Living cells are open systems that exist far away from a state of thermodynamical equilibrium. They utilize the high-grade chemical energy provided by food to produce ATP and re- lease ADP and Pi together with heat di...Living cells are open systems that exist far away from a state of thermodynamical equilibrium. They utilize the high-grade chemical energy provided by food to produce ATP and re- lease ADP and Pi together with heat dissipation. Living cells exist in a non-equilibrium steady state （NESS）, they replicate themselves and respond to various environmental changes via signal transduction pathways. Because the majority of cells exist at room temperature, the stochasticity of chemical reac- tions in the cells is unavoidable. Recent research into fluores- cent proteins and microscopy techniques have enabled us to observe the dynamic process of mRNA and proteins in single living bacterial cells [1], and these have resulted in new in- sights into regulation mechanisms in molecular biology, i.e., in cellular signal transduction pathways.展开更多
We present a mean field study of a propagation-tumover lattice model, which was proposed by Hodges and Crabtree [Proc. Nat. Acad. Sci. 109, 13296 （2012）] for understanding how posttranslational histone marks modulat...We present a mean field study of a propagation-tumover lattice model, which was proposed by Hodges and Crabtree [Proc. Nat. Acad. Sci. 109, 13296 （2012）] for understanding how posttranslational histone marks modulate gene expression in mammalian ceils. The kinetics of the lattice model consists of nucleation, propagation and turnover mechanisms, and exhibits second-order phase transition for the histone marking domain. We showed rigorously that the dynamics essentially depends on a non-dimensional parameter k = k＋/k-, the ratio between the propagation and turnover rates, which has been observed in the simulations. We then studied the lowest order mean field approximation, and observed the phase transition with an analytically obtained critical parameter. The boundary layer analysis was utilized to investigate the structure of the decay profile of the mark density. We also studied the higher order mean field approximation to achieve sharper estimate of the critical transition parameter and more detailed features. The comparison between the simulation and theoretical results shows the validity of our theory.展开更多
基金supported by the National Natural Science Foundation of China(Grant Nos.11174011,and 91130005)the National Key Basic Research Project of China(Grant No.2015CB910300)
文摘Living cells are open systems that exist far away from a state of thermodynamical equilibrium. They utilize the high-grade chemical energy provided by food to produce ATP and re- lease ADP and Pi together with heat dissipation. Living cells exist in a non-equilibrium steady state （NESS）, they replicate themselves and respond to various environmental changes via signal transduction pathways. Because the majority of cells exist at room temperature, the stochasticity of chemical reac- tions in the cells is unavoidable. Recent research into fluores- cent proteins and microscopy techniques have enabled us to observe the dynamic process of mRNA and proteins in single living bacterial cells [1], and these have resulted in new in- sights into regulation mechanisms in molecular biology, i.e., in cellular signal transduction pathways.
基金supported by the National Natural Science Foundation of China (Grant Nos. 11174011, 11021463, 11421101, and 91530322)
文摘We present a mean field study of a propagation-tumover lattice model, which was proposed by Hodges and Crabtree [Proc. Nat. Acad. Sci. 109, 13296 （2012）] for understanding how posttranslational histone marks modulate gene expression in mammalian ceils. The kinetics of the lattice model consists of nucleation, propagation and turnover mechanisms, and exhibits second-order phase transition for the histone marking domain. We showed rigorously that the dynamics essentially depends on a non-dimensional parameter k = k＋/k-, the ratio between the propagation and turnover rates, which has been observed in the simulations. We then studied the lowest order mean field approximation, and observed the phase transition with an analytically obtained critical parameter. The boundary layer analysis was utilized to investigate the structure of the decay profile of the mark density. We also studied the higher order mean field approximation to achieve sharper estimate of the critical transition parameter and more detailed features. The comparison between the simulation and theoretical results shows the validity of our theory.
