Aptamers are a type of single-chain oligonucleotide that can combine with a specific target.Due to their simple preparation,easy modification,stable structure and reusability,aptamers have been widely applied as bioch...Aptamers are a type of single-chain oligonucleotide that can combine with a specific target.Due to their simple preparation,easy modification,stable structure and reusability,aptamers have been widely applied as biochemical sensors for medicine,food safety and environmental monitoring.However,there is little research on aptamer-target binding mechanisms,which limits their application and development.Computational simulation has gained much attention for revealing aptamer-target binding mechanisms at the atomic level.This work summarizes the main simulation methods used in the mechanistic analysis of aptamer-target complexes,the characteristics of binding between aptamers and different targets(metal ions,small organic molecules,biomacromolecules,cells,bacteria and viruses),the types of aptamer-target interactions and the factors influencing their strength.It provides a reference for further use of simulations in understanding aptamer-target binding mechanisms.展开更多
In order to simulate the instability phenomenon of a nonaqueous phase liquid(NAPL) dissolution front in a computational model, the intrinsic characteristic length is commonly used to determine the length scale at whic...In order to simulate the instability phenomenon of a nonaqueous phase liquid(NAPL) dissolution front in a computational model, the intrinsic characteristic length is commonly used to determine the length scale at which the instability of the NAPL dissolution front can be initiated. This will require a huge number of finite elements if a whole NAPL dissolution system is simulated in the computational model. Even though modern supercomputers might be used to tackle this kind of NAPL dissolution problem, it can become prohibitive for commonly-used personal computers to do so. The main purpose of this work is to investigate whether or not the whole NAPL dissolution system of an annular domain can be replaced by a trapezoidal domain, so as to greatly reduce the requirements for computer efforts. The related simulation results have demonstrated that when the NAPL dissolution system under consideration is in a subcritical state, if the dissolution pattern around the entrance of an annulus domain is of interest, then a trapezoidal domain cannot be used to replace an annular domain in the computational simulation of the NAPL dissolution system.However, if the dissolution pattern away from the vicinity of the entrance of an annulus domain is of interest, then a trapezoidal domain can be used to replace an annular domain in the computational simulation of the NAPL dissolution system. When the NAPL dissolution system under consideration is in a supercritical state, a trapezoidal domain cannot be used to replace an annular domain in the computational simulation of the NAPL dissolution system.展开更多
According to the recently developed single-trough floating machine with the world's largest volume(inflatable mechanical agitation flotation machine with volume of 320 m3) in China, the gas-fluid two-phase flow in...According to the recently developed single-trough floating machine with the world's largest volume(inflatable mechanical agitation flotation machine with volume of 320 m3) in China, the gas-fluid two-phase flow in flotation cell was simulated using computational fluid dynamics method. It is shown that hexahedral mesh scheme is more suitable for the complex structure of the flotation cell than tetrahedral mesh scheme, and a mesh quality ranging from 0.7 to 1.0 is obtained. Comparative studies of the standard k-ε, k-ω and realizable k-ε turbulence models were carried out. It is indicated that the standard k-ε turbulence model could give a result relatively close to the practice and the liquid phase flow field is well characterized. In addition, two obvious recirculation zones are formed in the mixing zones, and the pressure on the rotor and stator is well characterized. Furthermore, the simulation results using improved standard k-ε turbulence model show that surface tension coefficient of 0.072, drag model of Grace and coefficient of 4, and lift coefficient of 0.001 can be achieved. The research results suggest that gas-fluid two-phase flow in large flotation cell can be well simulated using computational fluid dynamics method.展开更多
The finite element method was used to solve fluid dynamic interaction problems between the crust and mantle of the Earth. To consider different mechanical behaviours, the lithosphere consisting of the crust and upper ...The finite element method was used to solve fluid dynamic interaction problems between the crust and mantle of the Earth. To consider different mechanical behaviours, the lithosphere consisting of the crust and upper mantle was simulated as fluid-saturated porous rocks, while the upper aesthenospheric part of the mantle was simulated as viscous fluids. Since the whole lithosphere was computationally simulated, the dynamic interaction between the crust and the upper mantle was appropriately considered. In particular, the mixing of mantle fluids and crustal fluids was simulated in the corresponding computational model. The related computational simulation results from an example problem demonstrate that the mantle fluids can flow into the crust and mix with the crustal fluids due to the resulting convective flows in the crust-mantle system. Likewise, the crustal fluids can also flow into the upper mantle and mix with the mantle fluids. This kind of fluids mixing and exchange is very important to the better understanding of the governing processes that control the ore body formation and mineralization in the upper crust of the Earth.展开更多
Homogeneity and heterogeneity are two totally different concepts in nature.At the particle length scale,rocks exhibit strong heterogeneity in their constituents and porosities.When the heterogeneity of porosity obeys ...Homogeneity and heterogeneity are two totally different concepts in nature.At the particle length scale,rocks exhibit strong heterogeneity in their constituents and porosities.When the heterogeneity of porosity obeys the random uniform distribution,both the mean value and the variance of porosities in the heterogeneous porosity field can be used to reflect the overall heterogeneous characteristics of the porosity field.The main purpose of this work is to investigate the effects of porosity heterogeneity on chemical dissolution front instability in fluid-saturated rocks by the computational simulation method.The related computational simulation results have demonstrated that:1) since the propagation speed of a chemical dissolution front is inversely proportional to the difference between the final porosity and the mean value of porosities in the initial porosity field,an increase in the extent of the porosity heterogeneity can cause an increase in the mean value of porosities in the initial porosity field and an increase in the propagation speed of the chemical dissolution front.2) An increase in the variance of porosities in the initial porosity field can cause an increase in the instability probability of the chemical dissolution front in the fluid-saturated rock.3) The greater the mean value of porosities in the initial porosity field,the quicker the irregular morphology of the chemical dissolution front changes in the supercritical chemical dissolution systems.This means that the irregular morphology of a chemical dissolution front grows quicker in a porosity field of heterogeneity than it does in that of homogeneity when the chemical dissolution system is at a supercritical stage.展开更多
Many scientific and engineering problems need to use numerical methods and algorithms to obtain computational simulation results because analytical solutions are seldom available for them.The chemical dissolution-fron...Many scientific and engineering problems need to use numerical methods and algorithms to obtain computational simulation results because analytical solutions are seldom available for them.The chemical dissolution-front instability problem in fluid-saturated porous rocks is no exception.Since this kind of instability problem has both the conventional(i.e.trivial)and the unconventional(i.e.nontrivial)solutions,it is necessary to examine the effects of different numerical algorithms,which are used to solve chemical dissolution-front instability problems in fluid-saturated porous rocks.Toward this goal,two different numerical algorithms associated with the commonly-used finite element method are considered in this paper.In the first numerical algorithm,the porosity,pore-fluid pressure and acid/solute concentration are selected as basic variables,while in the second numerical algorithm,the porosity,velocity of pore-fluid flow and acid/solute concentration are selected as basic variables.The particular attention is paid to the effects of these two numerical algorithms on the computational simulation results of unstable chemical dissolution-front propagation in fluid-saturated porous rocks.The related computational simulation results have demonstrated that:1)the first numerical algorithm associated with the porosity-pressure-concentration approach can realistically simulate the evolution processes of unstable chemical dissolution-front propagation in chemical dissolution systems.2)The second numerical algorithm associated with the porosity-velocity-concentration approach fails to simulate the evolution processes of unstable chemical dissolution-front propagation.3)The extra differential operation is the main source to result in the failure of the second numerical algorithm.展开更多
In order to lower the power consumption and improve the coefficient of resource utilization of current cloud computing systems, this paper proposes two resource pre-allocation algorithms based on the ＂shut down the r...In order to lower the power consumption and improve the coefficient of resource utilization of current cloud computing systems, this paper proposes two resource pre-allocation algorithms based on the ＂shut down the redundant, turn on the demanded＂ strategy here. Firstly, a green cloud computing model is presented, abstracting the task scheduling problem to the virtual machine deployment issue with the virtualization technology. Secondly, the future workloads of system need to be predicted： a cubic exponential smoothing algorithm based on the conservative control（CESCC） strategy is proposed, combining with the current state and resource distribution of system, in order to calculate the demand of resources for the next period of task requests. Then, a multi-objective constrained optimization model of power consumption and a low-energy resource allocation algorithm based on probabilistic matching（RA-PM） are proposed. In order to reduce the power consumption further, the resource allocation algorithm based on the improved simulated annealing（RA-ISA） is designed with the improved simulated annealing algorithm. Experimental results show that the prediction and conservative control strategy make resource pre-allocation catch up with demands, and improve the efficiency of real-time response and the stability of the system. Both RA-PM and RA-ISA can activate fewer hosts, achieve better load balance among the set of high applicable hosts, maximize the utilization of resources, and greatly reduce the power consumption of cloud computing systems.展开更多
The main objectives were to (1) calculate the total volatile organic compounds (TVOCs) inhalation dose, (2) analyze the proportions of human’s inhaled contaminant dose from different sources, and (3) present a newly ...The main objectives were to (1) calculate the total volatile organic compounds (TVOCs) inhalation dose, (2) analyze the proportions of human’s inhaled contaminant dose from different sources, and (3) present a newly defined ratio of relative inhalation dose level (RIDL) to assess indoor air quality (IAQ). A user defined function based on CFD (computational fluid dynamics) was developed, which integrated human motion model with TVOCs emission model in a high sidewall air supply ventilation mode. Based on simulation results of 10 cases, it is shown that the spatial concentration distribution of TVOCs is affected by human motion. TVOCs diffusion characteristic of building material is the most effective way to impact the TVOCs inhalation dose. From the RIDL index, case A-2 has the most serious IAQ problem, while case D-1 is of the best IAQ.展开更多
文摘Aptamers are a type of single-chain oligonucleotide that can combine with a specific target.Due to their simple preparation,easy modification,stable structure and reusability,aptamers have been widely applied as biochemical sensors for medicine,food safety and environmental monitoring.However,there is little research on aptamer-target binding mechanisms,which limits their application and development.Computational simulation has gained much attention for revealing aptamer-target binding mechanisms at the atomic level.This work summarizes the main simulation methods used in the mechanistic analysis of aptamer-target complexes,the characteristics of binding between aptamers and different targets(metal ions,small organic molecules,biomacromolecules,cells,bacteria and viruses),the types of aptamer-target interactions and the factors influencing their strength.It provides a reference for further use of simulations in understanding aptamer-target binding mechanisms.
基金Project(11272359)supported by the National Natural Science Foundation of China
文摘In order to simulate the instability phenomenon of a nonaqueous phase liquid(NAPL) dissolution front in a computational model, the intrinsic characteristic length is commonly used to determine the length scale at which the instability of the NAPL dissolution front can be initiated. This will require a huge number of finite elements if a whole NAPL dissolution system is simulated in the computational model. Even though modern supercomputers might be used to tackle this kind of NAPL dissolution problem, it can become prohibitive for commonly-used personal computers to do so. The main purpose of this work is to investigate whether or not the whole NAPL dissolution system of an annular domain can be replaced by a trapezoidal domain, so as to greatly reduce the requirements for computer efforts. The related simulation results have demonstrated that when the NAPL dissolution system under consideration is in a subcritical state, if the dissolution pattern around the entrance of an annulus domain is of interest, then a trapezoidal domain cannot be used to replace an annular domain in the computational simulation of the NAPL dissolution system.However, if the dissolution pattern away from the vicinity of the entrance of an annulus domain is of interest, then a trapezoidal domain can be used to replace an annular domain in the computational simulation of the NAPL dissolution system. When the NAPL dissolution system under consideration is in a supercritical state, a trapezoidal domain cannot be used to replace an annular domain in the computational simulation of the NAPL dissolution system.
基金Project(51074027)supported by the National Natural Science Foundation of China
文摘According to the recently developed single-trough floating machine with the world's largest volume(inflatable mechanical agitation flotation machine with volume of 320 m3) in China, the gas-fluid two-phase flow in flotation cell was simulated using computational fluid dynamics method. It is shown that hexahedral mesh scheme is more suitable for the complex structure of the flotation cell than tetrahedral mesh scheme, and a mesh quality ranging from 0.7 to 1.0 is obtained. Comparative studies of the standard k-ε, k-ω and realizable k-ε turbulence models were carried out. It is indicated that the standard k-ε turbulence model could give a result relatively close to the practice and the liquid phase flow field is well characterized. In addition, two obvious recirculation zones are formed in the mixing zones, and the pressure on the rotor and stator is well characterized. Furthermore, the simulation results using improved standard k-ε turbulence model show that surface tension coefficient of 0.072, drag model of Grace and coefficient of 4, and lift coefficient of 0.001 can be achieved. The research results suggest that gas-fluid two-phase flow in large flotation cell can be well simulated using computational fluid dynamics method.
基金Project(10872219) supported by the National Natural Science Foundation of China
文摘The finite element method was used to solve fluid dynamic interaction problems between the crust and mantle of the Earth. To consider different mechanical behaviours, the lithosphere consisting of the crust and upper mantle was simulated as fluid-saturated porous rocks, while the upper aesthenospheric part of the mantle was simulated as viscous fluids. Since the whole lithosphere was computationally simulated, the dynamic interaction between the crust and the upper mantle was appropriately considered. In particular, the mixing of mantle fluids and crustal fluids was simulated in the corresponding computational model. The related computational simulation results from an example problem demonstrate that the mantle fluids can flow into the crust and mix with the crustal fluids due to the resulting convective flows in the crust-mantle system. Likewise, the crustal fluids can also flow into the upper mantle and mix with the mantle fluids. This kind of fluids mixing and exchange is very important to the better understanding of the governing processes that control the ore body formation and mineralization in the upper crust of the Earth.
基金Project(11272359)supported by the National Natural Science Foundation of China
文摘Homogeneity and heterogeneity are two totally different concepts in nature.At the particle length scale,rocks exhibit strong heterogeneity in their constituents and porosities.When the heterogeneity of porosity obeys the random uniform distribution,both the mean value and the variance of porosities in the heterogeneous porosity field can be used to reflect the overall heterogeneous characteristics of the porosity field.The main purpose of this work is to investigate the effects of porosity heterogeneity on chemical dissolution front instability in fluid-saturated rocks by the computational simulation method.The related computational simulation results have demonstrated that:1) since the propagation speed of a chemical dissolution front is inversely proportional to the difference between the final porosity and the mean value of porosities in the initial porosity field,an increase in the extent of the porosity heterogeneity can cause an increase in the mean value of porosities in the initial porosity field and an increase in the propagation speed of the chemical dissolution front.2) An increase in the variance of porosities in the initial porosity field can cause an increase in the instability probability of the chemical dissolution front in the fluid-saturated rock.3) The greater the mean value of porosities in the initial porosity field,the quicker the irregular morphology of the chemical dissolution front changes in the supercritical chemical dissolution systems.This means that the irregular morphology of a chemical dissolution front grows quicker in a porosity field of heterogeneity than it does in that of homogeneity when the chemical dissolution system is at a supercritical stage.
基金Project(11272359)supported by the National Natural Science Foundation of China
文摘Many scientific and engineering problems need to use numerical methods and algorithms to obtain computational simulation results because analytical solutions are seldom available for them.The chemical dissolution-front instability problem in fluid-saturated porous rocks is no exception.Since this kind of instability problem has both the conventional(i.e.trivial)and the unconventional(i.e.nontrivial)solutions,it is necessary to examine the effects of different numerical algorithms,which are used to solve chemical dissolution-front instability problems in fluid-saturated porous rocks.Toward this goal,two different numerical algorithms associated with the commonly-used finite element method are considered in this paper.In the first numerical algorithm,the porosity,pore-fluid pressure and acid/solute concentration are selected as basic variables,while in the second numerical algorithm,the porosity,velocity of pore-fluid flow and acid/solute concentration are selected as basic variables.The particular attention is paid to the effects of these two numerical algorithms on the computational simulation results of unstable chemical dissolution-front propagation in fluid-saturated porous rocks.The related computational simulation results have demonstrated that:1)the first numerical algorithm associated with the porosity-pressure-concentration approach can realistically simulate the evolution processes of unstable chemical dissolution-front propagation in chemical dissolution systems.2)The second numerical algorithm associated with the porosity-velocity-concentration approach fails to simulate the evolution processes of unstable chemical dissolution-front propagation.3)The extra differential operation is the main source to result in the failure of the second numerical algorithm.
基金supported by the National Natural Science Foundation of China(6147219261202004)+1 种基金the Special Fund for Fast Sharing of Science Paper in Net Era by CSTD(2013116)the Natural Science Fund of Higher Education of Jiangsu Province(14KJB520014)
文摘In order to lower the power consumption and improve the coefficient of resource utilization of current cloud computing systems, this paper proposes two resource pre-allocation algorithms based on the ＂shut down the redundant, turn on the demanded＂ strategy here. Firstly, a green cloud computing model is presented, abstracting the task scheduling problem to the virtual machine deployment issue with the virtualization technology. Secondly, the future workloads of system need to be predicted： a cubic exponential smoothing algorithm based on the conservative control（CESCC） strategy is proposed, combining with the current state and resource distribution of system, in order to calculate the demand of resources for the next period of task requests. Then, a multi-objective constrained optimization model of power consumption and a low-energy resource allocation algorithm based on probabilistic matching（RA-PM） are proposed. In order to reduce the power consumption further, the resource allocation algorithm based on the improved simulated annealing（RA-ISA） is designed with the improved simulated annealing algorithm. Experimental results show that the prediction and conservative control strategy make resource pre-allocation catch up with demands, and improve the efficiency of real-time response and the stability of the system. Both RA-PM and RA-ISA can activate fewer hosts, achieve better load balance among the set of high applicable hosts, maximize the utilization of resources, and greatly reduce the power consumption of cloud computing systems.
基金Projects(2006BAJ02A08, 2006BAJ02A05) supported by the National Science and Technology Pillar Program Project during the 11th Five-Year Plan PeriodProject(2007-209) supported by the Excellent Youth Teacher of Ministry of Education of China
文摘The main objectives were to (1) calculate the total volatile organic compounds (TVOCs) inhalation dose, (2) analyze the proportions of human’s inhaled contaminant dose from different sources, and (3) present a newly defined ratio of relative inhalation dose level (RIDL) to assess indoor air quality (IAQ). A user defined function based on CFD (computational fluid dynamics) was developed, which integrated human motion model with TVOCs emission model in a high sidewall air supply ventilation mode. Based on simulation results of 10 cases, it is shown that the spatial concentration distribution of TVOCs is affected by human motion. TVOCs diffusion characteristic of building material is the most effective way to impact the TVOCs inhalation dose. From the RIDL index, case A-2 has the most serious IAQ problem, while case D-1 is of the best IAQ.
