BioNetSim,a Petri net-based software for modeling and simulating biochemistry processes,is developed,whose design and implement are presented in this pa-per,including logic construction,real-time access to KEGG(Kyoto ...BioNetSim,a Petri net-based software for modeling and simulating biochemistry processes,is developed,whose design and implement are presented in this pa-per,including logic construction,real-time access to KEGG(Kyoto Encyclopedia of Genes and Genomes),and BioModel database.Furthermore,glycolysis is simulated as an example of its application.BioNetSim is a helpful tool for researchers to download data,model biological network,and simulate complicated biochemistry processes.Gene regulatory networks,metabolic pathways,signaling pathways,and kinetics of cell interaction are all available in BioNetSim,which makes modeling more efficient and effective.Similar to other Petri net-based softwares,BioNetSim does well in graphic application and mathematic construction.Moreover,it shows several powerful predominances.(1)It creates models in database.(2)It realizes the real-time access to KEGG and BioModel and transfers data to Petri net.(3)It provides qualitative analysis,such as computation of constants.(4)It generates graphs for tracing the concentration of every molecule during the simulation processes.展开更多
Pressurized biochemical process derived from traditional activated sludge processes is an innovative technology for wastewater treatment.The main advantage of the pressurized process is that the oxygen transfer barrie...Pressurized biochemical process derived from traditional activated sludge processes is an innovative technology for wastewater treatment.The main advantage of the pressurized process is that the oxygen transfer barrier can be overcome by increasing the dissolved oxygen level.In this study,high concentration pesticide wastewater was treated by pressurized activated sludge process.It was found that the removal of chemical oxygen demand(COD)increased steadily with the increase of operating pressure,aeration time,and sludge concentration.When the operation pressure was 0.30 MPa and the aeration time was 6 hr,85.0%-92.5%COD,corresponding to an effluent COD of 230-370 mg/L,was removed from an influent COD of 2500-5000 mg/L.The obtained outlet COD concentration was lower than 350-450 mg/L for the identical process operated under the atmospheric pressure.In addition,pressurized biochemical process could produce a higher COD volumetric loading rate at 5.8-7.6 kg COD/(m^3.day),compared with 2.0-2.8 kg COD/(ma.day)using the same equipment at the atmospheric pressure.The COD concentration followed a modified Monod model with Vmax 2.31 day-1 and Ks 487 mg/L.展开更多
In order to confirm which process is the most important in the blood coagulation cascade,a dynamic model on the function of platelets in blood coagulation is presented based on biochemical experiments.Based on qualita...In order to confirm which process is the most important in the blood coagulation cascade,a dynamic model on the function of platelets in blood coagulation is presented based on biochemical experiments.Based on qualitative analysis and mathematical simulation,a series of conclusions about the influence of the activation rate of factor VIII and factor IX on the generation of thrombin(IIa)are drawn.It is evident that the pro-coagulation stimulus must exceed a threshold value to initiate the coagulation cascade.The value is related to the binding constant d_2 of the platelet. The stability of the equilibrium value is also related to the pro-coagulation stimulus. This article also evaluates the influence of the stimulus strength and the activated rate parameter of platelets on thrombin.The proportion of platelets activated at any given time is designated c.To each c,we obtain a maximum concentration of thrombin.It is evident that when the level of factor IX is below 1% of the normal level,the rate of thrombin generation reduces dramatically,resulting in severe bleeding tendency.展开更多
The applications of fluorescence resonance energy transfer(FRET)are coming to be one of the simplest and most accessible strategy with super-resolved optical measurements.Meanwhile,nanomaterials have become ideal for ...The applications of fluorescence resonance energy transfer(FRET)are coming to be one of the simplest and most accessible strategy with super-resolved optical measurements.Meanwhile,nanomaterials have become ideal for constructing FRET-based system,due to their unique advantages of tunable emission,broad absorption,and long fluorescence(FL)lifetime.The limitations of traditional FRET-based detections,such as the intrinsic FL,auto-FL,as well as the short FL lifetime,could be overcome with nanomaterials.Consequently,numbers of FRET-based nanomaterials have been constructed for precise,sensitive and selective detections in biological systems.They could act as both energy donors and/or acceptors in the optical energy transfer process for biological detections.Some other nanomaterials would not participate in the energy transfer process,but act as the excellent matrix for modifications.The review will be roughly classified into nanomaterial-involved and uninvolved ones.Different detection targets,such as nucleic acids,pathogenic microorganisms,proteins,heavy metal ions,and other applications will be reviewed.Finally,the other biological applications,including environmental evaluation and mechanism studies would also be summarized.展开更多
Natural hydrogen(H_(2)),generated by subsurface biochemical processes,critically facilitates abiotic methane formation,biological activity,and C/H cycling in Earth’s spheres[1].Natural hydrogen can be derived from ab...Natural hydrogen(H_(2)),generated by subsurface biochemical processes,critically facilitates abiotic methane formation,biological activity,and C/H cycling in Earth’s spheres[1].Natural hydrogen can be derived from abiotic and biotic origins,the former including degassing from deep-mantle hydrous minerals during high-pressure phase transitions,hydrothermal reactions of Fe(II)-bearing minerals/rocks in the mantle-lithosphere(e.g.serpentinization).展开更多
Photosynthesis is the most important biochemical process and the largest-scale process of matter and energy conversion on Earth.It is the process by which plants,algae,and certain bacteria convert light energy into ch...Photosynthesis is the most important biochemical process and the largest-scale process of matter and energy conversion on Earth.It is the process by which plants,algae,and certain bacteria convert light energy into chemical energy.Through photosynthesis,solar energy is used to transform carbon dioxide and water into organic matter(such as glucose)and oxygen.This process not only provides energy and growth materials for plants themselves,but also supplies food and oxygen for other organisms in the ecosystems.展开更多
基金supported by grants from the National Basic Research Program of China(973 Program)(Grant No.2012CB721000)the Key Project of Shanghai Science and Technology Commission(No.11JC1406400)the Research Innovation Project of Shanghai Education Commission(No.09YZ95).
文摘BioNetSim,a Petri net-based software for modeling and simulating biochemistry processes,is developed,whose design and implement are presented in this pa-per,including logic construction,real-time access to KEGG(Kyoto Encyclopedia of Genes and Genomes),and BioModel database.Furthermore,glycolysis is simulated as an example of its application.BioNetSim is a helpful tool for researchers to download data,model biological network,and simulate complicated biochemistry processes.Gene regulatory networks,metabolic pathways,signaling pathways,and kinetics of cell interaction are all available in BioNetSim,which makes modeling more efficient and effective.Similar to other Petri net-based softwares,BioNetSim does well in graphic application and mathematic construction.Moreover,it shows several powerful predominances.(1)It creates models in database.(2)It realizes the real-time access to KEGG and BioModel and transfers data to Petri net.(3)It provides qualitative analysis,such as computation of constants.(4)It generates graphs for tracing the concentration of every molecule during the simulation processes.
基金supported by the Education Bureau of Zhejiang Province(No.20070303)the National Key Science and Technology Project:Water Pollution Control and Treatment(No.2008ZX07101-006)
文摘Pressurized biochemical process derived from traditional activated sludge processes is an innovative technology for wastewater treatment.The main advantage of the pressurized process is that the oxygen transfer barrier can be overcome by increasing the dissolved oxygen level.In this study,high concentration pesticide wastewater was treated by pressurized activated sludge process.It was found that the removal of chemical oxygen demand(COD)increased steadily with the increase of operating pressure,aeration time,and sludge concentration.When the operation pressure was 0.30 MPa and the aeration time was 6 hr,85.0%-92.5%COD,corresponding to an effluent COD of 230-370 mg/L,was removed from an influent COD of 2500-5000 mg/L.The obtained outlet COD concentration was lower than 350-450 mg/L for the identical process operated under the atmospheric pressure.In addition,pressurized biochemical process could produce a higher COD volumetric loading rate at 5.8-7.6 kg COD/(m^3.day),compared with 2.0-2.8 kg COD/(ma.day)using the same equipment at the atmospheric pressure.The COD concentration followed a modified Monod model with Vmax 2.31 day-1 and Ks 487 mg/L.
基金The project supported by The Beijing Municipal Natural Sciences Foundation (3982005)
文摘In order to confirm which process is the most important in the blood coagulation cascade,a dynamic model on the function of platelets in blood coagulation is presented based on biochemical experiments.Based on qualitative analysis and mathematical simulation,a series of conclusions about the influence of the activation rate of factor VIII and factor IX on the generation of thrombin(IIa)are drawn.It is evident that the pro-coagulation stimulus must exceed a threshold value to initiate the coagulation cascade.The value is related to the binding constant d_2 of the platelet. The stability of the equilibrium value is also related to the pro-coagulation stimulus. This article also evaluates the influence of the stimulus strength and the activated rate parameter of platelets on thrombin.The proportion of platelets activated at any given time is designated c.To each c,we obtain a maximum concentration of thrombin.It is evident that when the level of factor IX is below 1% of the normal level,the rate of thrombin generation reduces dramatically,resulting in severe bleeding tendency.
基金the financial support provided by the National Key Research and Development Programof China(No.2019YFC1805600)the National Natural Science Foundation of China(NNSFC,No.21874012)the financial support provided by the NNSFC(No.21974010).
文摘The applications of fluorescence resonance energy transfer(FRET)are coming to be one of the simplest and most accessible strategy with super-resolved optical measurements.Meanwhile,nanomaterials have become ideal for constructing FRET-based system,due to their unique advantages of tunable emission,broad absorption,and long fluorescence(FL)lifetime.The limitations of traditional FRET-based detections,such as the intrinsic FL,auto-FL,as well as the short FL lifetime,could be overcome with nanomaterials.Consequently,numbers of FRET-based nanomaterials have been constructed for precise,sensitive and selective detections in biological systems.They could act as both energy donors and/or acceptors in the optical energy transfer process for biological detections.Some other nanomaterials would not participate in the energy transfer process,but act as the excellent matrix for modifications.The review will be roughly classified into nanomaterial-involved and uninvolved ones.Different detection targets,such as nucleic acids,pathogenic microorganisms,proteins,heavy metal ions,and other applications will be reviewed.Finally,the other biological applications,including environmental evaluation and mechanism studies would also be summarized.
基金supported by the National Key Research and Development Program of China(2022YFF0800304)the Science and Technology Project of China National Petroleum Corporation(2024DJ9301).
文摘Natural hydrogen(H_(2)),generated by subsurface biochemical processes,critically facilitates abiotic methane formation,biological activity,and C/H cycling in Earth’s spheres[1].Natural hydrogen can be derived from abiotic and biotic origins,the former including degassing from deep-mantle hydrous minerals during high-pressure phase transitions,hydrothermal reactions of Fe(II)-bearing minerals/rocks in the mantle-lithosphere(e.g.serpentinization).
文摘Photosynthesis is the most important biochemical process and the largest-scale process of matter and energy conversion on Earth.It is the process by which plants,algae,and certain bacteria convert light energy into chemical energy.Through photosynthesis,solar energy is used to transform carbon dioxide and water into organic matter(such as glucose)and oxygen.This process not only provides energy and growth materials for plants themselves,but also supplies food and oxygen for other organisms in the ecosystems.
