We develop a coarse grained （CG） approach for efficiently simulating calcium dynamics in the endoplasmic reticulum membrane based on a fine stochastic lattice gas model. By grouping neighboring microscopic sites tog...We develop a coarse grained （CG） approach for efficiently simulating calcium dynamics in the endoplasmic reticulum membrane based on a fine stochastic lattice gas model. By grouping neighboring microscopic sites together into CG cells and deriving CG reaction rates using local mean field approximation, we perform CG kinetic Monte Carlo （kMC） simulations and find the results of CG-kMC simulations are in excellent agreement with that of the microscopic ones. Strikingly, there is an appropriate range of coarse proportion rn, corresponding to the minimal deviation of the phase transition point compared to the microscopic one. For fixed m, the critical point increases monotonously as the system size increases, especially, there exists scaling law between the deviations of the phase transition point and the system size. Moreover, the CG approach provides significantly faster Monte Carlo simulations which are easy to implement and are directly related to the microscopics, so that one can study the system size effects at the cost of reasonable computational time.展开更多
In this work,an automated microfluidic chip that uses negative pressure to sample and analyze solutions with high temporal resolution was developed.The chip has a T-shaped channel for mixing the sample with a fluoresc...In this work,an automated microfluidic chip that uses negative pressure to sample and analyze solutions with high temporal resolution was developed.The chip has a T-shaped channel for mixing the sample with a fluorescent indicator,a flow-focusing channel for generating droplets in oil,and a long storage channel for incubating and detecting the droplets.By monitoring the fluorescence intensity of the droplets,the device could detect changes in solution accurately over time.The chip can generate droplets at frequencies of up to 42 Hz with a mixing ratio of 1:1 and a temporal resolution of 3–6 s.It had excellent linearity in detecting fluorescein solution in the concentration range 1–5μM.This droplet microfluidic chip provides several advantages over traditional methods,including high temporal resolution,stable droplet generation,and faster flow rates.This approach could be applied to monitoring calcium ions with a dynamic range from 102 to 107 nM and a detection limit of 10 nM.展开更多
This study addresses the fundamental principle of inter-synaptic interactions in synaptic cross-talk through homosynaptic and heterosynaptic plasticity by studying the intrinsic calcium signaling dynamics in spines. B...This study addresses the fundamental principle of inter-synaptic interactions in synaptic cross-talk through homosynaptic and heterosynaptic plasticity by studying the intrinsic calcium signaling dynamics in spines. Beyond the calcium influx into synapse through voltage gated calcium channels （VGCCs） and N-methyl-D-aspartate （NNMDA） receptors, the function of calcium released from internal store in mediating inter-synaptic cross-talk has barely been modeled. This work investigates how different sources of calcium contribute to inter-synaptic cross-talk and synaptic clustering. Based on experimental observations, we developed a mathematical model in one dimensional system with uniform distribution of spines with the connected dendrite. We modeled the biophysical process of calcium induced calcium release （CICR） in the dendritic smooth endoplasmic reticulum （SER）. Our model compared distinct roles of calcium diffusion, back propagated action potentials （bAPs） and CICR played in synaptic clustering and inter-synaptic cross-talk. The simulation result demonstrated that calcium signal extruded from spine into dendrite requires amplification by CICR before invading neighboring spines to induce plasticity. Our model predicted that initial calcium concentration in SER may discriminate between different types of neuronal activity and induce completely different synaptic potentiation and depression.展开更多
基金This work was supported by the National Natural Science Foundation of China （No.11205002）. Chuansheng Shen was also supported by the Key Scientific Research Fund of Anhui Provincial Education Department （No.KJ2012A189）.
文摘We develop a coarse grained （CG） approach for efficiently simulating calcium dynamics in the endoplasmic reticulum membrane based on a fine stochastic lattice gas model. By grouping neighboring microscopic sites together into CG cells and deriving CG reaction rates using local mean field approximation, we perform CG kinetic Monte Carlo （kMC） simulations and find the results of CG-kMC simulations are in excellent agreement with that of the microscopic ones. Strikingly, there is an appropriate range of coarse proportion rn, corresponding to the minimal deviation of the phase transition point compared to the microscopic one. For fixed m, the critical point increases monotonously as the system size increases, especially, there exists scaling law between the deviations of the phase transition point and the system size. Moreover, the CG approach provides significantly faster Monte Carlo simulations which are easy to implement and are directly related to the microscopics, so that one can study the system size effects at the cost of reasonable computational time.
基金We acknowledge support from the equipment research and development projects of the Chinese Academy of Sciences,“On-chip integrated optical biochemical detection key technology research and development team,”E11YTB1001.
文摘In this work,an automated microfluidic chip that uses negative pressure to sample and analyze solutions with high temporal resolution was developed.The chip has a T-shaped channel for mixing the sample with a fluorescent indicator,a flow-focusing channel for generating droplets in oil,and a long storage channel for incubating and detecting the droplets.By monitoring the fluorescence intensity of the droplets,the device could detect changes in solution accurately over time.The chip can generate droplets at frequencies of up to 42 Hz with a mixing ratio of 1:1 and a temporal resolution of 3–6 s.It had excellent linearity in detecting fluorescein solution in the concentration range 1–5μM.This droplet microfluidic chip provides several advantages over traditional methods,including high temporal resolution,stable droplet generation,and faster flow rates.This approach could be applied to monitoring calcium ions with a dynamic range from 102 to 107 nM and a detection limit of 10 nM.
基金We would like to thank Prof. Florentin Woergoetter, Dr. Christian Tetzlaff and Dr. Tomas Kulvicius for helpful discussions. This work is supported by Chinese Natural Science Foundation with 31601145, the Fundamental Research Funds for the Central Universities, and the Federal Ministry of Education and Research （BMBF） Germany to the Goettingen Bernstein Center for Computational Neuroscience Project D1. Y.L. conceived the experiment（s）, Z.Z. and Y.L. conducted the experiment（s）, Y.L. and Z.Z. analyzed the results, Y.L. wrote the paper. All authors reviewed the manuscript. The authors declare no competing interest.
文摘This study addresses the fundamental principle of inter-synaptic interactions in synaptic cross-talk through homosynaptic and heterosynaptic plasticity by studying the intrinsic calcium signaling dynamics in spines. Beyond the calcium influx into synapse through voltage gated calcium channels （VGCCs） and N-methyl-D-aspartate （NNMDA） receptors, the function of calcium released from internal store in mediating inter-synaptic cross-talk has barely been modeled. This work investigates how different sources of calcium contribute to inter-synaptic cross-talk and synaptic clustering. Based on experimental observations, we developed a mathematical model in one dimensional system with uniform distribution of spines with the connected dendrite. We modeled the biophysical process of calcium induced calcium release （CICR） in the dendritic smooth endoplasmic reticulum （SER）. Our model compared distinct roles of calcium diffusion, back propagated action potentials （bAPs） and CICR played in synaptic clustering and inter-synaptic cross-talk. The simulation result demonstrated that calcium signal extruded from spine into dendrite requires amplification by CICR before invading neighboring spines to induce plasticity. Our model predicted that initial calcium concentration in SER may discriminate between different types of neuronal activity and induce completely different synaptic potentiation and depression.
