论文发表

1.   Huang, Y.; Qu, J.; Wei, F.; Zhong, J.; Wu, Y.; Cai, M.; Gao, X.; Pearson, J. E.; Shuai, J. 

Anti-cross-correlation between open and closing time series of Markov channels.

Phys. Rev. E Under revision

2.   Li, Z.; Zhang, X.; Wang, Q.;Li, C.; Zhang, N.; Zhang, X.; Xu, B.; Ma, B.; Schrader, T.; Coates, L.; Kovalevsky, A.; Huang, Y.*; Wan, Q.*

 Understanding the pH-dependent reaction mechanism of a glycoside hydrolase using high resolution X-ray and neutron crystallography.

ACS Catal. (2018) 8:8058-8069 (IF=11.4).

3.   Huang, Y.; Yue, Z.; Tsai, C. C.; Henderson, J. A.; Shen, J.*

Predicting catalytic proton donors and nucleophiles in enzymes: how adding dynamics help elucidate the structure-function relationships.

J. Phys. Chem. Lett. (2018) 9:1179-1184 (IF=8.7).

4.   Huang, Y.; Harris, R. C.; Shen, J.*

Generalized Born based continuous constant pH molecular dynamics in Amber: Implementation, benchmarking and analysis.

J. Chem. Inf. Mod. (2018) 58:1372-1383 (IF=3.8).

5.   Huang, Y.; Chen, W.; Dotson, D. L.; Beckstein, O.; Shen, J.*

Mechanism of pH-dependent activation of the sodium-proton antiporter NhaA. 

Nat. Commun. (2016) 7:12940 (IF=12.4).

6.   Huang, Y.; Chen, W.; Wallace, J. A.; Shen, J.*

All-atom continuous constant pH molecular dynamics with particle mesh Ewald and titratable water.

J. Chem. Theory Comput. (2016) 12:5411-5421 (IF=5.4).

7.   Chen, W.; Huang, Y.; Shen, J.*

Conformational activation of a transmembrane proton channel from constant pH molecular dynamics.

J. Phys. Chem. Lett. (2016) 7:3961-3966 (IF=8.7).

8.   Ling, A.; Huang, Y.; Shuai, J.; Lan, Y.*

Channel based generating function approach to the stochastic Hodgkin-Huxley neuronal system.

Sci. Rep. (2016) 6:22662 (IF=4.1)

9.   Huang, Y.; Rudiger, S.*; Shuai, J.*

Accurate Langevin approaches to simulate Markovian channel dynamics.

Phys. Biol. (2015) 12:061001 (高亮文章，IF=1.6).

10.   Huang, Y.; Li, X.; Shuai, J.*

Langevin approach with scaled noise for stochastic channel dynamics in Hodgkin-Huxley neuron.

Chin. Phys. B (2015) 24:120501. (IF=1.3).

11. Qi, H.; Huang, Y.; Rudiger, S.; Shuai, J.*

Frequency and relative prevalence of calcium blips and puffs transition in a model of small IP3R clusters.

Biophys. J. (2014) 106:2553-2363 (IF=3.5).

12. Huang, Y.; Shuai, J.*

Induced dipoles incorporated into all-atom Zn protein simulations with multiscale modeling.

J. Phys. Chem. B (2013) 117:6138-6148 (IF=3.2).

13. Huang, Y.; Rudiger, S.; Shuai, J.*

Channel-based Langevin approach for the stochastic Hodgkin-Huxley neuron. 

Phys. Rev. E (2013) 87:012716 (IF=2.3).

14. Huang, Y.; Rudiger, S.; Shuai, J.*

Langevin approach for stochastic Hodgkin-Huxley dynamics with discretization of channel open fraction.

Phys. Lett. A (2013) 337: 3223-3227 (IF=1.9).

15. Huang, Y.; Rudiger, S.; Shuai, J.*

Modified langevin approach for a stochastic calcium puff model.

Eur. Phys. J. B (2011) 83:401-407 (IF=1.5).

16. Shuai, J.*; Huang, Y.; Rudiger, S.

Puff-wave transition in an inhomogeneous model for calcium signals.

Phys. Rev. E (2010) 81:041904 (IF=2.3)

软件开发

1.    2016-2018，分子动力学软件AMBER的CpHMD模块。主要贡献是实现基于隐性溶剂的CpHMD模拟（http://ambermd.org/）

参考文献：a) D.A. Case, I.Y. Ben-Shalom, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, D. Ghoreishi, M.K. Gilson, H. Gohlke, A.W. Goetz, D. Greene, R Harris, N. Homeyer, Y. Huang, S. Izadi, A. Kovalenko, T. Kurtzman, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, D.J. Mermelstein, K.M. Merz, Y. Miao, G. Monard, C. Nguyen, H. Nguyen, I. Omelyan, A. Onufriev, F. Pan, R. Qi, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, J. Shen, C.L. Simmerling, J. Smith, R. Salomon-Ferrer, J. Swails, R.C. Walker, J. Wang, H. Wei, R.M. Wolf, X. Wu, L. Xiao, D.M. York and P.A. Kollman (2018), AMBER 2018, University of California, San Francisco.（http://ambermd.org/doc12/Amber19.pdf） b) Huang, Y.; et al. J. Chem. Inf. Mod. 2018, 58:1372-1383。

2.    2015-2016，分子动力学软件CHARMM（版本c42）的CpHMD模块，主要贡献是实现基于PME（Particle-Mesh Ewald）显性溶剂的CpHMD模拟 （www.charmm.org）。

参考文献：Huang, Y.; et al. J. Chem. Theory Comput. 2016,12:5411-5421。

3.    2008-2012，基于CHARMM分子力场的蛋白质分子动力学软件，计算机软件著作权登记号：2014SR017052。创作人：黄艳东，帅建伟。 

参考文献：Huang, Y.; et al. J. Phys. Chem. B 2013,117:6138-6148。