Publications

S. Wu, H. Li, and A. Ma, “Exact reaction coordinates for flap opening in HIV-1 protease”, Proc. Natl. Acad. Sci. 119, e2214906119 (2022).
https://doi.org/10.1073/pnas.2214906119

S. Wu, H. Li, and A. Ma, “A Rigorous Method for Identifying a One-Dimensional Reaction Coordinate in Complex Molecules”, J. Chem. Theory Comput. 18, 2836–2844 (2022).
https://doi.org/10.1021/acs.jctc.2c00132

H. Li, S. Wu, and A. Ma, “Origin of Protein Quake: Energy Waves Conducted by a Precise Mechanical Machine”, J. Chem. Theory Comput. 18, 5692–5702 (2022).
https://doi.org/10.1021/acs.jctc.2c00514

W. Li and A. Ma, “A benchmark for reaction coordinates in the transition path ensemble”, J. Chem. Phys. 144, 134104 (2016).

W. Li and A. Ma, “Reaction mechanism and reaction coordinates from the viewpoint of energy flow”, J. Chem. Phys. 144, 114103 (2016).

W. Li and A. Ma, “Some studies on generalized coordinate sets for polyatomic molecules”, J. Chem. Phys. 143, 224103 (2015).

W. Li and A. Ma, “Reducing the cost of evaluating the committor by a fitting procedure”, J. Chem. Phys. 143, DOI: 174103 (2015).

W. Li and A. Ma, “Recent developments in methods for identifying reaction coordinates”, Molecular Simulation, 40, 784 (2014).

S. Solinet, K. Mahmud, S. Stewman, K. Ben EL Kadhi, B. Decellie, L. Talje, A. Ma, B. Kwok and S. Carreno, “The actin-binding ERM protein Moesin binds to and stabilizes microtubules at the cell cortex”, J. Cell Biol. 202, 251 (2013).

S. Mukherjee, J. D. D. Valencia, S. Stewman, S. Monnier, U. Rath, A. Asenjo, R. Charafeddine, J. Metz, H. Sosa, J. Ross, A. Ma and D. Sharp, “Human fidgetin is a microtubule severing enzyme and minus-end depolymerase that regulates mitosis”, Cell Cycle, 11, 2359 (2012).

J. Currie, Shannon Stewman, G. Schimizzi, K. Slep, A. Ma and S. Rogers, “The microtubule lattice and plus-end association of Drosophila Mini spindles is spatially regulated to fine-tune microtubule dynamics”, Mol. Biol. Cell, 22, 4343 (2011).

D. Zhang, K. Grode*, Shannon Stewman*, D. Diaz*, E. Liebling, J. Curie, D. Buster, A. Asenjo, H. Sosa, J. Ross*, A. Ma*, S. Rogers*, D. Sharp, "Drosophila Katanin is a microtubule depolymerase that regulates cortical-microtubule plus-end interactions and cell migration”, Nat. Cell Biol. 13, 361 (2011). * equal contribution.

A. Wainman, D. W. Buster, T. Duncan, J. Metz, A. Ma, D. J. Sharp, and J. G. Wakefield, “A new Augmin subunit, Msd1, demonstrates the importance of mitotic spindle-templated microtubule nucleation in the absence of functioning centrosomes”, Gene. Dev. 23, 1876 (2009).

V. Mennella, D. Y. Tan, D. W. Buster, A. B. Asenjo, U. Rath, A. Ma, H. Sosa and D. J. Sharp, “A novel phospho-regulatory site on the Kinesin-13 motor domain”, J. Cell Biol. 186, 481 (2009).

N. Fernandez, Q. Chang, D. W. Buster, D. J. Sharp and A. Ma, “A model for the regulatory network controlling the dynamics of kinetochore microtubule plus-ends and poleward flux in metaphase”, Proc. Nat. Acad. Sci. 106, 7846 (2009).

Y. Li, X. Qu, A. Ma, G. Smith, N. F. Scherer and A. R. Dinner, “Models of single-molecule experiments with periodic perturbations reveal hidden dynamics in RNA folding”, J. Phys. Chem. B, 113, 7579 (2009).

J. Hu, A. Ma and A. R. Dinner, “A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT”, Proc. Natl. Acad. Sci. USA, 105, 4615 (2008).

M. Zhang, J. B. Gong, A. Ma and S. A. Rice, “Infrared multiphoton induced isomerization and dissociation of FCN, ClCN and BrCN in liquid Ar: A classical simulation study”, J. Chem. Phys. 127, 144501 (2007).

A. Ma, J. Hu, M. Karplus and A. R. Dinner, “Alternative substrate binding modes and the implications for catalysis in uracil-DNA glycosylase”, Biochem. 45, 13687 (2006).

A. Ma, A. Nag and A. R. Dinner, “Dynamic coupling between reaction coordinates in a model for biomolecular isomerization”, J. Chem. Phys. 124, 144199 (2006).

J. Hu, A. Ma and A. R. Dinner, “Monte Carlo simulations of biomolecules: The MC module in CHARMM”, J. Comp. Chem. 27, 203 (2006).

J. B. Gong, A. Ma and S. A. Rice, “Binding cold molecules in an attractive inverse square potential”, Phys. Rev. A, 72, 063410 (2005).

J. B. Gong, A. Ma and S. A. Rice, “Controlled subnanosecond isomerization of HCN to CNH in solution”, J. Chem. Phys. 122, 204505 (2005).

J. B. Gong, A. Ma and S. A. Rice, “Isomerization and dissociation dynamics of HCN in a picosecond infrared laser field: A full-dimensional classical study”, J. Chem. Phys. 122, 144311 (2005).

A. Ma and A. R. Dinner, “Automatic method for identifying reaction coordinates in complex systems”, J. Phys. Chem. B, 109, 6769 (2005).

A. Ma and R. M. Stratt, “Multiphonon vibrational relaxation in liquids: Should it lead to an exponential-gap law?”, J. Chem. Phys. 121, 11217 (2004).

A. Ma and R. M. Stratt, “Selecting the information content of two-dimensional Raman spectra in liquids”, J. Chem. Phys. 119, 8500 (2003).

A. Ma and R. M. Stratt, “Multiphonon vibrational relaxation in liquids: An exploration of the idea and of the problems it causes for molecular dynamics algorithms”, J. Chem. Phys. 119, 6709 (2003).

A. Ma and R. M. Stratt, “What do we lear from two-dimensional Raman spectra by varying the polarization conditions?”, Bull. Korean Chem. Soc. [Special Issue on Multidimensional Vibrational Spectroscopy], 24, 1126 (2003).

A. Ma and R. M. Stratt, “The molecular origins of the two-dimensional Raman spectrum of an atomic liquid. II. Instantaneous-normal-mode theory”, J. Chem. Phys. 116, 4972 (2002).

A. Ma and R. M. Stratt, “The molecular origins of the two-dimensional Raman spectrum of an atomic liquid. I. Molecular dynamics simulation”, J. Chem. Phys. 116, 4962 (2002).

A. Ma and R. M. Stratt, “Fifth-order Raman spectrum of an atomic liquid: Simulation and instantaneous-normal-mode calculation”, Phys. Rev. Lett. 85, 1004 (2000).

Y. Wang, C. Liu, L. Sun and A. Ma, “Thermodynamic and kinetic study of the dissociation and isomerization of trifluoroacetyl fluoride”, Journal of Shandong University, 32, 302 (1997).

A. Ma, L. Sun, Y. Wang, C. Liu and C. Deng, “Theoretical study of the decompositions of CF₃CO and CF₃C(O)O radicals”, Chemical Journal of Chinese Universities, 17, 777 (1996).

L. Sun, A. Ma, Y. Wang and C. Liu, “Thermodynamic and kinetic study of gas-phase hydrolysis of CF₃C(O)F to CF₃COOH”, Acta Physico-Chimica Sinica, 12, 361 (1996).