14 citations · 39 across the 8 of their papers we have counts for
8 papers
Ultra-high-density local structure of liquid water
Cheng Yang, Chuanbiao Zhang, Fangfu Ye +1
The local structure of liquid water plays a key role in determining the anomalous properties of water. We run all-atom simulations for three microscopic water models, and use multi…
Jarzynski matrix equality: calculating free energy difference by non-equilibrium simulations with an arbitrary initial distribution
Biao Wan, Cheng Yang, Yanting Wang +1
The Jarzynski equality (JE), which relates works of non-equilibrium trajectories to the free energy difference of the initial and final states of the non-equilibrium process, provi…
Equilibrium sampling by re-weighting non-equilibrium simulation trajectories
Cheng Yang, Biao Wan, Shun Xu +2
With the traditional equilibrium molecular simulations, it is usually difficult to efficiently visit the whole conformational space in complex systems, which are separated into som…
Optimization of coarse-grained models: matching probability density in conformational space
Shijing Lu, Xin Zhou
Coarse-Graining (CG) models are low resolution approximation of high resolution models, such as all-atomic (AA) models. An effective CG model is expected to reproduce equilibrium v…
Structuring and sampling complex conformation space: Weighted ensemble dynamics simulations
Linchen Gong, Xin Zhou
Based on multiple simulation trajectories, which started from dispersively selected initial conformations, the weighted ensemble dynamics method is designed to robustly and systema…
Construction and Refinement of Coarse-Grained Models
Xin Zhou
A general scheme, which includes constructions of coarse-grained (CG) models, weighted ensemble dynamics (WED) simulations and cluster analyses (CA) of stable states, is presented…