Full Publications
Monograph/textbook:
- Qian, H. and Ge, H.: Stochastic Chemical Reaction Systems in Biology. in Lecture Notes on Mathematical Modeling in the Life Sciences (LMML) series. Springer (2021)
Selected Publications:
26. Yang, H.R. and Ge, H.: Fluctuation Theorems and Thermodynamic Inequalities for Nonequilibrium Processes Stopped at Stochastic Times. Physical Review E 108, L052104 (2023)
25. Guo, X.L., Tang, T., Duan, M.X., Zhang, L.* and Ge, H.*: The Nonequilibrium Mechanism of Noise-Enhanced Drug Synergy in HIV Latency Reactivation. iScience 25，104358 (2022) (*co-corresponding authors)
24. Ge, H., Jia, C. and Jin, X.: Martingale structure for general thermodynamic functionals of diffusion processes under second-order averaging. Journal of Statistical Physics 184:17 (2021)
23. Peng, Y.L., Qian, H., Beard, D. and Ge, H.*: Universal Relation Between Thermodynamic Driving Force and One-Way Fluxes in a Nonequilibrium Chemical Reaction with Complex Mechanism. Physical Review Research 2, 033089 (2020)
22. You, Z.Y., Li, L.Y., Lu, J.F. * and Ge, H. *: Integrated tempering enhanced sampling method as the infinite switching limit of simulated tempering. J. Chem. Phys. 149, 084114 (2018) (*co-corresponding authors)
21. Gao, S., …, Ge, H. *, Qiao, J. * and Tang, F.C. *: Tracing the temporal-spatial transcriptome landscapes of the human fetal digestive tract using single-cell RNA-sequencing. Nat. Cell Biol. 20, 721–734 (2018) (*co-corresponding authors)
20. Ge, H., Wu, P.P., Qian, H. and Xie, X.S.: Relatively slow stochastic gene-state switching in the presence of positive feedback significantly broadens the region of bimodality through stablizing the uninduced phenotypic state. Plos Comput. Biol. 14(3): e1006051 (2018)
19. Ge, H. and Qian, H.: Mathematical Formalism of Nonequilibrium Thermodynamics for Nonlinear Chemical Reaction Systems with General Rate Law. J. Stat. Phys. 166:190–209 (2017)
18. Ge, H., Jiang, D.Q. and Jia, C.: Cycle symmetry, limit theorems, and fluctuation theorems for diffusion processes on the circle. Stoc. Proc. Appl. 127: 1897–1925 (2017)
17. Ge, H. and Qian, H.: Mesoscopic kinetic basis of macroscopic chemical thermodynamics: A mathematical theory. Phys. Rev. E 94, 052150 (2016)
16. Zhao, Z.Q., Xie, X.S. and Ge, H.: Nonequilibrium Relaxation of Conformational Dynamics Facilitates Catalytic Reaction in an Elastic Network Model of T7 DNA Polymerase. J. Phys. Chem. B 120, 2869−2877 (2016)
15. Ge, H., Qian, H. and Xie, X.S.: Stochastic phenotype transition of a single cell in an intermediate region of gene state switching. Phys. Rev. Lett. 114, 078101 (2015)
14. Ge, H.: Mathematical laws of randomness. In Voices: Expanding the Biology Toolkit. Cell 163, 1306 (2015)
13. Ge, H.: Time reversibility and nonequilibrium thermodynamics of second-order stochastic processes. Phys. Rev. E 89, 022127 (2014)
12. Ge, H.: Stochastic Theory of Nonequilibrium Statistical Physics (review). Advances in Mathematics(China) 43, 161-174 (2014)
11. Chong, S.S., Chen, C.Y., Ge, H. and Xie, X.S.: Mechanism of transcriptional bursting in bacteria. Cell 158, 314–326 (2014)
10. Kim, S., Broströmer, E., Xing, D., Jin, J.S., Chong, S.S., Ge, H., Wang, S.Y., Gu, C., Yang, L., Gao, Y.Q., Su, X.D., Sun, Y.J. &Xie, X.S.: Probing allostery through DNA. Science 339 816 (2013)
9. Xu, X.L.#, Ge, H. #, Gu, C., Gao, Y. Q., Wang, S.Y., Thio, B., Hynes, J., Xie, X.S. and Cao, J.S.: Modeling spatial correlation of DNA deformation: DNA allostery in protein binding. J. Phys. Chem. B 117, 13378−13387 (2013) (#co-first-authors)
8. Ge, H., Qian, M. and Qian, H.: Stochastic theory of nonequilibrium steady states. Part II: Applications in chemical biophysics. Phys. Rep. 510, 87-118 (2012)
7. Ge, H., Pressé, S., Ghosh, K. and Dill, K.: Markov processes follow from the principle of maximum caliber. J. Chem. Phys. 136, 064108 (2012) (Research highlighted)
6. Ge, H.: Multivariable fluctuation theorems in the steady-state cycle kinetics of single enzyme with competing substrates. J. Phys. A: Math. Theor. 45 215002 (2012) (Research highlighted)
5. Ge, H. and Qian, H.: The physical origins of entropy production, free energy dissipation and their mathematical representations. Phys. Rev. E 81 051133 (2010)
4. Ge, H.: Extended forms of the second law for general time-dependent stochastic processes. Phys. Rev. E 80 021137 (2009)
3. Ge, H. and Qian, H.: Thermodynamic limit of a nonequilibrium steady state: Maxwell-type construction for a bistable biochemical system. Phys. Rev. Lett. 103, 148103 (2009)
2. Ge, H.: Waiting cycle times and generalized Haldane equality in the steady-state cycle kinetics of single enzymes. J. Phys. Chem. B 112 61-70 (2008)
1. Ge, H. and Jiang, D.Q.: Generalized Jarzynski’s equality of multidimensional inhomogeneous diffusion processes. J. Stat. Phys. 131 675–689 (2008)