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- Youfang Cao, Hsiao-Mei Lu, Jie Liang
- Proceedings of the National Academy of Sciences…
- 2010

Computational studies of biological networks can help to identify components and wirings responsible for observed phenotypes. However, studying stochastic networks controlling many biological processes is challenging. Similar to Schrödinger's equation in quantum mechanics, the chemical master equation (CME) provides a basic framework for understanding… (More)

- Yiming Li, Hsiao-Mei Lu, Ting-Wei Tang, S. M. Sze
- Mathematics and Computers in Simulation
- 2003

- Sëma Kachalo, Hsiao-Mei Lu, Jie Liang
- Physical review letters
- 2006

We study folding dynamics of proteinlike sequences on a square lattice using a physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of occupancy of all 802 075 conformations of 16 mers over 7 orders of time span. We find that (i) folding rates of these… (More)

- Hsiao-Mei Lu, Jie Liang
- Proteins
- 2008

To study protein nascent chain folding during biosynthesis, we investigate the folding behavior of models of hydrophobic and polar (HP) chains at growing length using both two-dimensional square lattice model and an optimized three-dimensional 4-state discrete off-lattice model. After enumerating all possible sequences and conformations of HP heteropolymers… (More)

- Ming Lin, Jian Zhang, Hsiao-Mei Lu, Rong Chen, Jie Liang
- The Journal of chemical physics
- 2011

Characterizing the conformations of protein in the transition state ensemble (TSE) is important for studying protein folding. A promising approach pioneered by Vendruscolo et al. [Nature (London) 409, 641 (2001)] to study TSE is to generate conformations that satisfy all constraints imposed by the experimentally measured φ values that provide information… (More)

- Youfang Cao, Hsiao-Mei Lu, Jie Liang
- Conference proceedings : ... Annual International…
- 2008

The genetic switch of phage lambda provides a paradigm for studying developmental biology and cell fate. Although there have been numerous experimental and theoretical studies, the mechanisms for switching efficiency, stability and robustness, maintenance of lysogenic state, and the induction lytic state are not fully understood. In this paper, a new method… (More)

- Ming Lin, Hsiao-Mei Lu, Rong Chen, Jie Liang
- The Journal of chemical physics
- 2008

Inferring three-dimensional structural information of biomacromolecules such as proteins from limited experimental data is an important and challenging task. Nuclear Overhauser effect measurements based on nucleic magnetic resonance, disulfide linking, and electron paramagnetic resonance labeling studies can all provide useful partial distance constraint… (More)

- Hsiao-Mei Lu, Jie Liang
- PLoS Computational Biology
- 2009

Large macromolecular assemblies are often important for biological processes in cells. Allosteric communications between different parts of these molecular machines play critical roles in cellular signaling. Although studies of the topology and fluctuation dynamics of coarse-grained residue networks can yield important insights, they do not provide… (More)

- Hsiao-Mei Lu, Jie Liang
- Conference proceedings : ... Annual International…
- 2007

The study of the dynamics of a complex system is an important problem that includes large macromolecular complexes, molecular interaction networks, and cell functional modules. Large macromolecular complexes in cellular machinery can be modeled as a connected network, as in the elastic or Gaussian network models as demonstrated by Bahar and colleagues. Here… (More)

- Hsiao-Mei Lu, Sumeet Gupta, Yang Dai
- BIOKDD
- 2003

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