Hsiao-Mei Lu

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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)
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)
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)
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)
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)
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)
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)
We study folding dynamics of protein-like sequences on square lattice by constructing a physically realizable move set that exhausts all possible conformational changes for a structure. By solving the master equation of 16-mer characterized by a 802,075times802,075 transition matrix, we monitor the time-dependent probabilities of occupancy of all(More)