CHIANG, Ying-Chih

Presidential Young Fellow

Assistant Professor

Education Background

Ph.D.(University of Heidelberg, Germany)

Research Field
computational biology; theoretical chemistry; non-equilibrium physics
Email
chiangyc@cuhk.edu.cn
Biography

Prof. Ying-Chih Chiang graduated from National Taiwan University in 2004 and obtained her Ph.D. degree in theoretical chemistry in 2012 from the University of Heidelberg, Germany.  She went on to study biophysics in the Department of Physics at The Chinese University of Hong Kong (CUHK), where she developed a VMD plugin for an efficient free energy scan that can be applied to computer-aided lead optimization.  During this period, she also studied the evolution of enzymes using computational methods.  After her post-doctoral research at CUHK, she was awarded a Newton International Fellowship from the Royal Society UK.  With this fellowship she joined the School of Chemistry at the University of Southampton, where she investigated the antibiotic resistance of MRSA and developed a new non-equilibrium method for free energy calculations.  During her PhD and postdoctoral research, she published 23 papers and was cited 359 times.  In March 2020, she joined The Chinese University of Hong Kong, Shenzhen as an assistant professor.

Personal Website: https://mypage.cuhk.edu.cn/academics/chiangyc/

Academic Publications

List of Publications

1. Y.-C. Chiang, M. T. Y. Wong and J. W. Essex.  Molecular Dynamics Simulations of Anti-biotic Ceftaroline at The Allosteric Site of Penicillin-Binding Protein 2a (PBP2a). Accept-ed by Isr. J. Chem.

2. Y.-C. Chiang, S. Engin, P. Bao, F. Otto, P. Kolorenc, P. Votavova, T. Miteva, J. Gao, N. Sisourat. Molecular bond-breaking induced by Interatomic Coulombic Decay. Phys. Rev. A 100, 052701 (2019).

3. Y.-C. Chiang, O. Levsh, C. K. Lam, J.-K. Weng and Y. Wang.  Structural and dynamic ba-sis of substrate permissiveness in hydroxy-cinnamoyl-transferase (HCT). PLOS Comput. Biol. 14, e1006511 (2018).

4. G. Liou, Y.-C. Chiang, Y. Wang and J.-K. Weng.  Mechanistic basis for the evolution of chalcone synthase catalytic cysteine reactivity in land plants. J. Biol. Chem. 293, 18601-18612 (2018).

5. F. Otto, Y.-C. Chiang and D. Peláez.  Accuracy of Potfit-based potential representations and its impact on the performance of (ML-)MCTDH.  Chem. Phys. 509, 116-130 (2018). 

6. A. Haller, Y.-C. Chiang, M. Menger, E. F. Aziz, and A. Bande.  Strong field control of the interatomic Coulombic decay process in quantum dots. Chem. Phys. 482, 135-145 (2017). 

7. O. Levsh, Y.-C. Chiang, C. F. Tung, J. P. Noel, Y. Wang, and J.-K. Weng.  Dynamic con-formational states dictate selectivity toward native substrate in a substrate-permissive acyl-transferase. Biochemistry. 55, 6314-6326 (2016). 

8. Y.-C. Chiang, Y. T. Pang, and Y. Wang.  The role of intramolecular nonbonded interaction and angle sampling in single-step free energy perturbation. J. Chem. Phys. 145, 234109 (2016).

9. Y.-C. Chiang and Y. Wang.  Virtual substitution scan via single-step free energy perturba-tion. Biopolymers. 105, 324-336 (2016).

10. F. Trinter, J. B. Williams, M. Weller, M. Waitz, M. Pitzer, J. Voigtsberger, C. Schober, G. Kastirke, C. Müller, C. Goihl, P. Burzynski, F. Wiegandt, R. Wallauer, A. Kalinin, L. Ph. H. Schmidt, M. S. Schöffler, Y.-C. Chiang, K. Gokhberg, T. Jahnke and, R. Dörner.  A Single Atom Antenna. J. Phys. Conf. Ser. 635, 112099 (2015). 

11.  G. Jabbari, S. Klaiman, Y.-C. Chiang, F. Trinter, T. Jahnke and K. Gokhberg.  Ab initio calculation of ICD widths in photoexcited HeNe.  J. Chem. Phys. 140, 224305 (2014). 

12. T. Miteva, Y.-C. Chiang, P. Kolorenc, A. I. Kuleff, L. S. Cederbaum and K. Gokhberg.  The effect of the partner atom on the spectra of interatomic Coulombic decay triggered by reso-nant Auger processes. J. Chem. Phys. 141, 164303 (2014). 

13. T. Miteva, Y.-C. Chiang, P. Kolorenc, A. I. Kuleff, K. Gokhberg and L. S. Cederbaum.  In-teratomic Coulombic decay following resonant core excitation of Ar in argon dimer.  J. Chem. Phys. 141, 064307 (2014). 

14. Y.-C. Chiang, S. Klaiman, F. Otto and L. S. Cederbaum.  The exact wavefunction factoriza-tion of a vibronic coupling system.  J. Chem. Phys. 140, 054104 (2014). 

15. F. Trinter, J. B. Williams, M. Weller, M. Waitz, M. Pitzer, J. Voigtsberger, C. Schober, G. Kastirke, C. Müller, C. Goihl, P. Burzynski, F. Wiegandt, R. Wallauer, A. Kalinin, L. Ph. H. Schmidt, M. S. Schöffler, Y.-C. Chiang, K. Gokhberg, T. Jahnke, and R. Dörner.  Vibra-tionally resolved decay width of Interatomic Coulombic Decay in HeNe. Phys. Rev. Lett. 111, 233004 (2013). 

16. S. Kopelke, Y.-C. Chiang, K. Gokhberg and L. S. Cederbaum.  Quenching molecular pho-todissociation by intermolecular Coulombic decay. J. Chem. Phys. 137, 034302 (2012). 

17. Y.-C. Chiang, F. Otto, H.-D. Meyer and L. S. Cederbaum.  Kinetic energy release in frag-mentation processes following electron emission: A time-dependent approach.  J. Chem. Phys. 136, 114111 (2012). 

18. T. Ouchi, K. Sakai, H. Fukuzawa, I. Higuchi, Ph. V. Demekhin, Y.-C. Chiang, S. D. Stoychev, A. I. Kuleff, T. Mazza, M. Schöffler, K. Nagaya, M. Yao, Y. Tamenori, N. Saito and K. Ueda.  Interatomic Coulombic decay following Ne 1s Auger decay in NeAr.  Phys. Rev. A 83, 053415 (2011). 

19. Ph. V. Demekhin, Y.-C. Chiang and L. S. Cederbaum.  Resonant Auger decay of the core-excited C*O molecule in intense X-ray laser fields.  Phys. Rev. A 84, 033417 (2011). 

20. Y.-C. Chiang, F. Otto, H.-D. Meyer and L. S. Cederbaum.  Interrelation between the distri-butions of kinetic energy release and emitted electron energy following the decay of elec-tronic states. Phys. Rev. Lett. 107, 173001 (2011). 

21. L. S. Cederbaum, Y.-C. Chiang, Ph. V. Demekhin and N. Moiseyev.  Resonant Auger decay of molecules in intense X-ray laser fields: Light-induced strong nonadiabatic effects. Phys. Rev. Lett. 106, 123001 (2011). 

22. V. Averbukh, Ph. V. Demekhin, P. Kolorenč, S. Scheit, S. D. Stoychev, A. I. Kuleff, Y.-C. Chiang, K. Gokhberg, S. Kopelke, N. Sisourat, and L. S. Cederbaum.  Interatomic electron-ic decay processes in singly and multiply ionized clusters.  J. Electron. Spectrosc. Relat. Phenom. 183, 36-47 (2011). 

23. Y.-C. Chiang, P. V. Demekhin, A. I. Kuleff, S. Scheit and L. S. Cederbaum.  Linewidth and lifetime of atomic levels and the time evolution of spectra and coincidence spectra. Phys. Rev. A 81, 032511 (2010). 

24. Ph. V. Demekhin, Y.-C. Chiang, S. D. Stoychev, P. Kolorenc, S. Scheit, A. I. Kuleff, F. Tarantelli and L. S. Cederbaum.  Interatomic Coulombic decay and its dynamics in NeAr following K-LL Auger transition in the Ne atom.  J. Chem. Phys. 131, 104303 (2009). 、

 

List of Contributed Scientific Software
1. The preconditioner routine for the complex Davidson diagonalization method in the Hei-delberg MCTDH software package (Fortran). See: https://www.pci.uni-heidelberg.de/tc/usr/mctdh/doc/index.html.

2. Software for the quantum molecular dynamics in diatomic molecules under an intense laser field (Fortran).  This code is available on request.

3. Software for the exact factorization wavefunction ansatz for nonadiabatic coupling (Fortran/Matlab). This code is available on request.

4. Virtual Substitution Scan (VSS), a software that post-processes a single MD trajectory for free energy calculations. The code is available at https://github.com/YingChihChiang/VSS. Implemented for the VMD platform using Tcl-C API.

5. ParseFEP plugin for analyzing NAMD free energy calculation output files. I/O bugfix and 3-fold speedup. See: https://www.ks.uiuc.edu/Research/vmd/plugins/parsefep/. Implement-ed in Tcl.

6Software RAFEP for harmonic oscillator potentials and for Lennard-Jones fluids (Py-thon/C++). The code will be made public through an online code repository once our paper is published.