD methods based on the transformation to curvilinear coordinates using body-fitted grids have been proposed, e.g., stand staggered grid(SSG) with interpolation, nonstaggered grid, rotated staggered grid(RSG), and fully staggered. The FD based on the RSG is somewhat superior to others because it satisfies the spatial distribution of the wave equation without additional memory and computational requirements; furthermore, it is simpler to implement. We use the RSG FD method to transform the firstorder stress–velocity equation in the curvilinear coordinates system and introduce the highprecision adaptive, unilateral mimetic finite-difference(UMFD) method to process the freeboundary conditions of an irregular surface. The numerical results suggest that the precision of the solution is higher than that of the vacuum formalism. When the minimum wavelength is low, UMFD avoids the surface wave dispersion. We compare FD methods based on RSG, SEM, and nonstaggered grid and infer that all simulation results are consistent but the computational efficiency of the RSG FD method is higher than the rest.展开更多
The Drag-Free and Attitude Control System(DFACS)is a critical platform for various space missions,including high precision satellite navigation,geoscience and gravity field measurement,and space scientific experiments...The Drag-Free and Attitude Control System(DFACS)is a critical platform for various space missions,including high precision satellite navigation,geoscience and gravity field measurement,and space scientific experiments.This paper presents a comprehensive review of over sixty years of research on the design and dynamics model of DFACS.Firstly,we examine the open literature on DFACS and its applications in Drag-Free missions,providing readers with necessary background information on the field.Secondly,we analyze the system configurations and main characteristics of different DFACSs,paying particular attention to the coupling mechanism between the system configuration and dynamics model.Thirdly,we summarize the dynamics modeling methods and main dynamics models of DFACS from multiple perspectives,including common fundamentals and specific applications.Lastly,we identify current challenges and technological difficulties in the system design and dynamics modeling of DFACS,while suggesting potential avenues for future research.This paper aims to provide readers with a comprehensive understanding of the state-of-the-art in DFACS research,as well as the future prospects and challenges in this field.展开更多
In this work, a novel thermal–hydraulic–mechanical (THM) coupling model is developed, where the real geological parameters of the reservoir properties are embedded. Accordingly, nine schemes of CO_(2) injection well...In this work, a novel thermal–hydraulic–mechanical (THM) coupling model is developed, where the real geological parameters of the reservoir properties are embedded. Accordingly, nine schemes of CO_(2) injection well (IW) and CH_(4) production well (PW) are established, aiming to explore the behavior of free gases after CO_(2) is injected into the depleted Wufeng–Longmaxi shale. The results indicate the free CH4 or CO2 content in the shale fractures/matrix is invariably heterogeneous. The CO_(2) involvement facilitates the ratio of free CH_(4)/CO_(2) in the matrix to that in the fractures declines and tends to be stable with time. Different combinations of IW–PWs induce a difference in the ratio of the free CH4 to the free CO_(2), in the ratio of the free CH_(4)/CO_(2) in the matrix to that in the fractures, in the content of the recovered free CH_(4), and in the content of the trapped free CO_(2). Basically, when the IW locates at the bottom Wufeng–Longmaxi shale, a farther IW–PWs distance allows more CO2 in the free phase to be trapped;furthermore, no matter where the IW is, a shorter IW–PWs distance benefits by getting more CH_(4) in the free phase recovered from the depleted Wufeng–Longmaxi shale. Hopefully, this work is helpful in gaining knowledge about the shale-based CO_(2) injection technique.展开更多
Many interesting characteristics of sea ice drift depend on the atmospheric drag coefficient （Ca） and oceanic drag coefficient （Cw）. Parameterizations of drag coefficients rather than constant values provide us a ...Many interesting characteristics of sea ice drift depend on the atmospheric drag coefficient （Ca） and oceanic drag coefficient （Cw）. Parameterizations of drag coefficients rather than constant values provide us a way to look insight into the dependence of these characteristics on sea ice conditions. In the present study, the parameterized ice drag coefficients are included into a free-drift sea ice dynamic model, and the wind factor a and the deflection angle θ between sea ice drift and wind velocity as well as the ratio of Ca to Cw are studied to investigate their dependence on the impact factors such as local drag coefficients, floe and ridge geometry. The results reveal that in an idealized steady ocean, Ca/Cw increases obviously with the increasing ice concentration for small ice floes in the marginal ice zone, while it remains at a steady level （0.2-0.25） for large floes in the central ice zone. The wind factor a increases rapidly at first and approaches a steady level of 0.018 when A is greater than 20%. And the deflection angle ~ drops rapidly from an initial value of approximate 80° and decreases slowly as A is greater than 20% without a steady level like a. The values of these parameters agree well with the previously reported observations in Arctic. The ridging intensity is an important parameter to determine the dominant contribution of the ratio of skin friction drag coefficient （Cs＇/Cs） and the ratio of ridge form drag coefficient （Cr＇/Cr） to the value of Ca/Cw, a, and 8, because of the dominance of ridge form drag for large ridging intensity and skin friction for small ridging intensity among the total drag forces. Parameterization of sea ice drag coefficients has the potential to be embedded into ice dynamic models to better account for the variability of sea ice in the transient Arctic Ocean.展开更多
Abstract Methane （CH4） emissions from paddy rice fields substantially contribute to the dramatic increase of this greenhouse gas in the atmosphere. Due to great concern about climate change, it is necessary to predi...Abstract Methane （CH4） emissions from paddy rice fields substantially contribute to the dramatic increase of this greenhouse gas in the atmosphere. Due to great concern about climate change, it is necessary to predict the effects of the dramatic increase in atmospheric carbon dioxide （CO2） on CH4 emissions from paddy rice fields. CH4MOD 1.0 is the most widely validated model for simulating CH4 emissions from paddy rice fields exposed to ambient CO2 （hereinafter referred to as aCO2）. We upgraded the model to CH4MOD 2.0 by： （a） modifying the description of the influences of soil Eh and the water regime on CH4 production; （b） adding new features to reflect the regulatory effects of atmospheric CO2 upon methanogenic substrates, soil Eh during drainages, and vascular CH4 transport; and （c） adding a new feature to simulate the influences of nitrogen （N） addition rates on methanogenic substrates under elevated CO2 （hereinafter referred to as eCO2） condition. Validation with 109 observation cases under aC02 condition showed that CHaMOD 2.0 possessed a minor systematic bias in the prediction of seasonally accumulated methane emissions （SAM）. Validation with observations in free-air CO2 enrichment （FACE） experiments in temperate and subtropical climates showed that CH4MOD 2.0 successfully simulated the effects of eCO2 upon SAM from paddy rice fields incorporated with various levels of previous crop residues and/or N fertilizer. Our results imply that CH4MOD 2.0 provides a potential approach for estimating of the effects of elevated atmospheric CO2 upon CHa emissions from regional or global paddy rice fields with various management practices in a changing climate.展开更多
Alternative mechanisms of toxic effects induced by 2,3,7,8-tetrachlorodibenzo-p-dioxin（TCDD）, instead of the binding to aryl hydrocarbon receptor（AhR）, have been taken into consideration. It has been recently show...Alternative mechanisms of toxic effects induced by 2,3,7,8-tetrachlorodibenzo-p-dioxin（TCDD）, instead of the binding to aryl hydrocarbon receptor（AhR）, have been taken into consideration. It has been recently shown that TCDD reduces rapidly the activity of CK2（casein kinase II） both in vivo and in vitro. It is found that TCDD has high molecular similarities to the known inhibitors of CK2 catalytic subunit（CK2a）. This suggests that TCDD could also be an ATP-competitive inhibitor of CK2a. In this work, docking TCDD to CK2 was carried out based on the two structures of CK2a from maize and human, respectively. The binding free energies of the predicted CK2a-TCDD complexes estimated by the molecular mechanics/Poisson-Boltzmann surface area（MM/PBSA） method are from -85.1 kJ/mol to -114.3 kJ/mol for maize and are from -96.1 kJ/mol to -118.2 kJ/mol for human, which are comparable to those estimated for the known inhibitor and also ATP with CK2a. The energetic analysis also reveals that the van der Waals interaction is the dominant contribution to the binding free energy. These results are also useful for designing new drugs for a target of overexpressing CK2 in cancers.展开更多
The possible inclusion modes of berberine（Berb） with β-cyclodextrin（BCD） in aqueous solution were predicted by molecular docking,molecular dynamics（MD） simulation and binding free energy calculations.Firstly,th...The possible inclusion modes of berberine（Berb） with β-cyclodextrin（BCD） in aqueous solution were predicted by molecular docking,molecular dynamics（MD） simulation and binding free energy calculations.Firstly,the molecular docking result reveals that the docking conformations of Berb appeared in two clusters ranked in two opposite orientations.Then,10 ns MD simulation was performed separately on the lowest energy conformation of each orientation（Mode I and Mode II） obtained by molecular docking.Moreover,based on the trajectories from MD simulation,the binding free energies of the two different modes were calculated by the Molecular Mechanics/Poisson Boltzmann surface area（MM/PBSA） method.Through analyzing the binding free energies of Berb with BCD,we found that Mode II was the preferential inclusion mode,which was in good agreement with the experimental result.In addition,the computed results show that the main impetus for the complex was the van der Waals interaction,but the solvation energy and the entropy change produced an adverse effect on the complex.展开更多
Atmospheric oxidizing capacity(AOC)is an essential driving force of troposphere chemistry and self-cleaning,but the definition of AOC and its quantitative representation remain uncertain.Driven by national demand for ...Atmospheric oxidizing capacity(AOC)is an essential driving force of troposphere chemistry and self-cleaning,but the definition of AOC and its quantitative representation remain uncertain.Driven by national demand for air pollution control in recent years,Chinese scholars have carried out studies on theories of atmospheric chemistry and have made considerable progress in AOC research.This paper will give a brief review of these developments.First,AOC indexes were established that represent apparent atmospheric oxidizing ability(AOIe)and potential atmospheric oxidizing ability(AOIp)based on aspects of macrothermodynamics and microdynamics,respectively.A closed study refined the quantitative contributions of heterogeneous chemistry to AOC in Beijing,and these AOC methods were further applied in Beijing-Tianjin-Hebei and key areas across the country.In addition,the detection of ground or vertical profiles for atmospheric OH·,HO_(2)·,NO_(3)·radicals and reservoir molecules can now be obtained with domestic instruments in diverse environments.Moreover,laboratory smoke chamber simulations revealed heterogeneous processes involving reactions of O_(3)and NO_(2),which are typical oxidants in the surface/interface atmosphere,and the evolutionary and budgetary implications of atmospheric oxidants reacting under multispecies,multiphase and multi-interface conditions were obtained.Finally,based on the GRAPES-CUACE adjoint model improved by Chinese scholars,simulations of key substances affecting atmospheric oxidation and secondary organic and inorganic aerosol formation have been optimized.Normalized numerical simulations of AOIe and AOIp were performed,and regional coordination of AOC was adjusted.An optimized plan for controlling O_(3)and PM2.5was analyzed by scenario simulation.展开更多
Meshfree method offers high accuracy and computational capability and constructs the shape function without relying on predefined elements. We comparatively analyze the global weak form meshfree methods, such as eleme...Meshfree method offers high accuracy and computational capability and constructs the shape function without relying on predefined elements. We comparatively analyze the global weak form meshfree methods, such as element-free Galerkin method （EFGM）, the point interpolation method （PIM）, and the radial point interpolation method （RPIM）. Taking two dimensional Poisson equation as an example, we discuss the support-domain dimensionless size, the field nodes, and background element settings with respect to their effect on calculation accuracy of the meshfree method. RPIM and EFGM are applied to controlled- source two-dimensional electromagnetic modeling with fixed shape parameters. The accuracy of boundary conditions imposed directly and by a penalty function are discussed in the case of forward modeling of two-dimensional magnetotellurics in a homogeneous medium model. The coupling algorithm of EFG-PIM and EFG-RPIM are generated by integrating the PIM or RPIM and EFGM. The results of the numerical modeling suggest the following. First, the proposed meshfree method and corresponding coupled methods are well-suited for electromagnetic numerical modeling. The accuracy of the algorithm is the highest when the support-domain dimensionless size is 1.0 and the distribution of field nodes is consistent with the nodes of background elements. Second, the accuracy of PIM and RPIM are lower than that of EFGM for the Poisson equation but higher than EFGM for the homogeneous medium MT response. Third, RPIM overcomes the matrix inversion problem of PIM and has a wider selection of support-domain dimensionless sizes as compared to RPIM.展开更多
A thermodynamic integration dual-transform method was firstly applied to calculating the relative hydration free energies of 99m TcO-N 2S 2 complexes. The relationship between the brain uptakes(B.U.) of ...A thermodynamic integration dual-transform method was firstly applied to calculating the relative hydration free energies of 99m TcO-N 2S 2 complexes. The relationship between the brain uptakes(B.U.) of 99m TcO-N 2S 2 complexes with different substituted functional groups and their relative hydration free energies was investigated. The simulation results show that the experiment brain uptake(B.U.) data are strongly influenced by the relative hydration free energies of 99m TcO-N 2S 2 complexes, thus the simulations can provide the useful information for the medicine design of 99m Tc brain imaging agents.展开更多
Carboxyltransferase domain（CT） of acetyl-coenzyme A carboxylase（ACCase, EC 6.4.1.2） from a family of Poaceae is an important target of commercial herbicide APPs for controlling grass weed growth. As the abuse of A...Carboxyltransferase domain（CT） of acetyl-coenzyme A carboxylase（ACCase, EC 6.4.1.2） from a family of Poaceae is an important target of commercial herbicide APPs for controlling grass weed growth. As the abuse of APPs herbicides, the resistant ACCase due to the mutation of a single residue（Ile→Leu）, which is located in CT active site, is emergent in many populations and species of Poaceae. So it is urgent to understand the resistant mechanism so as to design new effect herbicides. Herein lies the complex of CT dimmer from Lolium rigidum and herbicide haloxyfop successfully constructed for wild type enzyme and Ile/Leu mutant, respectively, providing a basis for explaining the resistance from microscopic structure. Moreover, the binding free energy difference between wild type and mutant enzymes was predicted in good agreement with the known observation, and the various contributions to it were analyzed, by Molecular mechanics-Poisson-Boltzmann surface area（MM-PBSA） method. The results indicate the van der Waals interaction difference between the protein and inhibitor, -22.94 kJ/mol of CT wild type lower than that of mutant, is the major reason for resistance. Structure analysis further suggests that van der Waals interaction difference is originated from the steric hindrance between the side chain of mutated residue Leu and the chiral methyl group of haloxyfop. All these findings enhance the understanding of resistant mechanism of ACCase to herbicide by Ile/Leu mutation and provide an important clue for the rational design of high effective herbicides.展开更多
Development of the orbital-free (OF) approach of the density functional theory (DFT) may result in a power instrument for modeling of complicated nanosystems with a huge number of atoms. A key problem on this way is c...Development of the orbital-free (OF) approach of the density functional theory (DFT) may result in a power instrument for modeling of complicated nanosystems with a huge number of atoms. A key problem on this way is calculation of the kinetic energy. We demonstrate how it is possible to create the OF kinetic energy functionals using results of Kohn-Sham calculations for single atoms. Calculations provided with these functionals for dimers of sp-elements of the C, Si, and Ge periodic table rows show a good accordance with the Kohn-Sham DFT results.展开更多
In this paper, a numerical simulation has been carried out on unsteady hydromagnetic free convection near a moving infinite flat plate in a rotating medium. The temperatures involved are assumed to be very high so tha...In this paper, a numerical simulation has been carried out on unsteady hydromagnetic free convection near a moving infinite flat plate in a rotating medium. The temperatures involved are assumed to be very high so that the radiative heat transfer is significant, which renders the problem highly non-linear even with the assumption of a differential approximation for the radiative heat flux. A numerical method based on the Nakamura scheme has been employed to obtain the temperature and velocity distributions which are depicted graphically. The effects of the different parameters entering into the problem have been discussed extensively.展开更多
A mathematical model incorporating animal TB and Human TB transmission is formulated and analysed in order to determine the role of animal TB and human TB in the overall TB transmission and also, to determine the para...A mathematical model incorporating animal TB and Human TB transmission is formulated and analysed in order to determine the role of animal TB and human TB in the overall TB transmission and also, to determine the parameters which govern the transmission of the TB disease. The model has five classes namely susceptible, exposed animal TB, and exposed human TB, infectious and recovery. The model assumed that there are two classes for infected individuals, those who acquired TB through animal and those who acquire TB from human. Qualitative results show that the model has the disease-free equilibrium and at least one endemic equilibrium that is locally asymptotically stable. The study includes numerical simulations as a way of supporting the analytical results. Graphical results indicate that animal TB has major contribution on overall TB transmission and the TB transmission can be reduced by ensuring intervention to both Animal TB and Human TB. Furthermore the equations indicate that there is at least one endemic equilibrium which translates that t animal and human have the contribution on TB transmission. This shows that both animals and humans together with fast progressors have contribution on TB transmissions.展开更多
基金supported by the National Nature Science Foundation of China(Nos.41504102 and 41604037)National Science and Technology Major Project(No.2016ZX05015-006)Yangtze University Youth Found(No.2015cqn32)
文摘Finite-difference(FD) methods are widely used in seismic forward modeling owing to their computational efficiency but are not readily applicable to irregular topographies. Thus, several FD methods based on the transformation to curvilinear coordinates using body-fitted grids have been proposed, e.g., stand staggered grid(SSG) with interpolation, nonstaggered grid, rotated staggered grid(RSG), and fully staggered. The FD based on the RSG is somewhat superior to others because it satisfies the spatial distribution of the wave equation without additional memory and computational requirements; furthermore, it is simpler to implement. We use the RSG FD method to transform the firstorder stress–velocity equation in the curvilinear coordinates system and introduce the highprecision adaptive, unilateral mimetic finite-difference(UMFD) method to process the freeboundary conditions of an irregular surface. The numerical results suggest that the precision of the solution is higher than that of the vacuum formalism. When the minimum wavelength is low, UMFD avoids the surface wave dispersion. We compare FD methods based on RSG, SEM, and nonstaggered grid and infer that all simulation results are consistent but the computational efficiency of the RSG FD method is higher than the rest.
基金This research was supported by National Key R&D Program of China:Gravitational Wave Detection Project,China(Nos.2021YFC2202601,2021YFC2202603)National Natural Science Foundation of China(No.12172288).
文摘The Drag-Free and Attitude Control System(DFACS)is a critical platform for various space missions,including high precision satellite navigation,geoscience and gravity field measurement,and space scientific experiments.This paper presents a comprehensive review of over sixty years of research on the design and dynamics model of DFACS.Firstly,we examine the open literature on DFACS and its applications in Drag-Free missions,providing readers with necessary background information on the field.Secondly,we analyze the system configurations and main characteristics of different DFACSs,paying particular attention to the coupling mechanism between the system configuration and dynamics model.Thirdly,we summarize the dynamics modeling methods and main dynamics models of DFACS from multiple perspectives,including common fundamentals and specific applications.Lastly,we identify current challenges and technological difficulties in the system design and dynamics modeling of DFACS,while suggesting potential avenues for future research.This paper aims to provide readers with a comprehensive understanding of the state-of-the-art in DFACS research,as well as the future prospects and challenges in this field.
基金This study was financially supported by the National Natural Science Foundation of China(Grant Nos.51704197 and 11872258)。
文摘In this work, a novel thermal–hydraulic–mechanical (THM) coupling model is developed, where the real geological parameters of the reservoir properties are embedded. Accordingly, nine schemes of CO_(2) injection well (IW) and CH_(4) production well (PW) are established, aiming to explore the behavior of free gases after CO_(2) is injected into the depleted Wufeng–Longmaxi shale. The results indicate the free CH4 or CO2 content in the shale fractures/matrix is invariably heterogeneous. The CO_(2) involvement facilitates the ratio of free CH_(4)/CO_(2) in the matrix to that in the fractures declines and tends to be stable with time. Different combinations of IW–PWs induce a difference in the ratio of the free CH4 to the free CO_(2), in the ratio of the free CH_(4)/CO_(2) in the matrix to that in the fractures, in the content of the recovered free CH_(4), and in the content of the trapped free CO_(2). Basically, when the IW locates at the bottom Wufeng–Longmaxi shale, a farther IW–PWs distance allows more CO2 in the free phase to be trapped;furthermore, no matter where the IW is, a shorter IW–PWs distance benefits by getting more CH_(4) in the free phase recovered from the depleted Wufeng–Longmaxi shale. Hopefully, this work is helpful in gaining knowledge about the shale-based CO_(2) injection technique.
基金The National Natural Science Foundation of China under contracts Nos 41276191 and 41306207the Public Science and Technology Research Funds Projects of Ocean under contract No.201205007-05the Global Change Research Program of China under contract No.2015CB953901
文摘Many interesting characteristics of sea ice drift depend on the atmospheric drag coefficient （Ca） and oceanic drag coefficient （Cw）. Parameterizations of drag coefficients rather than constant values provide us a way to look insight into the dependence of these characteristics on sea ice conditions. In the present study, the parameterized ice drag coefficients are included into a free-drift sea ice dynamic model, and the wind factor a and the deflection angle θ between sea ice drift and wind velocity as well as the ratio of Ca to Cw are studied to investigate their dependence on the impact factors such as local drag coefficients, floe and ridge geometry. The results reveal that in an idealized steady ocean, Ca/Cw increases obviously with the increasing ice concentration for small ice floes in the marginal ice zone, while it remains at a steady level （0.2-0.25） for large floes in the central ice zone. The wind factor a increases rapidly at first and approaches a steady level of 0.018 when A is greater than 20%. And the deflection angle ~ drops rapidly from an initial value of approximate 80° and decreases slowly as A is greater than 20% without a steady level like a. The values of these parameters agree well with the previously reported observations in Arctic. The ridging intensity is an important parameter to determine the dominant contribution of the ratio of skin friction drag coefficient （Cs＇/Cs） and the ratio of ridge form drag coefficient （Cr＇/Cr） to the value of Ca/Cw, a, and 8, because of the dominance of ridge form drag for large ridging intensity and skin friction for small ridging intensity among the total drag forces. Parameterization of sea ice drag coefficients has the potential to be embedded into ice dynamic models to better account for the variability of sea ice in the transient Arctic Ocean.
基金supported by the National Natural Science Foundation of China (40675075, 40425010)the Chinese Academy of Sciences (KZCX3-SW-440,KZCX2-yw-204)the European Union (NitroEurope IP 017841)
文摘Abstract Methane （CH4） emissions from paddy rice fields substantially contribute to the dramatic increase of this greenhouse gas in the atmosphere. Due to great concern about climate change, it is necessary to predict the effects of the dramatic increase in atmospheric carbon dioxide （CO2） on CH4 emissions from paddy rice fields. CH4MOD 1.0 is the most widely validated model for simulating CH4 emissions from paddy rice fields exposed to ambient CO2 （hereinafter referred to as aCO2）. We upgraded the model to CH4MOD 2.0 by： （a） modifying the description of the influences of soil Eh and the water regime on CH4 production; （b） adding new features to reflect the regulatory effects of atmospheric CO2 upon methanogenic substrates, soil Eh during drainages, and vascular CH4 transport; and （c） adding a new feature to simulate the influences of nitrogen （N） addition rates on methanogenic substrates under elevated CO2 （hereinafter referred to as eCO2） condition. Validation with 109 observation cases under aC02 condition showed that CHaMOD 2.0 possessed a minor systematic bias in the prediction of seasonally accumulated methane emissions （SAM）. Validation with observations in free-air CO2 enrichment （FACE） experiments in temperate and subtropical climates showed that CH4MOD 2.0 successfully simulated the effects of eCO2 upon SAM from paddy rice fields incorporated with various levels of previous crop residues and/or N fertilizer. Our results imply that CH4MOD 2.0 provides a potential approach for estimating of the effects of elevated atmospheric CO2 upon CHa emissions from regional or global paddy rice fields with various management practices in a changing climate.
基金Supported by the International Science and Technology Cooperation Program of China（No.2010DFA31710）, the National Natural Science Foundation of China（No.10974008）, the Doctoral Fund of Innovation from Beijing University of Technology （China）, and the Project from the Italian Association for Cancer Research（No.IG10412）.
文摘Alternative mechanisms of toxic effects induced by 2,3,7,8-tetrachlorodibenzo-p-dioxin（TCDD）, instead of the binding to aryl hydrocarbon receptor（AhR）, have been taken into consideration. It has been recently shown that TCDD reduces rapidly the activity of CK2（casein kinase II） both in vivo and in vitro. It is found that TCDD has high molecular similarities to the known inhibitors of CK2 catalytic subunit（CK2a）. This suggests that TCDD could also be an ATP-competitive inhibitor of CK2a. In this work, docking TCDD to CK2 was carried out based on the two structures of CK2a from maize and human, respectively. The binding free energies of the predicted CK2a-TCDD complexes estimated by the molecular mechanics/Poisson-Boltzmann surface area（MM/PBSA） method are from -85.1 kJ/mol to -114.3 kJ/mol for maize and are from -96.1 kJ/mol to -118.2 kJ/mol for human, which are comparable to those estimated for the known inhibitor and also ATP with CK2a. The energetic analysis also reveals that the van der Waals interaction is the dominant contribution to the binding free energy. These results are also useful for designing new drugs for a target of overexpressing CK2 in cancers.
基金Supported by the National Natural Science Foundation of China(No. 20975081)the Open Foundation of the Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of Ministry of Education,China(No.KF09014)the Northwest University Graduate Cross-discipline Funds,China(No.09YJC18)
文摘The possible inclusion modes of berberine（Berb） with β-cyclodextrin（BCD） in aqueous solution were predicted by molecular docking,molecular dynamics（MD） simulation and binding free energy calculations.Firstly,the molecular docking result reveals that the docking conformations of Berb appeared in two clusters ranked in two opposite orientations.Then,10 ns MD simulation was performed separately on the lowest energy conformation of each orientation（Mode I and Mode II） obtained by molecular docking.Moreover,based on the trajectories from MD simulation,the binding free energies of the two different modes were calculated by the Molecular Mechanics/Poisson Boltzmann surface area（MM/PBSA） method.Through analyzing the binding free energies of Berb with BCD,we found that Mode II was the preferential inclusion mode,which was in good agreement with the experimental result.In addition,the computed results show that the main impetus for the complex was the van der Waals interaction,but the solvation energy and the entropy change produced an adverse effect on the complex.
基金supported by the Ministry of Science and Technology of the People’s Republic of China(No.2017YFC0210000)the Young Talent Project of the Center for Excellence in Regional Atmospheric Environment,CAS(No.CERAE202002)+1 种基金the National Natural Science Foundation of China(No.41705110)Beijing Major Science and Technology Project(No.Z211100004321006)。
文摘Atmospheric oxidizing capacity(AOC)is an essential driving force of troposphere chemistry and self-cleaning,but the definition of AOC and its quantitative representation remain uncertain.Driven by national demand for air pollution control in recent years,Chinese scholars have carried out studies on theories of atmospheric chemistry and have made considerable progress in AOC research.This paper will give a brief review of these developments.First,AOC indexes were established that represent apparent atmospheric oxidizing ability(AOIe)and potential atmospheric oxidizing ability(AOIp)based on aspects of macrothermodynamics and microdynamics,respectively.A closed study refined the quantitative contributions of heterogeneous chemistry to AOC in Beijing,and these AOC methods were further applied in Beijing-Tianjin-Hebei and key areas across the country.In addition,the detection of ground or vertical profiles for atmospheric OH·,HO_(2)·,NO_(3)·radicals and reservoir molecules can now be obtained with domestic instruments in diverse environments.Moreover,laboratory smoke chamber simulations revealed heterogeneous processes involving reactions of O_(3)and NO_(2),which are typical oxidants in the surface/interface atmosphere,and the evolutionary and budgetary implications of atmospheric oxidants reacting under multispecies,multiphase and multi-interface conditions were obtained.Finally,based on the GRAPES-CUACE adjoint model improved by Chinese scholars,simulations of key substances affecting atmospheric oxidation and secondary organic and inorganic aerosol formation have been optimized.Normalized numerical simulations of AOIe and AOIp were performed,and regional coordination of AOC was adjusted.An optimized plan for controlling O_(3)and PM2.5was analyzed by scenario simulation.
基金supported by the National Nature Science Foundation of China(Grant No.40874055)the Natural Science Foundation of the Hunan Province,China(Grant No.14JJ2012)
文摘Meshfree method offers high accuracy and computational capability and constructs the shape function without relying on predefined elements. We comparatively analyze the global weak form meshfree methods, such as element-free Galerkin method （EFGM）, the point interpolation method （PIM）, and the radial point interpolation method （RPIM）. Taking two dimensional Poisson equation as an example, we discuss the support-domain dimensionless size, the field nodes, and background element settings with respect to their effect on calculation accuracy of the meshfree method. RPIM and EFGM are applied to controlled- source two-dimensional electromagnetic modeling with fixed shape parameters. The accuracy of boundary conditions imposed directly and by a penalty function are discussed in the case of forward modeling of two-dimensional magnetotellurics in a homogeneous medium model. The coupling algorithm of EFG-PIM and EFG-RPIM are generated by integrating the PIM or RPIM and EFGM. The results of the numerical modeling suggest the following. First, the proposed meshfree method and corresponding coupled methods are well-suited for electromagnetic numerical modeling. The accuracy of the algorithm is the highest when the support-domain dimensionless size is 1.0 and the distribution of field nodes is consistent with the nodes of background elements. Second, the accuracy of PIM and RPIM are lower than that of EFGM for the Poisson equation but higher than EFGM for the homogeneous medium MT response. Third, RPIM overcomes the matrix inversion problem of PIM and has a wider selection of support-domain dimensionless sizes as compared to RPIM.
基金Supported by the NationalNaturalScience Foundation of China( No.30 170 2 30 ,10 174 0 0 5 and2 0 0 710 0 5 ) and BeijingNatural Science Foundation( No.5 0 32 0 0 2)
文摘A thermodynamic integration dual-transform method was firstly applied to calculating the relative hydration free energies of 99m TcO-N 2S 2 complexes. The relationship between the brain uptakes(B.U.) of 99m TcO-N 2S 2 complexes with different substituted functional groups and their relative hydration free energies was investigated. The simulation results show that the experiment brain uptake(B.U.) data are strongly influenced by the relative hydration free energies of 99m TcO-N 2S 2 complexes, thus the simulations can provide the useful information for the medicine design of 99m Tc brain imaging agents.
基金Supported by the National Natural Science Foundation of China(Nos.20802025, 30870539, 20432010 and 20672045)
文摘Carboxyltransferase domain（CT） of acetyl-coenzyme A carboxylase（ACCase, EC 6.4.1.2） from a family of Poaceae is an important target of commercial herbicide APPs for controlling grass weed growth. As the abuse of APPs herbicides, the resistant ACCase due to the mutation of a single residue（Ile→Leu）, which is located in CT active site, is emergent in many populations and species of Poaceae. So it is urgent to understand the resistant mechanism so as to design new effect herbicides. Herein lies the complex of CT dimmer from Lolium rigidum and herbicide haloxyfop successfully constructed for wild type enzyme and Ile/Leu mutant, respectively, providing a basis for explaining the resistance from microscopic structure. Moreover, the binding free energy difference between wild type and mutant enzymes was predicted in good agreement with the known observation, and the various contributions to it were analyzed, by Molecular mechanics-Poisson-Boltzmann surface area（MM-PBSA） method. The results indicate the van der Waals interaction difference between the protein and inhibitor, -22.94 kJ/mol of CT wild type lower than that of mutant, is the major reason for resistance. Structure analysis further suggests that van der Waals interaction difference is originated from the steric hindrance between the side chain of mutated residue Leu and the chiral methyl group of haloxyfop. All these findings enhance the understanding of resistant mechanism of ACCase to herbicide by Ile/Leu mutation and provide an important clue for the rational design of high effective herbicides.
文摘Development of the orbital-free (OF) approach of the density functional theory (DFT) may result in a power instrument for modeling of complicated nanosystems with a huge number of atoms. A key problem on this way is calculation of the kinetic energy. We demonstrate how it is possible to create the OF kinetic energy functionals using results of Kohn-Sham calculations for single atoms. Calculations provided with these functionals for dimers of sp-elements of the C, Si, and Ge periodic table rows show a good accordance with the Kohn-Sham DFT results.
文摘In this paper, a numerical simulation has been carried out on unsteady hydromagnetic free convection near a moving infinite flat plate in a rotating medium. The temperatures involved are assumed to be very high so that the radiative heat transfer is significant, which renders the problem highly non-linear even with the assumption of a differential approximation for the radiative heat flux. A numerical method based on the Nakamura scheme has been employed to obtain the temperature and velocity distributions which are depicted graphically. The effects of the different parameters entering into the problem have been discussed extensively.
文摘A mathematical model incorporating animal TB and Human TB transmission is formulated and analysed in order to determine the role of animal TB and human TB in the overall TB transmission and also, to determine the parameters which govern the transmission of the TB disease. The model has five classes namely susceptible, exposed animal TB, and exposed human TB, infectious and recovery. The model assumed that there are two classes for infected individuals, those who acquired TB through animal and those who acquire TB from human. Qualitative results show that the model has the disease-free equilibrium and at least one endemic equilibrium that is locally asymptotically stable. The study includes numerical simulations as a way of supporting the analytical results. Graphical results indicate that animal TB has major contribution on overall TB transmission and the TB transmission can be reduced by ensuring intervention to both Animal TB and Human TB. Furthermore the equations indicate that there is at least one endemic equilibrium which translates that t animal and human have the contribution on TB transmission. This shows that both animals and humans together with fast progressors have contribution on TB transmissions.
